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This article is part of the series on:
Introduction to Genetics
General flow: DNA > RNA > Protein
special transfers (RNA > RNA,
RNA > DNA, Protein > Protein)
Genetic code
Transcription
Transcription (Transcription factors,
RNA Polymerase,promoter)
Prokaryotic / Archaeal / Eukaryotic
post-transcriptional modification
(hnRNA,Splicing)
Translation
Translation (Ribosome,tRNA)
Prokaryotic / Archaeal / Eukaryotic
post-translational modification
(functional groups, peptides,
structural changes
)
gene regulation
epigenetic regulation
(Genomic imprinting)
transcriptional regulation
post-transcriptional regulation
(sequestration,
alternative splicing,miRNA)
translational regulation
post-translational regulation
(reversible,irreversible)
ask a question , edit
.
A representation of the 3D structure of myoglobin showing coloured alpha helices.
^ The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ There are three common secondary structures in proteins, namely alpha helices, beta sheets and turns .
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

This protein was the first to have its structure solved by X-ray crystallography.
.Proteins (also known as polypeptides) are organic compounds made of amino acids arranged in a linear chain and folded into a globular form.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ Peptides that contain many amino acids are called polypeptides or proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Amino acids in proteins(or polypeptides) are joined together by peptide bonds.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.^ If the amine and carboxylic acid functional groups in amino acids join together to form amide bonds, a chain of amino acid units, called a peptide , is formed.
  • Proteins 2 February 2010 16:52 UTC www.cem.msu.edu [Source type: Reference]

^ Once 50 amino acids get together by peptide bond, this is what scientists have called a protein.
  • John Berardi - Protein Super Feature 2 February 2010 16:52 UTC www.johnberardi.com [Source type: Academic]

^ Amino acids in proteins(or polypeptides) are joined together by peptide bonds.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ When gene mutations occur within an amino acid sequence, mutant proteins are formed.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

[1] .In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine—and in certain archaeapyrrolysine.^ Since the remaining entries are generally so much smaller, this suggests that these remaining entries correspond to amino acid replacements that are almost always disruptive.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ There are about 20 different amino acids commonly found in plant and animal proteins.

^ Codons which are a series of three RNA bases, code for each of the twenty different amino acids .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins.^ There are several different types of post-translational modifications of proteins.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Protein requirements and physical activity.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ Auto-modification of protein is another common form of post-translational modification.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.^ All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Protein-protein association involves the specific complementary recognition of two macromolecules to form a stable assembly (Jones and Thornton, 1995).
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ They were able to form protein-like chains from a mixture of 18 common amino acids at only 70C in the presence of phosphoric acid, and dubbed these protein-like chains protenoids.

[2]
.Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells.^ Protein is a part of every cell of your body.

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Proteins are one of the classes of bio-macromolecules, alongside polysaccharides and nucleic acids, that make up the primary constituents of living things.

.Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism.^ All enzymes are proteins and are vital for the body's metabolism.

^ Many proteins are enzymes or subunits of enzymes.

^ In addition, proteins such as enzymes, hormones, and neurotransmitters are responsible for metabolic regulation; hemoglobin and myoglobin are responsible for transport; and immunoglobulins are responsible for immune function.
  • John Berardi - Protein Super Feature 2 February 2010 16:52 UTC www.johnberardi.com [Source type: Academic]

.Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape.^ Muscles are composed largely of the proteins myosin and actin.

^ Other proteins play structural or mechanical roles, such as those that form the struts and joints of the cytoskeleton.

^ Proteins are essential to the structure and function of all living cells and viruses.

.Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle.^ Whey proteins modulate immune responses.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

^ The entirety of proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of proteins found in a particular cell type under a particular type of stimulation, are referred to as the proteome of the organism or cell type respectively.

^ Differential effect of dietary protein type on the B-cll and T-cell immune respone in mice.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

.Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food.^ Incomplete protein foods, such as vegetables, lack several essential amino acids.
  • The A-Z Protein Supplements Guide | Muscle & Strength 2 February 2010 16:52 UTC www.muscleandstrength.com [Source type: FILTERED WITH BAYES]

^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ The ones that the animals cannot synthesize are called essential amino acids.
  • Protein Requirements for Good Dog Nutrition 2 February 2010 16:52 UTC www.peteducation.com [Source type: Academic]
  • Protein Requirements for Good Cat Nutrition 28 January 2010 0:42 UTC www.peteducation.com [Source type: Academic]

.Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ All protein, whether plant or animal, is broken down into the individual amino acids before the body uses it.
  • Protein for Vegetarians (& the myth of incomplete proteins) 2 February 2010 16:52 UTC michaelbluejay.com [Source type: FILTERED WITH BAYES]

^ Amino acids are the building blocks of protein.
  • The A-Z Protein Supplements Guide | Muscle & Strength 2 February 2010 16:52 UTC www.muscleandstrength.com [Source type: FILTERED WITH BAYES]

.Proteins were first described by the Dutch chemist Gerhardus Johannes Mulder and named by the Swedish chemist Jöns Jakob Berzelius in 1838. The central role of proteins in living organisms was however not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was a protein.^ The best known role of proteins is that of an enzyme.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ The Swedish chemist Jöns Jacob Berzelius was believed to be the first to use the term protein in 1836.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ All living organisms need to synthesis proteins and all cells of an organism need to synthesize proteins, therefore, it is not hard to imagine that ribosomes are a major constituent of all cells of all organisms.

[3] .The first protein to be sequenced was insulin, by Frederick Sanger, who won the Nobel Prize for this achievement in 1958. The first protein structures to be solved were hemoglobin and myoglobin, by Max Perutz and Sir John Cowdery Kendrew, respectively, in 1958.[4][5] The three-dimensional structures of both proteins were first determined by x-ray diffraction analysis; Perutz and Kendrew shared the 1962 Nobel Prize in Chemistry for these discoveries.^ It has the aim of determining the three-dimensional structure of proteins from their amino acid sequences.

^ X-ray structure of a protein-conducting channel.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Protein structure determination .
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification.^ To characterise protein-protein interactions, a number of chromatography techniques are used especially affinity chromatography.

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ The other way is using domain, which refers to the proteins function, or different areas of function within the protein.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, and mass spectrometry.^ Proteomics is the large-scale study of proteins, particularly their structures and functions.

^ With an elucidated structure, it is then possible to study that protein's function.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ The other way is using domain, which refers to the proteins function, or different areas of function within the protein.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

Contents

Biochemistry

Resonance structures of the peptide bond that links individual amino acids to form a protein polymer.
.Most proteins are linear polymers built from series of up to 20 different L-α-amino acids.^ Different types of proteins are comprised of different amounts of individual amino acids.

^ The kinds of amino acids that appear on the inside and the outside of a protein are different.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Amino acids are the building blocks of protein.
  • The A-Z Protein Supplements Guide | Muscle & Strength 2 February 2010 16:52 UTC www.muscleandstrength.com [Source type: FILTERED WITH BAYES]

.All amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded.^ Branched-chain amino acid metabolism.
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

^ There are twenty common amino acids .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ This shape is determined by bonding interactions between the side chains of neighboring amino acids .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO–NH amide moiety into a fixed conformation.^ The only large scale replacements of concern are those in which B and D have different secondary or tertiary structures.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ A comparison of rat and human milk makes the difference quite clear: protein comprises only 7% of the calorie content of human milk, while rat milk contains 20% protein.

^ Different conformations of a protein differ only in the angle of rotation about the bonds of the backbone and amino acid side-chains.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

[6] .The side chains of the standard amino acids, detailed in the list of standard amino acids, have a great variety of chemical structures and properties; it is the combined effect of all of the amino acid side chains in a protein that ultimately determines its three-dimensional structure and its chemical reactivity.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ Properties of amino acids .
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ It has the aim of determining the three-dimensional structure of proteins from their amino acid sequences.

[7]
Chemical structure of the peptide bond (left) and a peptide bond between leucine and threonine (right).
.The amino acids in a polypeptide chain are linked by peptide bonds.^ Peptides that contain many amino acids are called polypeptides or proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Amino acids in proteins(or polypeptides) are joined together by peptide bonds.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Branched-chain amino acid metabolism.
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

.Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone.[8] The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ The central carbon atom is called the C alpha -atom and is a chiral centre.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ A molecule that contains two or more amino acids (the molecules that join together to form proteins).
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone.^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Regular secondary structure conformations in segments of a polypeptide chain occur when all the bond angles in that polypeptide segment are equal to each other, and all the bond angles are equal.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ The remaining dihedral angles are the source of essentially all the interesting variability in protein conformation.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

[9] .The end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus, whereas the end with a free amino group is known as the N-terminus or amino terminus.^ Intake of free amino acids after resistance exercise stimulates net muscle protein synthesis.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

^ Folding@home is another distributed computing program used to elucidate the correct folding and structure of a protein based on its known amino acid sequence.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ As a result, only free protein molecules that are identical in amino acid sequence to the prion protein can be recruited into the growing fiber.

.The words protein, polypeptide, and peptide are a little ambiguous and can overlap in meaning.^ Peptides that contain many amino acids are called polypeptides or proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Amino acids in proteins(or polypeptides) are joined together by peptide bonds.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ This means that there is little to be gained in protein evolution by concatenating portions of existing protein sequences to generate proteins having new shapes.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

.Protein is generally used to refer to the complete biological molecule in a stable conformation, whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable three-dimensional structure.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ Peptides that contain many amino acids are called polypeptides or proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Amino acids in proteins(or polypeptides) are joined together by peptide bonds.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.However, the boundary between the two is not well defined and usually lies near 20–30 residues.^ When this study was repeated in young women, there was no difference between the two diets in protein turnover (20).
  • John Berardi - Protein Super Feature 2 February 2010 16:52 UTC www.johnberardi.com [Source type: Academic]

^ If all positions were 1/4 constrained, then there would be five typical residues at each position, and two proteins from the family would agree on about 20 percent of their sequence.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

[10] .Polypeptide can refer to any single linear chain of amino acids, usually regardless of length, but often implies an absence of a defined conformation.^ Each polypeptide chain is made up of a certain sequence of amino acids.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Branched-chain amino acid metabolism.
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

^ The branch-chain amino acids (BCAAs) .
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

Synthesis

The DNA sequence of a gene encodes the amino acid sequence of a protein.
.Proteins are assembled from amino acids using information encoded in genes.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ N- terminal protein amino acid acetylation .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

.Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein.^ When gene mutations occur within an amino acid sequence, mutant proteins are formed.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ N- terminal protein amino acid acetylation .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

.The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example AUG (adenine-uracil-guanine) is the code for methionine.^ Codons which are a series of three RNA bases, code for each of the twenty different amino acids .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ These 8 are called the essential amino acids.

