Protein

thumb|A representation of the 3D structure of the protein [[myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).]]

Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.

A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. 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. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can work together to achieve a particular function, and they often associate to form stable protein complexes.

Once formed, proteins only exist for a certain period and are then degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly, often by the proteasome, which is a large protein assembly itself. These proteins are degraded either due to being targeted (ubiquitin ligases can mark a protein for destruction) or due to being unstable or damaged.

Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Some proteins have structural or mechanical functions, such as actin and myosin in muscle, and the cytoskeleton's scaffolding proteins that maintain cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for metabolic use.

History and etymology

Discovery and early studies

Proteins have been studied and recognized since the 1700s by Antoine Fourcroy and others, Vegetable (plant) proteins studied in the late 1700s and early 1800s included gluten, plant albumin, gliadin, and legumin. Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula, C₄₀₀H₆₂₀N₁₀₀O₁₂₀P₁S₁. "in the lead", or "standing in front", Thomas Burr Osborne compiled a detailed review of the vegetable proteins at the Connecticut Agricultural Experiment Station. Osborne, alongside Lafayette Mendel, established several nutritionally essential amino acids in feeding experiments with laboratory rats. Diets lacking an essential amino acid stunts the rats' growth, consistent with Liebig's law of the minimum. The final essential amino acid to be discovered, threonine, was identified by William Cumming Rose.

The difficulty in purifying proteins impeded work by early protein biochemists. Proteins could be obtained in large quantities from blood, egg whites, and keratin, but individual proteins were unavailable. In the 1950s, the Armour Hot Dog Company purified 1 kg of 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. The central role of proteins as enzymes in living organisms that catalyzed reactions was not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was in fact a protein.

The first protein to have its amino acid chain sequenced was insulin, by Frederick Sanger, in 1949. 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.

Structure

thumb|upright=1.15|[[John Kendrew with model of myoglobin in progress]]

With the development of X-ray crystallography, it became possible to determine protein structures as well as their sequences. The first protein structures to be solved were hemoglobin by Max Perutz and myoglobin by John Kendrew, in 1958.

Classification

Proteins are primarily classified by sequence and structure, although other classifications are commonly used. Especially for enzymes the EC number system provides a functional classification scheme. Similarly, gene ontology classifies both genes and proteins by their biological and biochemical function, and by their intracellular location.

Sequence similarity is used to classify proteins both in terms of evolutionary and functional similarity. This may use either whole proteins or protein domains, especially in multi-domain proteins. Protein domains allow protein classification by a combination of sequence, structure and function, and they can be combined in many ways. In an early study of 170,000 proteins, about two-thirds were assigned at least one domain, with larger proteins containing more domains (e.g. proteins larger than 600 amino acids having an average of more than 5 domains).

Biochemistry

thumb|upright=1.35|Chemical structure of the peptide bond (bottom) and the three-dimensional structure of a peptide bond between an [[alanine and an adjacent amino acid (top/inset). The bond itself is made of the CHON elements.]]

thumb|upright=1.35|[[Resonance (chemistry)|Resonance structures of the peptide bond that links individual amino acids to form a protein polymer]]

Most proteins consist of linear polymers built from series of up to 20 <small>L</small>-α-amino acids. All proteinogenic amino acids have a common structure where an α-carbon is bonded to an amino group, a carboxyl group, and a variable side chain. Only proline differs from this basic structure as its side chain is cyclical, bonding to the amino group, limiting protein chain flexibility. The peptide bond has two resonance forms that confer some double-bond character to the backbone. The alpha carbons are roughly coplanar with the nitrogen and the carbonyl (C=O) group. The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone. One consequence of the N-C(O) double bond character is that proteins are somewhat rigid. By convention, peptide sequences are written N-terminus to C-terminus, correlating with the order in which proteins are synthesized by ribosomes.

The words protein, polypeptide, and peptide are a little ambiguous and can overlap in meaning. 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 3D structure. But the boundary between the two is not well defined and usually lies near 20–30 residues.