^ Sometimes several codons code for the same amino acid.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon.^ There are twenty common amino acids .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ A typical protein may contain 500 or more amino acids.

^ Sometimes several codons code for the same amino acid.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

[11] .Genes encoded in DNA are first transcribed into pre-messenger RNA (mRNA) by proteins such as RNA polymerase.^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ RNA gene cluster code for three similar, unusual Gly-tRNAs that may be used in the synthesis of the peptidoglycan in the cell wall but not in protein synthesis .

^ Plicamycin binds to DNA and prevents cells from making RNA and proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.Most organisms then process the pre-mRNA (also known as a primary transcript) using various forms of post-transcriptional modification to form the mature mRNA, which is then used as a template for protein synthesis by the ribosome.^ To reiterate the process of protein synthesis: .

^ This is too low for most people to use as a primary source of protein.
  • Lowcarb Vegetarian Protein Sources 2 February 2010 16:52 UTC immuneweb.org [Source type: FILTERED WITH BAYES]

^ Auto-modification of protein is another common form of post-translational modification.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.In prokaryotes the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid.^ Furthermore, a useless gene produces a protein that either fails to fold properly or has no useful function in the organism.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

.In contrast, eukaryotes make mRNA in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm, where protein synthesis then takes place.^ In Eukaryotes, transcription occurs in the nucleus, whereas translation occurs in the cytoplasm of a cell.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ The translation of mRNA into protein by a ribosome takes place within the cytosol.

^ RNA gene cluster code for three similar, unusual Gly-tRNAs that may be used in the synthesis of the peptidoglycan in the cell wall but not in protein synthesis .

.The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ Amino acids and whey protein increase protein synthesis in the elderly.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

^ Protein synthesis is influence synergistically by postexercise amino acid supplementation.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

[12]
.The process of synthesizing a protein from an mRNA template is known as translation.^ From an RNA template , proteins are synthesized.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Ribosomes consist of two subunits that fit together and work as one to translate the mRNA into a polypeptide chain during protein synthesis.

^ The template for correct addition of individual amino acids is the mRNA, yet both tRNAs and rRNAs are involved in the process.

.The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes.^ Codons which are a series of three RNA bases, code for each of the twenty different amino acids .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ This proprietary precision blend of various proteins offers a complete fast acting and time released delivery for optimal amino acid transport for faster recovery...
  • Whey Protein Powders & 100 Whey Protein 2 February 2010 16:52 UTC www.nutraplanet.com [Source type: Academic]

^ Sometimes several codons code for the same amino acid.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.The enzyme aminoacyl tRNA synthetase "charges" the tRNA molecules with the correct amino acids.^ Each tRNA, and the amino acid it carries, are recognized by individual aminoacyl-tRNA synthetases.

^ Accurate recognition of the correct amino acid as well as the correct tRNA is different for each aminoacyl-tRNA synthetase.

^ It is absolutely necessary that the discrimination of correct amino acid and correct tRNA be made by a given synthetase prior to release of the aminoacyl-tRNA from the enzyme.

.The growing polypeptide is often termed the nascent chain.^ Often it is necessary to isolate these proteins in order to determine their structure and polypeptide chain sequence.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

Proteins are always biosynthesized from N-terminus to C-terminus.[11]
.The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass, which is normally reported in units of daltons (synonymous with atomic mass units), or the derivative unit kilodalton (kDa).^ Peptides that contain many amino acids are called polypeptides or proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ A typical protein may contain 500 or more amino acids.

^ N- terminal protein amino acid acetylation .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

.Yeast proteins are on average 466 amino acids long and 53 kDa in mass.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ A protein is a long train of amino acids linked together.

^ N- terminal protein amino acid acetylation .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

[10] .The largest known proteins are the titins, a component of the muscle sarcomere, with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ Flood your muscles with amino acids .

^ N- terminal protein amino acid acetylation .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

[13]

Chemical synthesis

.Short proteins can also be synthesized chemically by a family of methods known as peptide synthesis, which rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield.^ The current method for synthesizing protein in vitro retraces the pathway of the central dogma as postulated by Crick .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ By the same token, during protein refeeding (or simply high protein feeding) it appears that liver proteins are the first to be synthesized.
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

^ For example, when leucine is oxidized, it produces ketoisocaproate (KIC) which may play a positive role in protein synthesis (10).
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

[14] .Chemical synthesis allows for the introduction of non-natural amino acids into polypeptide chains, such as attachment of fluorescent probes to amino acid side chains.^ Each polypeptide chain is made up of a certain sequence of amino acids.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Branched-chain amino acid metabolism.
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

^ The branch-chain amino acids (BCAAs) .
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

[15] .These methods are useful in laboratory biochemistry and cell biology, though generally not for commercial applications.^ A secretory pathway is a term used to describe different methods that cells use to transport material from the Golgi apparatus to the outside.

^ The influence of wastewater treatment processes on enterobacterial community physiology was examined at the single-cell level by using culture-independent methods .

^ According to these results, both biomass and SCP production can be manipulated and optimized for commercial use by varying the environmental factors used here.

.Chemical synthesis is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native tertiary structure.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ Amino acids and whey protein increase protein synthesis in the elderly.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

^ Peptides that contain many amino acids are called polypeptides or proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction.[16]

Structure of proteins

.
Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase.
^ The number of possible structures that proteins may possess is extremely large, as highlighted by the Levinthal paradox.

^ De novo- or ab initio- protein modelling methods seek to build three-dimensional protein models "from scratch".

^ The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

.Left: all-atom representation colored by atom type.^ An elegant representation is the ball-and-stick type in which atoms are drawn as coloured spheres and their bonds as rod-like connections.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.Middle: Simplified representation illustrating the backbone conformation, colored by secondary structure.^ Regular secondary structure conformations in segments of a polypeptide chain occur when all the bond angles in that polypeptide segment are equal to each other, and all the bond angles are equal.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ The alpha-helix and beta-structure conformations for polypeptide chains are generally the most thermodynamically stable of the regular secondary structures.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Turns may be viewed as a weak link in the polypeptide chain, allowing the other secondary structures (helix and sheet) to determine the conformational outcome.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).
.Most proteins fold into unique 3-dimensional structures.^ A protein can be in a folded or unfolded state, and if it is folded, it may fold into a variety of structures.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Proteins are amino acid chains, made up from 20 different L-α-amino acids, also referred to as residues, that fold into unique three-dimensional protein structures.

^ Random coils are the unique and rapidly changing structures of proteins which are denatured.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.The shape into which a protein naturally folds is known as its native conformation.^ The shape into a which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids.

^ When a protein folds it samples a number of conformations.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Chaperones are proteins that help fold other proteins into their functional conformations.

[17] .Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states.^ Protein and amino acids.
  • The Protein Paradox: Part I 28 January 2010 0:42 UTC www.mikementzer.com [Source type: Academic]

^ Properties of amino acids .
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ The shape into a which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids.

[18] Biochemists often refer to four distinct aspects of a protein's structure:[19]
.
  • Primary structure: the amino acid sequence.
  • Secondary structure: regularly repeating local structures stabilized by hydrogen bonds.^ The secondary structures are held together by hydrogen bonds.

    ^ The sequence of the different amino acids is considered the primary structure of the peptide or protein.

    ^ Structure and mechanism of an amino acid antiporter.
    • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

    .The most common examples are the alpha helix, beta sheet and turns.^ The alpha-helix and beta-structure conformations for polypeptide chains are generally the most thermodynamically stable of the regular secondary structures.
    • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

    ^ The hairpin consists of antiparallel beta sheets with a sharp turn between them.
    • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

    ^ Like the 3 10 helix, one turn of pi helix is sometimes found at the ends of regular alpha helices.
    • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

    .Because secondary structures are local, many regions of different secondary structure can be present in the same protein molecule.
  • Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structures to one another.^ The "tertiary structure" describes how these secondary structures are combined in the protein.
    • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

    ^ Tertiary structure is best described as the overall geometric shape of the protein.
    • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

    ^ Secondary structures are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structural motifs to one another Quaternary structure: the shape or structure that results from the union of more than one protein molecule, usually called subunit proteins subunits in this context, which function as part of the larger assembly or protein complex.

    .Tertiary structure is generally stabilized by nonlocal interactions, most commonly the formation of a hydrophobic core, but also through salt bridges, hydrogen bonds, disulfide bonds, and even post-translational modifications.^ The tertiary structure is held together primarily by hydrophobic interactions but hydrogen bonds, ionic interactions, and disulfide bonds are usually involved too.

    ^ Both of these structures describe hydrogen bond interactions between amino acids in the protein.
    • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

    ^ The secondary structures are held together by hydrogen bonds.

    .The term "tertiary structure" is often used as synonymous with the term fold.^ In more formal terms, this is the prediction of protein tertiary structure from primary structure.

    ^ Protein Stability To be biologically active, proteins must adopt specific folded three-dimensional, tertiary structures.
    • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

    The Tertiary structure is what controls the basic function of the protein.
  • Quaternary structure: the structure formed by several protein molecules (polypeptide chains), usually called protein subunits in this context, which function as a single protein complex.
Proteins are not entirely rigid molecules. .In addition to these levels of structure, proteins may shift between several related structures while they perform their functions.^ In addition to these levels of structure, proteins may shift between several similar structures in performing of their biological function.

^ Knowledge of the proteome requires knowledge of (1) the structure of the proteins in the proteome and (2) the functional interaction between the proteins.

^ There are structural differences between these two globular proteins.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations", and transitions between them are called conformational changes. Such changes are often induced by the binding of a substrate molecule to an enzyme's active site, or the physical region of the protein that participates in chemical catalysis.^ The "tertiary structure" describes how these secondary structures are combined in the protein.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations," and transitions between them are called conformational changes.

^ A change in the tertiary and/or quaternary conformation of a protein results in a subsequent change in the function of the protein; this is highly significant as many proteins are in fact enzymes possessing active sites with extreme sensitivity to the substrate .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.In solution proteins also undergo variation in structure through thermal vibration and the collision with other molecules.^ Through genetic engineering, researchers can alter the sequence and hence the structure, "targeting", susceptibility to regulation and other properties of a protein.

^ The term denaturation denotes the response of the native protein to heat, acid, alkali, and a variety of other chemical and physical agents which cause marked changes in the protein structure.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ There are a number of other variables we can look at as well, which more effectively establish the unique properties of whey: protein synthesis, protein breakdown, and speed of digestion.
  • Bulk Nutrition - Whey Protein by David Tolson 2 February 2010 16:52 UTC www.bulknutrition.com [Source type: Academic]

[20]
.
Molecular surface of several proteins showing their comparative sizes.
^ Protein sizes range from this lower limit to several hundred residues in multi-functional proteins.

^ Whey protein, creatine and carbohydrate also showed great increases in type II muscle fiber size, compared to a carbohydrate and creatine group.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

From left to right are: immunoglobulin G (IgG, an antibody), hemoglobin, insulin (a hormone), adenylate kinase (an enzyme), and glutamine synthetase (an enzyme).
.Proteins can be informally divided into three main classes, which correlate with typical tertiary structures: globular proteins, fibrous proteins, and membrane proteins.^ In bacteria , proteins are divided into three main classes: integral , peripheral , and lipid-anchored .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Progress of membrane protein structure determination .
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ The signal that marks plasma membrane proteins for incorporation into MVB is mono-ubiquitination.
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

.Almost all globular proteins are soluble and many are enzymes.^ Many proteins are enzymes or subunits of enzymes.

^ Nearly all the biological catalysts known as enzymes are proteins.

^ In fact, almost all of the non-polar (hydrophobic) residues are clustered in a "hydrophobic core" of the protein, so this constraint is quite severe.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

.Fibrous proteins are often structural, such as collagen, the major component of connective tissue, or keratin, the protein component of hair and nails.^ It is a major structural component of all cells: skin, hair, nails and bone.

^ Pepsin is the only proteolytic enzyme that digests collagen , which is the major protein of connective tissue .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Hair, nails, skin contain protein.

.Membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane.^ There, the nascent protein is inserted into a protein channel that passes through the ER membrane.

^ Transmembrane proteins The amino acid chain of transmembrane proteins, which often are transmembrane receptors, passes through a membrane one or several times.

^ Transport proteins are embedded in the bilayer and allow passage of molecules through a channel.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

[21]
.A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration, are called dehydrons.^ Both of these structures describe hydrogen bond interactions between amino acids in the protein.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ The presence in the serum albumin fraction of glutamylcysteine groups (rare in food protein) and the specific intramolecular bond as related to the undenatured conformation of the molecule are considered to be key factors in the glutathione-promoting activity of the protein mixture.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

^ When such side chains are on the surface of a protein, they form hydrogen bonds with water.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

[22]

Structure determination

.Discovering the tertiary structure of a protein, or the quaternary structure of its complexes, can provide important clues about how the protein performs its function.^ The "tertiary structure" describes how these secondary structures are combined in the protein.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ The function of a protein is highly dependent on its tertiary structure .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Most proteins can function immediately when they have been properly folded into the appropriate tertiary or quaternary structure.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Common experimental methods of structure determination include X-ray crystallography and NMR spectroscopy, both of which can produce information at atomic resolution.^ The output of experimentally determined protein structures, typically by time-consuming and relatively expensive X-ray crystallography or NMR spectroscopy, is lagging far behind the output of protein sequences.

^ High-resolution x-ray structure of human aquaporin 5.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ To identify and characterise proteins mass spectrometry, X-ray crystallography, and NMR are used.

.Dual polarisation interferometry is a quantitative analytical method for measuring the overall protein conformation and conformational changes due to interactions or other stimulus.^ So in other words, whey protein has the highest biological value (value that measures how well the body can absorb and utilize a protein) of any protein.
  • Protein Supplements – Fitness and bodybuilding supplements! 2 February 2010 16:52 UTC proteinsupplementsplus.com [Source type: FILTERED WITH BAYES]

^ Proteins are naturally dry and chewy when cooked by methods other than boiling or slow roasting.

^ With completion of a rough draft of the human genome, many researchers are now looking at how genes and proteins interact to form other proteins.

.Circular dichroism is another laboratory technique for determining internal beta sheet/ helical composition of proteins.^ The plot which develops from a large sampling of these angle pairs is known as a Ramachandran plot , and it has distinct areas for helices , beta-sheets , and left-handed helices .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Another irregularity found in antiparallel beta-sheets is the hydrogen-bonding of two residues from one strand with one residue from another called a beta bulge (as shown above).
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ There are two major secondary structures commonly found in proteins: the alpha helix and the beta (pleated) sheet .
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Cryoelectron microscopy is used to produce lower-resolution structural information about very large protein complexes, including assembled viruses;[23] a variant known as electron crystallography can also produce high-resolution information in some cases , especially for two-dimensional crystals of membrane proteins.^ Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Membrane Proteins of Known 3D Structure ( Table description ) .
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ High-resolution structure of the OmpA membrane domain.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

[24] .Solved structures are usually deposited in the Protein Data Bank (PDB), a freely available resource from which structural data about thousands of proteins can be obtained in the form of Cartesian coordinates for each atom in the protein.^ Early in protein research there was some concern about needing to combine proteins so that all essential proteins were available at each meal.

^ Gels formed by aggregation of proteins are of the fourth type, and they usually occur under conditions of partial denaturation.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Crystal structure of the ligand-free G-protein-coupled receptor opsin.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

[25]
.Many more gene sequences are known than protein structures.^ The correlation between protein structure and sequence is even more elusive than the correlation between structure and function.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Every single whole plant food has more than 2.5% protein, and they all have more than 10% except for fruit.
  • Protein for Vegetarians (& the myth of incomplete proteins) 2 February 2010 16:52 UTC michaelbluejay.com [Source type: FILTERED WITH BAYES]

^ Clearly if these massive animals are eating only plants, then plants have more than sufficient protein.
  • Protein for Vegetarians (& the myth of incomplete proteins) 2 February 2010 16:52 UTC michaelbluejay.com [Source type: FILTERED WITH BAYES]

.Further, the set of solved structures is biased toward proteins that can be easily subjected to the conditions required in X-ray crystallography, one of the major structure determination methods.^ X-ray structure of a protein-conducting channel.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Protein structure determination .
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Progress of membrane protein structure determination .
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

.In particular, globular proteins are comparatively easy to crystallize in preparation for X-ray crystallography.^ To identify and characterise proteins mass spectrometry, X-ray crystallography, and NMR are used.

^ It is also often necessary to make protein in vitro to provide the amount needed for studies such as X-Ray crystallography of proteins, which requires about 15mg/ml of a protein.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Most of the current information we have obtained concerning a protein's structure has been acquired either by NMR or X-Ray crystallography.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Membrane proteins, by contrast, are difficult to crystallize and are underrepresented in the PDB.[26] Structural genomics initiatives have attempted to remedy these deficiencies by systematically solving representative structures of major fold classes.^ Also, from [Service 97]: pairs of natural proteins differing in up to 70% of their amino acid sequences virtually always fold up in to the same general 3D structure.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Therefore, changing enough of the amino acids is likely to change the secondary structure, and thus change the protein fold.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Folding@home is another distributed computing program used to elucidate the correct folding and structure of a protein based on its known amino acid sequence.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Protein structure prediction methods attempt to provide a means of generating a plausible structure for proteins whose structures have not been experimentally determined.^ Reference is made to all of the protein types whose structures have been determined.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Protein structure determination .
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Progress of membrane protein structure determination .
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

Cellular functions

.Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes.^ A protein that pumps substances out of cells.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ These procedures tend to require vast computational resources, and have thus only been carried out for tiny proteins.

^ This means that these interactions have to be specified by a considerable amount of information on the protein surface.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

[10] .With the exception of certain types of RNA, most other biological molecules are relatively inert elements upon which proteins act.^ While whey protein is superior to other types of protein powders, there is also a significant difference between available whey proteins on the market a difference that is sometimes difficult to understand or even detect.
  • Daily Protein Plus™ - Whey Protein Isolate with Fiber and Mangosteen | Chocolate, or Vanilla 2 February 2010 16:52 UTC www.wellnessresources.com [Source type: Academic]

^ This means the protein contains truly useful components in their highest quality and most biologically active condition.
  • Daily Protein Plus™ - Whey Protein Isolate with Fiber and Mangosteen | Chocolate, or Vanilla 2 February 2010 16:52 UTC www.wellnessresources.com [Source type: Academic]

^ Certain highly polar molecules are so effective in altering or disrupting the local water structure that when dissolved in water they can have a drastic effect on other solute molecules.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.Proteins make up half the dry weight of an Escherichia coli cell, whereas other macromolecules such as DNA and RNA make up only 3% and 20%, respectively.^ Plicamycin binds to DNA and prevents cells from making RNA and proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ DNA binding nucleotide binding protein binding RNA binding .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

[27] .The set of proteins expressed in a particular cell or cell type is known as its proteome.^ The cell then over expresses our gene as a protein.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation.

^ Prions have also been confirmed to be the only type of infectious proteins known.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

The enzyme hexokinase is shown as a simple ball-and-stick molecular model. To scale in the top right-hand corner are two of its substrates, ATP and glucose.
.The chief characteristic of proteins that also allows their diverse set of functions is their ability to bind other molecules specifically and tightly.^ Various molecules and ions are able to bind to specific sites on proteins.

^ Protein binding Structural Molecule Activity .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ The other way is using domain, which refers to the proteins function, or different areas of function within the protein.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or "pocket" on the molecular surface.^ Various molecules and ions are able to bind to specific sites on proteins.