Abundance in cells

A typical bacterial cell, e.g. E. coli and Staphylococcus aureus, is estimated to contain about 2 million proteins. Smaller bacteria, such as Mycoplasma or spirochetes contain fewer molecules, on the order of 50,000 to 1 million. By contrast, eukaryotic cells are larger and thus contain much more protein. For instance, yeast cells have been estimated to contain about 50 million protein molecules and human cells on the order of 1 to 3 billion. The concentration of individual protein copies ranges from a few molecules per cell up to 20 million. Not all genes coding proteins are expressed in most cells and their number depends on, for example, cell type and external stimuli. For instance, of the 20,000 or so proteins encoded by the human genome, only 6,000 are detected in lymphoblastoid cells. The most abundant protein in nature is thought to be RuBisCO, an enzyme that catalyzes the incorporation of carbon dioxide into organic matter in photosynthesis. Plants can consist of as much as 1% by weight of this enzyme.

Synthesis

Biosynthesis

thumb|A ribosome produces a protein using mRNA as template.

thumb|class=skin-invert-image|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. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. 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. 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. For instance, yeast proteins are on average 466 amino acids long and 53 kDa in mass. Domains usually have specific functions, such as enzymatic activities (e.g. kinase) or they serve as binding modules.|center]]

Sequence motif

Short amino acid sequences within proteins often act as recognition sites for other proteins. For instance, SH3 domains typically bind to short PxxP motifs (i.e. 2 prolines [P], separated by two unspecified amino acids [x], although the surrounding amino acids may determine the exact binding specificity). Many such motifs has been collected in the Eukaryotic Linear Motif (ELM) database.

Cellular functions

Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes. The set of proteins expressed in a particular cell or cell type is known as its proteome.

Transmembrane proteins can serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse. Membrane proteins contain internal channels that allow such molecules to enter and exit the cell. 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. for example, enzyme kinetics studies explore the chemical mechanism of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules. By contrast, in vivo experiments can provide information about the physiological role of a protein in the context of a cell or even a whole organism, and can often provide more information about protein behavior in different contexts. In silico studies use computational methods to study proteins.

Protein purification

Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography; Another applicable technique is cofractionation in sucrose (or other material) gradients using isopycnic centrifugation.

In silico simulation of dynamical processes

A more complex computational problem is the prediction of intermolecular interactions, such as in molecular docking,

Chemical analysis

The total nitrogen content of organic matter is mainly formed by the amino groups in proteins. The total Kjeldahl nitrogen (TKN) is a measure of nitrogen widely used in the analysis of (waste) water, soil, food, feed and organic matter in general. As the name suggests, the Kjeldahl method is applied. More sensitive methods are available.

Digestion

thumb|class=skin-invert-image|230px|Hydrolysis of protein. X = HCl and heat for industrial proteolysis. X = protease for biological proteolysis

In the absence of catalysts, proteins are slow to hydrolyze. The breakdown of proteins to small peptides and amino acids (proteolysis) is a step in digestion; these breakdown products are then absorbed in the small intestine<!--jejunum-->. The hydrolysis of proteins relies on enzymes called proteases or peptidases. Proteases, which are themselves proteins, come in several types according to the particular peptide bonds that they cleave as well as their tendency to cleave peptide bonds at the terminus of a protein (exopeptidases) vs peptide bonds at the interior of the protein (endopeptidases). Pepsin is an endopeptidase in the stomach. Subsequent to the stomach, the pancreas secretes other proteases to complete the hydrolysis, these include trypsin and chymotrypsin.

Protein hydrolysis is employed commercially as a means of producing amino acids from bulk sources of protein, such as blood meal, feathers, keratin. Such materials are treated with hot hydrochloric acid, which effects the hydrolysis of the peptide bonds.