^ Molecule: Retinol binding protein 4 .
  • BioVendor R&D - Products \ Proteins 2 February 2010 16:52 UTC www.biovendor.com [Source type: Academic]

^ The strength of ligand-protein binding is a property of the binding site known as affinity.

.This binding ability is mediated by the tertiary structure of the protein, which defines the binding site pocket, and by the chemical properties of the surrounding amino acids' side chains.^ Properties of amino acids .
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Branched-chain amino acid metabolism.
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

^ The branch-chain amino acids (BCAAs) .
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

.Protein binding can be extraordinarily tight and specific; for example, the ribonuclease inhibitor protein binds to human angiogenin with a sub-femtomolar dissociation constant (<10−15 M) but does not bind at all to its amphibian homolog onconase (>1 M).^ C binding protein kinase C inhibitor activity .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Hello, All of the sites that I have read state that the number of necessary grams of protein depend on your weight and they all give examples.
  • How Much Protein Should I Eat in a Day? | Project Swole 2 February 2010 16:52 UTC www.projectswole.com [Source type: General]

.Extremely minor chemical changes such as the addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding; for example, the aminoacyl tRNA synthetase specific to the amino acid valine discriminates against the very similar side chain of the amino acid isoleucine.^ Branched-chain amino acid metabolism.
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

^ The branch-chain amino acids (BCAAs) .
  • Protein, Part 4: Amino Acid Kinetics and Adaptations 28 January 2010 0:42 UTC www.thinkmuscle.com [Source type: Academic]

^ Incomplete protein foods, such as vegetables, lack several essential amino acids.
  • The A-Z Protein Supplements Guide | Muscle & Strength 2 February 2010 16:52 UTC www.muscleandstrength.com [Source type: FILTERED WITH BAYES]

[28]
.Proteins can bind to other proteins as well as to small-molecule substrates.^ Molecule: Retinol binding protein 4 .
  • BioVendor R&D - Products \ Proteins 2 February 2010 16:52 UTC www.biovendor.com [Source type: Academic]

^ So in other words, whey protein has the highest biological value (value that measures how well the body can absorb and utilize a protein) of any protein.
  • Protein Supplements – Fitness and bodybuilding supplements! 2 February 2010 16:52 UTC proteinsupplementsplus.com [Source type: FILTERED WITH BAYES]

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.When proteins bind specifically to other copies of the same molecule, they can oligomerize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers.^ Various molecules and ions are able to bind to specific sites on proteins.

^ Molecule: Retinol binding protein 4 .
  • BioVendor R&D - Products \ Proteins 2 February 2010 16:52 UTC www.biovendor.com [Source type: Academic]

^ ATP binding nucleotide binding protein binding structural molecule activity .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

.Protein–protein interactions also regulate enzymatic activity, control progression through the cell cycle, and allow the assembly of large protein complexes that carry out many closely related reactions with a common biological function.^ G1 phase of mitotic cell cycle positive regulation of cell proliferation protein folding regulation of progression through cell cycle .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ A protein that helps control many cell functions, including cell division and cell death.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Enzymatic activity is not the only important function of proteins.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Proteins can also bind to, or even be integrated into, cell membranes.^ Plicamycin binds to DNA and prevents cells from making RNA and proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Provenge injected into patients may stimulate T lymphocytes to kill tumor cells that express the prostate protein.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Describes cells that do not have a protein to which the hormone progesterone will bind.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.The ability of binding partners to induce conformational changes in proteins allows the construction of enormously complex signaling networks.^ The binding affinity of hemoglobin's four oxygen binding sites increases with each oxygen bound because the protein undergoes a conformational change.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ An excellent example of this is the conformational changes undergone by hemoglobin as it binds oxygen.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Apart from their involvement in the stabilization of molecules, they contribute to the ability of molecules to undergo changes in conformation and interact with each other.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

[29] .Importantly, as interactions between proteins are reversible, and depend heavily on the availability of different groups of partner proteins to form aggregates that are capable to carry out discrete sets of function, study of the interactions between specific proteins is a key to understand important aspects of cellular function, and ultimately the properties that distinguish particular cell types[30][31].^ Functional properties of proteins-polysaccharide mixtures.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Knowledge of the proteome requires knowledge of (1) the structure of the proteins in the proteome and (2) the functional interaction between the proteins.

^ Numerous examples of specific binding can be observed in biological systems: where proteins are directed to the correct compartments of cells by binding to other proteins; protein messengers bind to protein receptors on the outer surface of cell membranes to send signals between cells; proteins form structural connections between cells; some inhibitors of enzymes are proteins; proteins are modified and degraded by enzymes; interaction between different protein subunits are the basis of allosteric changes in multimers, and protein-protein interactions underlie very large-scale movements in organisms, such as muscle contraction.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

Enzymes

.The best-known role of proteins in the cell is as enzymes, which catalyze chemical reactions.^ The best known role of proteins is that of an enzyme.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Nearly all the biological catalysts known as enzymes are proteins.

^ Proteases are the major enzymes that catalyze protein degradation.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Enzymes are usually highly specific and accelerate only one or a few chemical reactions.^ An enzyme's active site is typically going to be specific for just one conformation of a molecular substrate.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ For example, protein catabolism requires only a few enzymes termed proteases.

.Enzymes carry out most of the reactions involved in metabolism, as well as manipulating DNA in processes such as DNA replication, DNA repair, and transcription.^ It blocks an enzyme involved in many functions of the cell, including the repair of DNA damage.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ An enzyme involved in many functions of the cell, including the repair of DNA damage.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ A measure of how well a patient is able to perform ordinary tasks and carry out daily activities.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.Some enzymes act on other proteins to add or remove chemical groups in a process known as post-translational modification.^ The best known role of proteins is that of an enzyme.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ There are several different types of post-translational modifications of proteins.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

^ Auto-modification of protein is another common form of post-translational modification.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

About 4,000 reactions are known to be catalyzed by enzymes.[32] .The rate acceleration conferred by enzymatic catalysis is often enormous — as much as 1017-fold increase in rate over the uncatalyzed reaction in the case of orotate decarboxylase (78 million years without the enzyme, 18 milliseconds with the enzyme).^ The critical flow rate (i.e., the fluid flow rate necessary to remove film diffusion resistance) approximately doubles with each 10 degree C rise in reaction temperature .

^ At 10 degrees C, at least a 10-fold reduction of the pathogen occurred, except in the beef without gravy .

^ The enzymatic activity per weight unit of enzyme is greater in the case of benzonase that in reported data for other nucleases insolubilized on corn cob by the same procedure.

[33]
.The molecules bound and acted upon by enzymes are called substrates.^ Other functions include such things as binding substrates and catalyzing important changes without chemically acting on the bound substrate.
  • Protein - BBWiki 2 February 2010 16:52 UTC bbwiki.tamu.edu [Source type: Academic]

.Although enzymes can consist of hundreds of amino acids, it is usually only a small fraction of the residues that come in contact with the substrate, and an even smaller fraction — 3 to 4 residues on average — that are directly involved in catalysis.^ Only a small fraction of the gelatin may be involved in the ordered domains.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ When protein is listed on a nutrition label it only refers to the amount of complete proteins in the food, though the food may be very strong in a subset of the essential amino acids.

^ Since the remaining entries are generally so much smaller, this suggests that these remaining entries correspond to amino acid replacements that are almost always disruptive.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

[34] .The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site.^ Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Since side chains at an active site are in an interior environment when the two proteins join, they should be at least as constrained as interior residues.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ The active site is external to the membrane, but the so-called Jaw Region contributes to membrane binding.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

Cell signaling and ligand binding

Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigen
.Many proteins are involved in the process of cell signaling and signal transduction.^ Vertebrata) cell adhesion signal transduction .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Rho protein signal transduction .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Rho protein signal transduction signal transduction .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

.Some proteins, such as insulin, are extracellular proteins that transmit a signal from the cell in which they were synthesized to other cells in distant tissues.^ Some also include other proteins such as milk proteins and/or egg.
  • Protein Supplements – Fitness and bodybuilding supplements! 2 February 2010 16:52 UTC proteinsupplementsplus.com [Source type: FILTERED WITH BAYES]

^ Once a protein molecule is broken down into its individual units, amino acids, they are transported to muscle cells via the bloodstream to be used as the building blocks for muscle tissue.

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.Others are membrane proteins that act as receptors whose main function is to bind a signaling molecule and induce a biochemical response in the cell.^ Molecule: Retinol binding protein 4 .
  • BioVendor R&D - Products \ Proteins 2 February 2010 16:52 UTC www.biovendor.com [Source type: Academic]

^ Numerous examples of specific binding can be observed in biological systems: where proteins are directed to the correct compartments of cells by binding to other proteins; protein messengers bind to protein receptors on the outer surface of cell membranes to send signals between cells; proteins form structural connections between cells; some inhibitors of enzymes are proteins; proteins are modified and degraded by enzymes; interaction between different protein subunits are the basis of allosteric changes in multimers, and protein-protein interactions underlie very large-scale movements in organisms, such as muscle contraction.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.Many receptors have a binding site exposed on the cell surface and an effector domain within the cell, which may have enzymatic activity or may undergo a conformational change detected by other proteins within the cell.^ Serine, threonine, and asparagine are also the binding sites of carbohydrates that are attached to the surface of many proteins.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Numerous examples of specific binding can be observed in biological systems: where proteins are directed to the correct compartments of cells by binding to other proteins; protein messengers bind to protein receptors on the outer surface of cell membranes to send signals between cells; proteins form structural connections between cells; some inhibitors of enzymes are proteins; proteins are modified and degraded by enzymes; interaction between different protein subunits are the basis of allosteric changes in multimers, and protein-protein interactions underlie very large-scale movements in organisms, such as muscle contraction.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

[35]
.Antibodies are protein components of adaptive immune system whose main function is to bind antigens, or foreign substances in the body, and target them for destruction.^ Proteins are components of some antibodies.

^ To keep the body’s immune system functioning properly.
  • The A-Z Protein Supplements Guide | Muscle & Strength 2 February 2010 16:52 UTC www.muscleandstrength.com [Source type: FILTERED WITH BAYES]

^ And proteins called antibodies are important components of your immune system, warding off foreign particles like bacteria.

.Antibodies can be secreted into the extracellular environment or anchored in the membranes of specialized B cells known as plasma cells.^ A tumor that begins in plasma cells (white blood cells that produce antibodies).
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ They are inserted into the membrane by translocation, until the process is interrupted by a stop-transfer sequence, also called a membrane anchor sequence.

^ Protein targeting in bacteria Bacteria do not have organelles they can send proteins to, but some proteins are incorporated into the plasma membrane or secreted into the environment.

.Whereas enzymes are limited in their binding affinity for their substrates by the necessity of conducting their reaction, antibodies have no such constraints.^ Proteins are the basis of body structures such as skin and hair and of substances such as enzymes, cytokines, and antibodies.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ The side chains confer important properties on a protein such as the ability to bind ligands and catalyse biochemical reactions.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

An antibody's binding affinity to its target is extraordinarily high.[36]
.Many ligand transport proteins bind particular small biomolecules and transport them to other locations in the body of a multicellular organism.^ So in other words, whey protein has the highest biological value (value that measures how well the body can absorb and utilize a protein) of any protein.
  • Protein Supplements – Fitness and bodybuilding supplements! 2 February 2010 16:52 UTC proteinsupplementsplus.com [Source type: FILTERED WITH BAYES]

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ With completion of a rough draft of the human genome, many researchers are now looking at how genes and proteins interact to form other proteins.

.These proteins must have a high binding affinity when their ligand is present in high concentrations, but must also release the ligand when it is present at low concentrations in the target tissues.^ The strength of ligand-protein binding is a property of the binding site known as affinity.

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Fat mass decreases with low protein and high protein intakes.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

.The canonical example of a ligand-binding protein is haemoglobin, which transports oxygen from the lungs to other organs and tissues in all vertebrates and has close homologs in every biological kingdom.^ A arsenite transporter, ATP- binding, homolog 1 .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Now, a 0 =1 and the other a i may be estimated as follows: Since about 1/4 of all mutations cause a protein to misfold, one can let a i+1 = (3/4)a i initially.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

[37] .Lectins are sugar-binding proteins which are highly specific for their sugar moieties.^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ DNA binding sugar binding unfolded protein binding zinc ion binding .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Protein interactions are highly specific, meaning that a given protein will interact with only a few others.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

.Lectins typically play a role in biological recognition phenomena involving cells and proteins.^ Protein supplementation plays a big role in providing essential building blocks that help regulate the body in an incredible number of ways.
  • Protein Powders Supplements at the Lowest Prices! 2 February 2010 16:52 UTC www.a1supplements.com [Source type: General]

^ Protein-protein association involves the specific complementary recognition of two macromolecules to form a stable assembly (Jones and Thornton, 1995).
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Since proteins are involved in practically every function performed by a cell, the mechanisms for controlling these functions therefore depend on controlling protein activity.

[38] .Receptors and hormones are highly specific binding proteins.^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ ATP binding ATPase activity hydrolase activity nucleotide binding thyrotropin- releasing hormone receptor binding transcription factor binding .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ E receptor binding beta- amyloid binding heparin binding lipid transporter activity phospholipid binding tau protein binding .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

.Transmembrane proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions.^ Once a protein molecule is broken down into its individual units, amino acids, they are transported to muscle cells via the bloodstream to be used as the building blocks for muscle tissue.

^ One of a family of small proteins found in white blood cells in pigs.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ However only a small selection of molecules are involved in specific binding (Zuckerkandl,1975) which is a property of individual proteins.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse.^ In fact, almost all of the non-polar (hydrophobic) residues are clustered in a "hydrophobic core" of the protein, so this constraint is quite severe.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ To date there have been very few direct measurements of the hydrophobic interaction between dissolved non-polar molecules, mainly because they are so insoluble.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Polar or charged side chains cannot be buried without destabilizing a protein.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

.Membrane proteins contain internal channels that allow such molecules to enter and exit the cell.^ A molecule that contains two or more amino acids (the molecules that join together to form proteins).
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ A molecule that contains both protein and glycosaminoglycans, which are a type of polysaccharide.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ A process in which a phosphate group is added to a molecule, such as a sugar or a protein.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.Many ion channel proteins are specialized to select for only a particular ion; for example, potassium and sodium channels often discriminate for only one of the two ions.^ In particular, it could only have had one or a very small number of proteins.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Thus the expected number of species having a second-generation new shape of protein would be about 10 -10 , which is much less than one.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ One species can be expected to generate about 10 -15 new beneficial shape proteins per 10 5 generations, for a total of about 10 -5 expected beneficial new shapes of proteins in all of evolutionary history.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

[39]

Structural proteins

.Structural proteins confer stiffness and rigidity to otherwise-fluid biological components.^ In addition to these levels of structure, proteins may shift between several similar structures in performing of their biological function.

^ Protein Stability To be biologically active, proteins must adopt specific folded three-dimensional, tertiary structures.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Structure and function of an essential component of the outer membrane protein assembly machine.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

.Most structural proteins are fibrous proteins; for example, actin and tubulin are globular and soluble as monomers, but polymerize to form long, stiff fibers that comprise the cytoskeleton, which allows the cell to maintain its shape and size.^ The intact protein is comprised of eight monomers.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ If P > R, then in 10 5 generations, one could expect all R replacements to occur, at most, and the expected number of new beneficial protein shapes produced in this species would be R B .
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ It is also clear that the sizes and shapes of non-polar solute molecules are fairly critical in determining the water structure adopted around them.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.Collagen and elastin are critical components of connective tissue such as cartilage, and keratin is found in hard or filamentous structures such as hair, nails, feathers, hooves, and some animal shells.^ Proteoglycans are found in cartilage and other connective tissues.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ It is used as structural material for cells and tissues, keratin of skin and elastin of connective tissue to name a few.
  • Protein Powders Supplements at the Lowest Prices! 2 February 2010 16:52 UTC www.a1supplements.com [Source type: General]

^ The filamentous material that makes up the cytoskeleton of cells and much of the structure of animals is also protein: microtubules, actin, intermediate filaments, collagen and keratin are components of skin, hair, and cartilage.

[40]
.Other proteins that serve structural functions are motor proteins such as myosin, kinesin, and dynein, which are capable of generating mechanical forces.^ Another class are the motor proteins such as myosin, kinesin, and dynein.

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Given the usefulness of known protein structures in such valuable tasks as rational drug design, this is a highly active field of research.

.These proteins are crucial for cellular motility of single celled organisms and the sperm of many multicellular organisms which reproduce sexually.^ Even if special mechanisms operated in the evolution of one-celled creatures, there are undoubtedly many proteins and shapes of proteins that only appear in multicellular organisms, and these must have evolved from others by currently existing genetic mechanisms.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation.

^ Since proteins are involved in practically every function performed by a cell, the mechanisms for controlling these functions therefore depend on controlling protein activity.

.They also generate the forces exerted by contracting muscles.^ Different prostaglandins control blood pressure, contraction of smooth muscles, and other processes within tissues where they are made.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Different PGs control blood pressure, contraction of smooth muscles, and other processes within tissues where they are made.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

[41]

Methods of study

.As some of the most commonly studied biological molecules, the activities and structures of proteins are examined both in vitro and in vivo.^ ATP binding nucleotide binding protein binding structural molecule activity .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Protein binding Structural Molecule Activity .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ A molecule that contains both protein and glycosaminoglycans, which are a type of polysaccharide.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.In vitro studies of purified proteins in controlled environments are useful for learning how a protein carries out its function: for example, enzyme kinetics studies explore the chemical mechanism of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules.^ Use this article to figure out how much protein to eat.
  • How Much Protein Should I Eat in a Day? | Project Swole 2 February 2010 16:52 UTC www.projectswole.com [Source type: General]

^ It is also rarely possible to cancel out the effect of a mutation that interferes with the function of a protein.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ It is possible to give all of the protein, calories, vitamins and minerals a person needs using parenteral nutrition.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.By contrast, in vivo experiments on proteins' activities within cells or even within whole organisms can provide complementary information about where a protein functions and how it is regulated.^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Protein supplementation plays a big role in providing essential building blocks that help regulate the body in an incredible number of ways.
  • Protein Powders Supplements at the Lowest Prices! 2 February 2010 16:52 UTC www.a1supplements.com [Source type: General]

^ The entirety of proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of proteins found in a particular cell type under a particular type of stimulation, are referred to as the proteome of the organism or cell type respectively.

Protein purification

.In order to perform in vitro analysis, a protein must be purified away from other cellular components.^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Product has 77% of in vitro dry matter digestibility, hence can be used to supplement the feed components of ruminents and other monogastric animals.

^ A proteasome is a large protein complex that helps destroy other cellular proteins when they are no longer needed.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.This process usually begins with cell lysis, in which a cell's membrane is disrupted and its internal contents released into a solution known as a crude lysate.^ NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ In biology, cell proliferation occurs by a process known as cell division.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Protein targeting includes the mechanisms by which a biological cell transports proteins to the appropriate organelle for insertion into a membrane or secretion to the outside.

.The resulting mixture can be purified using ultracentrifugation, which fractionates the various cellular components into fractions containing soluble proteins; membrane lipids and proteins; cellular organelles, and nucleic acids.^ Once a protein molecule is broken down into its individual units, amino acids, they are transported to muscle cells via the bloodstream to be used as the building blocks for muscle tissue.

^ The signal that marks plasma membrane proteins for incorporation into MVB is mono-ubiquitination.
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

.Precipitation by a method known as salting out can concentrate the proteins from this lysate.^ By this method, in each protein the amino acid furthest below the standard reference is known as the limiting amino acid.

.Various types of chromatography are then used to isolate the protein or proteins of interest based on properties such as molecular weight, net charge and binding affinity.^ The strength of ligand-protein binding is a property of the binding site known as affinity.

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation.