Mechanical properties

The mechanical properties of proteins are highly diverse and are often central to their biological function, as in the case of proteins like keratin and collagen. For instance, the ability of muscle tissue to continually expand and contract is directly tied to the elastic properties of their underlying protein makeup. Beyond fibrous proteins, the conformational dynamics of enzymes and the structure of biological membranes, among other biological functions, are governed by the mechanical properties of the proteins. Outside of their biological context, the unique mechanical properties of many proteins, along with their relative sustainability when compared to synthetic polymers, have made them desirable targets for next-generation materials design.

Young's modulus, E, is calculated as the axial stress σ over the resulting strain ε. It is a measure of the relative stiffness of a material. In the context of proteins, this stiffness often directly correlates to biological function. For example, collagen, found in connective tissue, bones, and cartilage, and keratin, found in nails, claws, and hair, have observed stiffnesses that are several orders of magnitude higher than that of elastin, which is thought to give elasticity to structures such as blood vessels, pulmonary tissue, and bladder tissue, among others. In comparison to this, globular proteins, such as Bovine Serum Albumin, which float relatively freely in the cytosol and often function as enzymes (and thus undergoing frequent conformational changes) have comparably much lower Young's moduli.

The Young's modulus of a single protein can be found through molecular dynamics simulation. Using either atomistic force-fields, such as CHARMM or GROMOS, or coarse-grained forcefields like Martini, a single protein molecule can be stretched by a uniaxial force while the resulting extension is recorded in order to calculate the strain. Experimentally, methods such as atomic force microscopy can be used to obtain similar data. The internal dynamics of proteins involve subtle elastic and plastic deformations induced by viscoelastic forces, which can be probed by nano-rheology techniques.

At the macroscopic level, the Young's modulus of cross-linked protein networks can be obtained through more traditional mechanical testing. Experimentally observed values for a few proteins can be seen below.

{| class="wikitable"

|+Elasticity of various proteins

!Protein

!Protein class

!Young's modulus

|-

|keratin (cross-linked)

|fibrous

|1.5–10&nbsp;GPa

|-

|elastin (cross-linked)

|fibrous

|1&nbsp;MPa

|-

|resilin (cross-linked)

|fibrous

|1–2&nbsp;MPa

|}

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Viscosity

In addition to serving as enzymes within the cell, globular proteins often act as key transport molecules. For instance, Serum Albumins, a key component of blood, are necessary for the transport of a multitude of small molecules throughout the body.

Viscosity, η, is generally given is a measure of a fluid's resistance to deformation. It can be calculated as the ratio between the applied stress and the rate of change of the resulting shear strain, that is, the rate of deformation. Viscosity of complex liquid mixtures, such as blood, often depends strongly on temperature and solute concentration. For serum albumin, specifically bovine serum albumin, the following relation between viscosity and temperature and concentration can be used.

<math>\eta = \exp\left[ \frac{c}{\alpha-\beta\ c}\left(-B +D T + \frac{\Delta E}{R T}\right)\right] </math>

where c is the concentration, T is the temperature, R is the gas constant, and α, β, B, D, and ΔE are all material-based property constants. This equation has the form of an Arrhenius equation, assigning viscosity an exponential dependence on temperature and concentration.

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See also

References

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Further reading

; Textbooks

; History

External links

Databases and projects

• NCBI Entrez Protein database
• NCBI Protein Structure database
• Human Protein Reference Database
• Human Proteinpedia
• Folding@Home (Stanford University)
• Protein Databank in Europe (see also PDBeQuips, short articles and tutorials on interesting PDB structures)
• Research Collaboratory for Structural Bioinformatics (see also Molecule of the Month , presenting short accounts on selected proteins from the PDB)
• Proteopedia – Life in 3D: rotatable, zoomable 3D model with wiki annotations for every known protein molecular structure.
• UniProt the Universal Protein Resource

Tutorials and educational websites

• "An Introduction to Proteins" from HOPES (Huntington's Disease Outreach Project for Education at Stanford)
• Proteins: Biogenesis to Degradation – The Virtual Library of Biochemistry and Cell Biology