[42] .The level of purification can be monitored using various types of gel electrophoresis if the desired protein's molecular weight and isoelectric point are known, by spectroscopy if the protein has distinguishable spectroscopic features, or by enzyme assays if the protein has enzymatic activity.^ Therefore, should I use my desired weight to calculate the correct amount of protein that I should eat?
  • How Much Protein Should I Eat in a Day? | Project Swole 2 February 2010 16:52 UTC www.projectswole.com [Source type: General]

^ A sample of WE80BG derived from whey proteins showed the strongest anti-hypertensive activity (-21.2 +/- 16.9 mm Hg) with a medium level of ACE inhibitory activity (53.6%), and it was subjected to hydrophobic and gel filtration chromatography.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

^ Gels formed by aggregation of proteins are of the fourth type, and they usually occur under conditions of partial denaturation.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

.Additionally, proteins can be isolated according their charge using electrofocusing.^ In addition, there are whey protein isolates and whey protein concentrates.
  • Protein Supplements – Fitness and bodybuilding supplements! 2 February 2010 16:52 UTC proteinsupplementsplus.com [Source type: FILTERED WITH BAYES]

^ In addition the substrates of serine proteases are proteins, therefore, the complex formation between these enzymes and their substrates can provide useful information on protein-protein interactions.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

[43]
.For natural proteins, a series of purification steps may be necessary to obtain protein sufficiently pure for laboratory applications.^ Call a protein fold or family F r constrained if the probability is r that a random amino acid at a random position i on the protein will be typical for F. If F is r constrained, then the expected fraction of amino acid replacements necessary to obtain the fold or family F from a random protein without harmful replacements is 1-r.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ In actual proteins, it is usually necessary to replace at least 70 percent of the amino acids to obtain a different fold, so the stated assumptions are somewhat too liberal.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ The virus is changed in the laboratory to make human proteins, including the tumor markers called CEA and MUC-1, that may help immune cells in the body kill tumor cells.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.To simplify this process, genetic engineering is often used to add chemical features to proteins that make them easier to purify without affecting their structure or activity.^ Protein binding Structural Molecule Activity .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Without proper protein intake, IGF-1 levels can be lowered, making it harder for your body to utilize available growth hormone.
  • The A-Z Protein Supplements Guide | Muscle & Strength 2 February 2010 16:52 UTC www.muscleandstrength.com [Source type: FILTERED WITH BAYES]

^ Through genetic engineering, researchers can alter the sequence and hence the structure, "targeting", susceptibility to regulation and other properties of a protein.

.Here, a "tag" consisting of a specific amino acid sequence, often a series of histidine residues (a "His-tag"), is attached to one terminus of the protein.^ N- terminal protein amino acid acetylation .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Each protein is composed of a sequence of amino acids that join together and are then called "residues."
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Amino acids are the building blocks of protein.
  • The A-Z Protein Supplements Guide | Muscle & Strength 2 February 2010 16:52 UTC www.muscleandstrength.com [Source type: FILTERED WITH BAYES]

As a result, when the lysate is passed over a chromatography column containing nickel, the histidine residues ligate the nickel and attach to the column while the untagged components of the lysate pass unimpeded. .A number of different tags have been developed to help researchers purify specific proteins from complex mixtures.^ Thus, if a protein can be constructed by such insertions, it cannot be done in many different ways, so the number of subsequences limits the probability of this happening.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Specific roles of protein-phospholipid interactions in the yeast cytochrome bc 1 complex structure.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Conclusion: Conclusion: Results are discussed in relation to the potential development of complex-mixture dairy products into health-modulating products.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

[44]

Cellular localization

Proteins in different cellular compartments and structures tagged with green fluorescent protein) (here, white).
.The study of proteins in vivo is often concerned with the synthesis and localization of the protein within the cell.^ RNA gene cluster code for three similar, unusual Gly-tRNAs that may be used in the synthesis of the peptidoglycan in the cell wall but not in protein synthesis .

^ The study of the structure and function of proteins, including the way they work and interact with each other inside cells.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ The study of protein expression in cancer cells may give information about a specific type of cancer, the best treatment to use, and how well a treatment works.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.Although many intracellular proteins are synthesized in the cytoplasm and membrane-bound or secreted proteins in the endoplasmic reticulum, the specifics of how proteins are targeted to specific organelles or cellular structures is often unclear.^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ The synthesis pauses while the ribosome-protein complex is transferred to an SRP receptor on the endoplasmic reticulum (ER, which is a membrane-bound organelle).

^ Regulated In regulated secretion, proteins are packaged as described in the constitutive pathway, but they are only secreted in response to a specific signal, such as neural or hormonal stimulation.

.A useful technique for assessing cellular localization uses genetic engineering to express in a cell a fusion protein or chimera consisting of the natural protein of interest linked to a "reporter" such as green fluorescent protein (GFP).^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ RNA gene cluster code for three similar, unusual Gly-tRNAs that may be used in the synthesis of the peptidoglycan in the cell wall but not in protein synthesis .

^ A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation.

[45] .The fused protein's position within the cell can be cleanly and efficiently visualized using microscopy,[46] as shown in the figure opposite.^ RNA gene cluster code for three similar, unusual Gly-tRNAs that may be used in the synthesis of the peptidoglycan in the cell wall but not in protein synthesis .

^ Intracellular concentrations of two conserved proteins, the growth-related protein Fis and the stationary-phase protein Dps, were analyzed by epifluoresence microscopy of uncultivated cells by using enterobacterial group-specific polyclonal fluorochrome-coupled antibodies .

^ Zentralbl Mikrobiol, 1991, 146(3), 181 - 4 Single cell protein production by Aspergillus niger and its evaluation; Singh A et al.; An efficient cellulolytic mold, Aspergillus niger AS-101 was used to produce single cell protein from alkalitreated corn cobs .

.Other methods for elucidating the cellular location of proteins requires the use of known compartmental markers for regions such as the ER, the Golgi, lysosomes/vacuoles, mitochondria, chloroplasts, plasma membrane, etc.^ G- protein complex plasma membrane .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ Golgi apparatus plasma membrane .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ ER- Golgi intermediate compartment extracellular region membrane .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

.With the use of fluorescently-tagged versions of these markers or of antibodies to known markers, it becomes much simpler to identify the localization of a protein of interest.^ To identify and characterise proteins mass spectrometry, X-ray crystallography, and NMR are used.

^ The polypeptide whilst folding may become trapped in the local energy well and cannot fold to the global energy minimum (kinetic hypothesis of protein folding, Wetlaufer, 1973; Wetlaufer and Ristow, 1973).
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Furthermore, because all known one-celled organisms have similar genetic mechanisms, it is reasonable to assume that these mechanisms were operating for a considerable portion of the time that these one-celled organisms evolved from simpler organisms having many fewer proteins.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

For example, indirect immunofluorescence will allow for fluorescence colocalization and demonstration of location. .Fluorescent dyes are used to label cellular compartments for a similar purpose.^ Using confocal laser scanning microscopy, we demonstrated that fluorescently labeled lactoferrin is endocytosed and can be visualized in the cytoplasm of primary osteoblastic cells.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

[47]
Other possibilities exist, as well. .For example, immunohistochemistry usually utilizes an antibody to one or more proteins of interest that are conjugated to enzymes yielding either luminescent or chromogenic signals that can be compared between samples, allowing for localization information.^ For example, one study found that whey stimulated protein synthesis by 68% compared to 31% for casein, but casein resulted in a higher net leucine balance (a marker of protein synthesis and degradation) over a seven hour period (1).
  • Bulk Nutrition - Whey Protein by David Tolson 2 February 2010 16:52 UTC www.bulknutrition.com [Source type: Academic]

^ One would expect, therefore, that proteins of different shapes would differ in considerably more than 70% of their amino acids at different positions in the protein.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Folds are identified with the three-dimensional structures of domains, so that a protein can have more than one fold.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

Another applicable technique is cofractionation in sucrose (or other material) gradients using isopycnic centrifugation.[48] .While this technique does not prove colocalization of a compartment of known density and the protein of interest, it does increase the likelihood, and is more amenable to large-scale studies.^ Proteomics is the large-scale study of proteins, particularly their structures and functions.

^ These new proteins could participate in new large scale replacements, and lead to more beneficial new shapes of "second generation" proteins.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ One study published in 1999 demonstrated that green tea does in fact increase metabolic rate.
  • Protein Supplements – Fitness and bodybuilding supplements! 2 February 2010 16:52 UTC proteinsupplementsplus.com [Source type: FILTERED WITH BAYES]

Finally, the gold-standard method of cellular localization is immunoelectron microscopy. .This technique also uses an antibody to the protein of interest, along with classical electron microscopy techniques.^ To characterise protein-protein interactions, a number of chromatography techniques are used especially affinity chromatography.

^ Intracellular concentrations of two conserved proteins, the growth-related protein Fis and the stationary-phase protein Dps, were analyzed by epifluoresence microscopy of uncultivated cells by using enterobacterial group-specific polyclonal fluorochrome-coupled antibodies .

^ Availability in both assays estimated using the slope-ratio technique wherein milligrams of available phosphorus per gram of RNA or single-cell protein was calculated .

The sample is prepared for normal electron microscopic examination, and then treated with an antibody to the protein of interest that is conjugated to an extremely electro-dense material, usually gold. This allows for the localization of both ultrastructural details as well as the protein of interest.[49]
.Through another genetic engineering application known as site-directed mutagenesis, researchers can alter the protein sequence and hence its structure, cellular localization, and susceptibility to regulation.^ Through genetic engineering, researchers can alter the sequence and hence the structure, "targeting", susceptibility to regulation and other properties of a protein.

^ Two such motifs are (i) a motif specific for DNA binding and (ii) a motif specific for calcium binding and is present in parvalbumin, calmodulin, troponin-C, and other proteins that bind calcium and thereby regulate cellular activities.
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ The genetic sequences of different proteins may be spliced together to create "chimeric" proteins that possess properties of both.

.This technique even allows the incorporation of unnatural amino acids into proteins, using modified tRNAs,[50] and may allow the rational design of new proteins with novel properties.^ Properties of amino acids .
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ A typical protein may contain 500 or more amino acids.

^ N- terminal protein amino acid acetylation .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

[51]

Proteomics and bioinformatics

.The total complement of proteins present at a time in a cell or cell type is known as its proteome, and the study of such large-scale data sets defines the field of proteomics, named by analogy to the related field of genomics.^ Proteomics is the large-scale study of proteins, particularly their structures and functions.

^ When the genome is defined by the sequence of nucleotides, the proteome cannot be limited to the sum of the sequences of the proteins present.

^ A piece of a protein found only on melanoma (a type of skin cancer) cells.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

.Key experimental techniques in proteomics include 2D electrophoresis,[52] which allows the separation of a large number of proteins, mass spectrometry,[53] which allows rapid high-throughput identification of proteins and sequencing of peptides (most often after in-gel digestion), protein microarrays,[54] which allow the detection of the relative levels of a large number of proteins present in a cell, and two-hybrid screening, which allows the systematic exploration of protein–protein interactions.^ Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis.

^ Key technologies for proteomics: 1-D electrophoresis and 2-D electrophoresis are for the separation and visualisation of proteins.

^ Protein standard in 1D and 2D SDS gel electrophoresis .
  • BioVendor R&D - Products \ Proteins 2 February 2010 16:52 UTC www.biovendor.com [Source type: Academic]

[55] The total complement of biologically possible such interactions is known as the interactome.[56] .A systematic attempt to determine the structures of proteins representing every possible fold is known as structural genomics.^ Protein structure determination .
  • Proteins 2 February 2010 16:52 UTC www.friedli.com [Source type: Academic]

^ Progress of membrane protein structure determination .
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Given the usefulness of known protein structures in such valuable tasks as rational drug design, this is a highly active field of research.

[57]
.The large amount of genomic and proteomic data available for a variety of organisms, including the human genome, allows researchers to efficiently identify homologous proteins in distantly related organisms by sequence alignment.^ ARP3 actin- related protein 3 homolog .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ With completion of a rough draft of the human genome, many researchers are now looking at how genes and proteins interact to form other proteins.

^ The complete proteome for an organism can be conceptualized as the complete set of proteins from all of the various cellular proteomes.

.Sequence profiling tools can perform more specific sequence manipulations such as restriction enzyme maps, open reading frame analyses for nucleotide sequences, and secondary structure prediction.^ In more formal terms, this is the prediction of protein tertiary structure from primary structure.

^ The reason for this is that predicting the structure of a protein from its amino acid sequence is a very hard problem.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ If there is 30% or more agreement in the amino acid sequences, the structure of the proteins will be similar.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

.From this data phylogenetic trees can be constructed and evolutionary hypotheses developed using special software like ClustalW regarding the ancestry of modern organisms and the genes they express.^ Finally, it is likely that some mutation to a useless gene would render it nonfunctional, producing a pseudogene, which would be unlikely to result in the evolution of a new protein of benefit to the organism.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ This means that these useless genes are likely actually harmful to the organism, more harmful than pseudogenes.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Furthermore, a useless gene produces a protein that either fails to fold properly or has no useful function in the organism.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

.The field of bioinformatics seeks to assemble, annotate, and analyze genomic and proteomic data, applying computational techniques to biological problems such as gene finding and cladistics.^ The term proteome was first used in 1995 and has been applied to several different types of biological systems.

^ A surprising finding of the Human Genome Project is that there are far fewer genes that code for proteins in the human genome than there are proteins in the human proteome (~22,000 genes vs ~200,000 proteins).

^ The proteome is larger than the genome, expecially in eukaryotes, in the sense there are more proteins than genes.

Structure prediction and simulation

.Complementary to the field of structural genomics, protein structure prediction seeks to develop efficient ways to provide plausible models for proteins whose structures have not yet been determined experimentally [58].^ Reference is made to all of the protein types whose structures have been determined.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Progress of membrane protein structure determination .
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Protein supplementation plays a big role in providing essential building blocks that help regulate the body in an incredible number of ways.
  • Protein Powders Supplements at the Lowest Prices! 2 February 2010 16:52 UTC www.a1supplements.com [Source type: General]

.The most successful type of structure prediction, known as homology modeling, relies on the existence of a "template" structure with sequence similarity to the protein being modeled; structural genomics' goal is to provide sufficient representation in solved structures to model most of those that remain.^ Comparative protein modelling uses previously solved structures as starting points, or templates.

^ PREDICTED: similar to Protein KIAA0841 isoform 1 .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

^ PREDICTED: similar to actin- related protein 2 .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

[59] .Although producing accurate models remains a challenge when only distantly related template structures are available, it has been suggested that sequence alignment is the bottleneck in this process, as quite accurate models can be produced if a "perfect" sequence alignment is known.^ In each case, a scoring function is used to assess the compatibility of the sequence to the structure, thus yielding possible three-dimensional models.

^ Comparative protein modelling uses previously solved structures as starting points, or templates.

^ Crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

[60] .Many structure prediction methods have served to inform the emerging field of protein engineering, in which novel protein folds have already been designed.^ Through genetic engineering, researchers can alter the sequence and hence the structure, "targeting", susceptibility to regulation and other properties of a protein.

^ In more formal terms, this is the prediction of protein tertiary structure from primary structure.

^ Also, from [Service 97]: pairs of natural proteins differing in up to 70% of their amino acid sequences virtually always fold up in to the same general 3D structure.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

[61] .A more complex computational problem is the prediction of intermolecular interactions, such as in molecular docking and protein–protein interaction prediction.^ In more formal terms, this is the prediction of protein tertiary structure from primary structure.

^ Specific roles of protein-phospholipid interactions in the yeast cytochrome bc 1 complex structure.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Also, many protein reactions require at least three proteins to interact, meaning even more constraints.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

[62]
.The processes of protein folding and binding can be simulated using such technique as molecular mechanics, in particular, molecular dynamics and Monte Carlo, which increasingly take advantage of parallel and distributed computing (Folding@Home project[63]; molecular modeling on GPU).^ However, the distributed computing project, Folding at home, is tackling such simulation difficulties.

^ Using production designs that take advantage of the bacterial and mammalian cell expression systems, BioVendor produces a wide range of HEK293 Cell-Expressed Recombinant Proteins , E.coli-Expressed Recombinant Proteins and Isolated Natural Proteins .
  • BioVendor R&D - Products \ Proteins 2 February 2010 16:52 UTC www.biovendor.com [Source type: Academic]

^ To attempt to predict protein structure de novo for larger proteins, we will need better algorithms and larger computational resources like those afforded by either powerful supercomputers (such as Blue Gene) or distributed computing (see Human Proteome Folding Project).

.The folding of small alpha-helical protein domains such as the villin headpiece[64] and the HIV accessory protein[65] have been successfully simulated in silico, and hybrid methods that combine standard molecular dynamics with quantum mechanics calculations have allowed exploration of the electronic states of rhodopsins.^ Direct simulation of protein folding via methods such as molecular dynamics is not generally tractable for both practical and theoretical reasons.

^ Therefore, only one such transfer of genetic material is feasible, so the total number of new folds obtainable this way and satisfying all constraints will be small.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Folds are identified with the three-dimensional structures of domains, so that a protein can have more than one fold.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

[66]

Nutrition

.Most microorganisms and plants can biosynthesize all 20 standard amino acids, while animals (including humans) must obtain some of the amino acids from the diet.^ These essential amino acids must be obtained through the diet or supplementation.

^ There are twenty amino acids commonly found in animal based proteins and eight of these are considered to be essential since the body cannot produce them on its own.

^ I bought some wey based protein powder as used by body builders, it has 22 grams protein, casein & lots of amino acids.
  • How Much Protein Should I Eat in a Day? | Project Swole 2 February 2010 16:52 UTC www.projectswole.com [Source type: General]

[27] .The amino acids that an organism cannot synthesize on its own are referred to as essential amino acids.^ These 8 are called the essential amino acids.

^ There are twenty amino acids commonly found in animal based proteins and eight of these are considered to be essential since the body cannot produce them on its own.

^ When protein is listed on a nutrition label it only refers to the amount of complete proteins in the food, though the food may be very strong in a subset of the essential amino acids.

.Key enzymes that synthesize certain amino acids are not present in animals — such as aspartokinase, which catalyzes the first step in the synthesis of lysine, methionine, and threonine from aspartate.^ There are twenty amino acids commonly found in animal based proteins and eight of these are considered to be essential since the body cannot produce them on its own.

^ Protein synthesis is influenced synergistically by postexercise amino acid supplementation, but the importance of the timing of protein intake remains unresolved.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

^ ResidueAtomNumber () Atom number of the first atom of the amino acid.

.If amino acids are present in the environment, microorganisms can conserve energy by taking up the amino acids from their surroundings and downregulating their biosynthetic pathways.^ Also, from [Service 97]: pairs of natural proteins differing in up to 70% of their amino acid sequences virtually always fold up in to the same general 3D structure.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Alanine, the first amino acid residue at the N-terminal end of beta was not present at this position in alpha .

^ N- linked glycosylation protein amino acid phosphorylation transmembrane receptor protein tyrosine kinase signaling pathway .
  • Urinary Exosome Protein Database. LKEM, DIR, NHLBI, NIH 28 January 2010 0:42 UTC dir.nhlbi.nih.gov [Source type: Academic]

.In animals, amino acids are obtained through the consumption of foods containing protein.^ Peptides that contain many amino acids are called polypeptides or proteins.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Different foods contain different ratios of the essential amino acids.

^ A typical protein may contain 500 or more amino acids.

.Ingested proteins are broken down through digestion, which typically involves denaturation of the protein through exposure to acid and hydrolysis by enzymes called proteases.^ Once a protein molecule is broken down into its individual units, amino acids, they are transported to muscle cells via the bloodstream to be used as the building blocks for muscle tissue.

^ The PDCAAS is based on whether or not a protein meets the human amino acid requirements (hence, incomplete proteins have lower scores) as well as how digestible the protein is.
  • Bulk Nutrition - Whey Protein by David Tolson 2 February 2010 16:52 UTC www.bulknutrition.com [Source type: Academic]

^ Studies with gastric and pancreatic proteinase digests of whey proteins indicate that enzyme specificity rather than extent of hydrolysis dictates the ACE inhibitory potency of whey hydrolysates.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

.Some ingested amino acids are used for protein biosynthesis, while others are converted to glucose through gluconeogenesis, or fed into the citric acid cycle.^ There are twenty amino acids commonly found in animal based proteins and eight of these are considered to be essential since the body cannot produce them on its own.

^ Once a protein molecule is broken down into its individual units, amino acids, they are transported to muscle cells via the bloodstream to be used as the building blocks for muscle tissue.

^ Whey protein rich in alpha-lactalbumin increases the ration of plasma tryptophan to the sum of the other large neutral amino acids and improves cognitive performance in stress vulnerable subjects.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

.This use of protein as a fuel is particularly important under starvation conditions as it allows the body's own proteins to be used to support life, particularly those found in muscle.^ Many bodybuilders use Protein to help build muscle in the body.

^ There are twenty amino acids commonly found in animal based proteins and eight of these are considered to be essential since the body cannot produce them on its own.

^ The entirety of proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of proteins found in a particular cell type under a particular type of stimulation, are referred to as the proteome of the organism or cell type respectively.

[67] .Amino acids are also an important dietary source of nitrogen.^ Bio-available Great Natural Source of High Potency Essential Amino Acids, including BCAA’s.
  • SALE Bulk Whey Protein 25lbs 400 serv American Sports Nutrition $139.95 Ephedra Diet Pills Bodybuilding Supplements Buy Weight Loss Prohormone Muscle Workout Products on sale! 18 September 2009 15:25 UTC www.worldclassnutrition.com [Source type: General]

^ Bio-available Great Natural Source of High Potency Essential Amino Acids, including BCAAs.
  • American Whey Protein 10lbs - Discount Offer $55.99 - i-Supplements� 2 February 2010 16:52 UTC www.i-supplements.com [Source type: General]

[citation needed]

History and etymology

.Proteins were recognized as a distinct class of biological molecules in the eighteenth century by Antoine Fourcroy and others, distinguished by the molecules' ability to coagulate or flocculate under treatments with heat or acid.^ A severe mental disorder in which a person loses the ability to recognize reality or relate to others.
  • Dictionary of Cancer Terms - National Cancer Institute 2 February 2010 16:52 UTC www.cancer.gov [Source type: Academic]

^ Proteins are one of the classes of bio-macromolecules, alongside polysaccharides and nucleic acids, that make up the primary constituents of living things.

^ Since prion proteins act on other molecules of their own kind, they can be considered as self-specific examples of a more general type of chaperone activity.

Noted examples at the time included albumin from egg whites, blood serum albumin, fibrin, and wheat gluten. .Dutch chemist Gerhardus Johannes Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula, C400H620N100O120P1S1.^ This could happen if the protein only involved biological mechanisms that were common among many organisms, but then the probabilities are about the same as if all these organisms belonged to the same population.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Not all prions are dangerous; in fact, prion-like proteins are found naturally in many (perhaps all) plants and animals.

^ Brandon: In my opinion, if you are trying to gain weight you should keep protein intake the same whether working out or not.
  • How Much Protein Should I Eat in a Day? | Project Swole 2 February 2010 16:52 UTC www.projectswole.com [Source type: General]

[68] .He came to the erroneous conclusion that they might be composed of a single type of (very large) molecule.^ Each subunit consists of one or two very large RNA molecules (known as ribosomal RNA or rRNA) and multiple smaller protein molecules.

^ Protein is a large, complex molecule composed of amino acids.

^ Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a an actin filament.

.The term "protein" to describe these molecules was proposed in 1838 by Mulder's associate Jöns Jakob Berzelius; protein is derived from the Greek word πρωτεῖος (proteios), meaning "primary"[69], "in the lead", or "standing in front".[70] Mulder went on to identify the products of protein degradation such as the amino acid leucine for which he found a (nearly correct) molecular weight of 131 Da.^ Protein is a large, complex molecule composed of amino acids.

^ These 8 are called the essential amino acids.

^ Proteins are highly complex molecules comprised of linked amino acids.

[68]
.The difficulty in purifying proteins in large quantities made them very difficult for early protein biochemists to study.^ Proteomics is the large-scale study of proteins, particularly their structures and functions.

^ Each subunit consists of one or two very large RNA molecules (known as ribosomal RNA or rRNA) and multiple smaller protein molecules.

^ Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a an actin filament.

.Hence, early studies focused on proteins that could be purified in large quantities, e.g., those of blood, egg white, various toxins, and digestive/metabolic enzymes obtained from slaughterhouses.^ Studies with gastric and pancreatic proteinase digests of whey proteins indicate that enzyme specificity rather than extent of hydrolysis dictates the ACE inhibitory potency of whey hydrolysates.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

^ I have increased my protein intake eating white eggs.
  • How Much Protein Should I Eat in a Day? | Project Swole 2 February 2010 16:52 UTC www.projectswole.com [Source type: General]

^ These new proteins could participate in new large scale replacements, and lead to more beneficial new shapes of "second generation" proteins.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

In the 1950s, the Armour Hot Dog Co. purified 1 kg of pure bovine pancreatic ribonuclease A and made it freely available to scientists; this gesture helped ribonuclease A become a major target for biochemical study for the following decades.[68]
.Linus Pauling is credited with the successful prediction of regular protein secondary structures based on hydrogen bonding, an idea first put forth by William Astbury in 1933.[71] Later work by Walter Kauzmann on denaturation,[72][73] based partly on previous studies by Kaj Linderstrøm-Lang,[74] contributed an understanding of protein folding and structure mediated by hydrophobic interactions.^ The secondary structures are held together by hydrogen bonds.

^ A fold is defined as a given collection of secondary structure elements with a specified topology, in a specified geometrical orientation.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Suppose (model A) that if this mutation occurs to a site outside the specified set of 34 sites, the mutation has a probability of one half of permitting the specified protein fold to form and for the protein to satisfy the constraints necessary for a functional protein (the right hydrogen bonding occurs, etc.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

.In 1949 Fred Sanger correctly determined the amino acid sequence of insulin, thus conclusively demonstrating that proteins consisted of linear polymers of amino acids rather than branched chains, colloids, or cyclols.^ It has the aim of determining the three-dimensional structure of proteins from their amino acid sequences.

^ Relation between glutamine, branched-chain amino acid, and protein metabolism.
  • Welcome to Whey Protein.com - Recent Studies 2 February 2010 16:52 UTC www.wheyprotein.com [Source type: Academic]

^ By amino acid sequencing 41 amino acids were determined .

[75] .The first atomic-resolution structures of proteins were solved by X-ray crystallography in the 1960s and by NMR in the 1980s.^ X-ray structure of a protein-conducting channel.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ High-resolution x-ray structure of human aquaporin 5.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ To identify and characterise proteins mass spectrometry, X-ray crystallography, and NMR are used.

.As of 2009, the Protein Data Bank has over 55,000 atomic-resolution structures of proteins.^ Structure of bacteriorhodopsin at 1.55 angstrom resolution.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

^ Structure of the protein subunits in the photosynthetic reaction centre of Rhodospeudomonas viridis at 3 Å resolution.
  • Membrane Proteins of Known Structure 2 February 2010 16:52 UTC blanco.biomol.uci.edu [Source type: Academic]

[76] .In more recent times, cryo-electron microscopy of large macromolecular assemblies[77] and computational protein structure prediction of small protein domains[78] are two methods approaching atomic resolution.^ In more formal terms, this is the prediction of protein tertiary structure from primary structure.

^ Two proteins sharing a domain might share a subsequence that is largely similar.
  • Problems in Protein Evolution 28 January 2010 0:42 UTC www.cs.unc.edu [Source type: Academic]

^ Prediction of structures for small proteins is now a perfectly realistic goal.

See also

Footnotes

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References

  • Branden C, Tooze J. (1999). Introduction to Protein Structure. New York: Garland Pub. ISBN 0-8153-2305-0. 
  • Murray RF, Harper HW, Granner DK, Mayes PA, Rodwell VW. (2006). Harper's Illustrated Biochemistry. New York: Lange Medical Books/McGraw-Hill. ISBN 0-07-146197-3. 
  • Van Holde KE, Mathews CK. (1996). Biochemistry. Menlo Park, Calif: Benjamin/Cummings Pub. Co., Inc. ISBN 0-8053-3931-0. 
  • Jörg von Hagen, VCH-Wiley 2008 Proteomics Sample Preparation. ISBN 978-3-527-31796-7

External links

Databases and projects

Tutorials and educational websites


Wiktionary

Up to date as of January 15, 2010

Definition from Wiktionary, a free dictionary

See also protein

German

Noun

Protein n. (genitive Proteins or Proteines, plural Proteine)
  1. protein

Simple English

Proteins are large molecules built from small units known as amino acids. These small pieces are stuck together with peptide bonds. They do different things depending on their shape. They can be found in meat or muscle. They are used for growth and repair, as well as for strengthening the bones. They help to make tissue and cells. They can be found in animals, plants, fungi, bacteria, and also in the human body. For example, muscles contain a lot of proteins. Body builders will eat foods with a lot of protein because exercise breaks down the muscles, allowing new protein to be used to rebuild them larger and stronger. Proteins form an important part in foods like milk, eggs, meat, fish, beans, and nuts. There are four things that determine what a protein will do. The first is the order that the amino acids are in. There are 20 amino acids, and they are all a bit different. The second is the little twists in the chain. The third is how the entire thing is folded up. The fourth is whether it's working with other proteins.

Animals eat proteins and break them down into amino acids in order to recombine them into other things needed, including other proteins and other amino acids. Animals have certain amino acids they are not able to create this way, and must get from their food. These are called "essential amino acids" and different animals have different amino acids they are not able to create. Meat contains all the essential amino acids humans need; most plants do not. However, eating a mixture of plants, such as both wheat and peanut butter, or rice and beans, provides all the essential amino acids needed. Soy products like tofu provide all the essential amino acids but are not the only way to get the protein you need. Amino acids are used to build new proteins that are used as enzymes, hormones, or antibodies. Protein is very important to have in your diet; it's basically what you are made of. Proteins are essential for life.

The scientist Jons Jacob Berzelius gave proteins their name,[1] but many other scientists have studied proteins.

References

Other websites

  • Protein from the Harvard School of Public Health


Citable sentences

Up to date as of December 12, 2010

Here are sentences from other pages on Protein, which are similar to those in the above article.








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