Protein 23634 224809379 2008-07-10T14:45:52Z TimVickers 1635280 remove material unsupported by reference [[Image:Myoglobin.png|thumb|200px|A representation of the 3D structure of [[myoglobin]] showing coloured [[alpha helix|alpha helices]]. This protein was the first to have its structure solved by [[X-ray crystallography]].]] {{otheruses4|a class of biomolecules|alternate uses, such as [[protein in nutrition]]|Protein (disambiguation)}} '''Proteins''' are large [[organic compound]]s made of [[amino acid]]s arranged in a linear chain and joined together by [[peptide bond]]s between the [[carboxyl]] and [[amino]] groups of adjacent amino acid [[Residue (chemistry)|residues]]. The sequence of amino acids in a protein is defined by a [[gene]] and encoded in the [[genetic code]]. Although this genetic code specifies 20 "standard" amino acids plus [[selenocysteine]] and - in certain archaea - [[pyrrolysine]], the residues in a protein are sometimes chemically altered in [[post-translational modification]]: either before the protein can function in the [[Cell (biology)|cell]], or as part of control mechanisms. Proteins can also work together to achieve a particular function, and they often associate to form stable [[protein complex|complex]]es.<ref>{{cite book | last = Maton | first = Anthea | authorlink = | coauthors = Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon Warner, David LaHart, Jill D. Wright | title = Human Biology and Health | publisher = Prentice Hall | date = 1993 | location = Englewood Cliffs, New Jersey, USA | pages = | url = | doi = | id = | isbn = 0-13-981176-1}}</ref> Like other biological [[macromolecules]] such as [[polysaccharide]]s and [[nucleic acid]]s, proteins are essential parts of organisms and participate in every process within [[cell (biology)|cell]]s. Many proteins are [[enzyme]]s that [[catalysis|catalyze]] biochemical reactions and are vital to [[metabolism]]. 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. Other proteins are important in [[cell signaling]], [[antibody|immune response]]s, [[cell adhesion]], and the [[cell cycle]]. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain [[essential amino acid]]s from food. Through the process of [[digestion]], animals break down ingested protein into free amino acids that are then used in metabolism. The word ''protein'' comes from the [[Greek language|Greek]] word ''πρώτα'' ("prota"), meaning "of primary importance." Proteins were first described and named by the Swedish chemist [[Jöns Jakob Berzelius]] in 1838. However, the central role of proteins in living organisms was not fully appreciated until 1926, when [[James B. Sumner]] showed that the enzyme [[urease]] was a protein.<ref>{{cite journal |author=Sumner, JB |title=The Isolation and Crystallization of the Enzyme Urease. Preliminary Paper |url=http://www.jbc.org/cgi/reprint/69/2/435.pdf?ijkey=028d5e540dab50accbf86e01be08db51ef49008f |journal=J Biol Chem |volume=69 |issue= |pages=435–41 |year=1926}}</ref> 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 included [[hemoglobin]] and [[myoglobin]], by [[Max Perutz]] and [[John Kendrew|Sir John Cowdery Kendrew]], respectively, in 1958.<ref>{{cite journal |author=Muirhead H, Perutz M |title=Structure of hemoglobin. A three-dimensional fourier synthesis of reduced human hemoglobin at 5.5&nbsp;A resolution |journal=Nature |volume=199 |issue=4894 |pages=633–8 |year=1963 |pmid=14074546 |doi=10.1038/199633a0}}</ref><ref>{{cite journal |author=Kendrew J, Bodo G, Dintzis H, Parrish R, Wyckoff H, Phillips D |title=A three-dimensional model of the myoglobin molecule obtained by x-ray analysis |journal=Nature |volume=181 |issue=4610 |pages=662–6 |year=1958 |pmid=13517261 | doi = 10.1038/181662a0 <!--Retrieved from CrossRef by DOI bot-->}}</ref> 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. ==Biochemistry== {{main|Amino acid|peptide bond}} [[Image:Peptide group resonance.png|thumb|300px|right|[[Resonance (chemistry)|Resonance]] structures of the [[peptide bond]] that links individual amino acids to form a protein [[polymer]].]] [[Image:Peptide bond.jpg|thumb|300px|right|Section of a protein structure showing serine and alanine residues linked together by peptide bonds. Carbons are shown in white and hydrogens are omitted for clarity.]] Proteins are linear polymers built from 20 different <small>L</small>-α-[[amino acid]]s. All amino acids possess common structural features, including an [[alpha carbon|α carbon]] to which an [[amino]] group, a [[carboxyl]] group, and a variable [[side chain]] are [[chemical bond|bonded]]. Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO&ndash;NH amide moiety into a fixed conformation.<ref name=''Nelson''>Nelson, D. L. and Cox, M. M. (2005) Lehninger's Principles of Biochemistry, 4th Edition, W. H. Freeman and Company, New York.</ref> The side chains of the standard amino acids, detailed in the [[list of standard amino acids]], have different chemical properties that produce three-dimensional protein structure and are therefore critical to protein function. The amino acids in a polypeptide chain are linked by [[peptide bond]]s formed in a [[dehydration reaction]]. 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.'' The peptide bond has two [[resonance (chemistry)|resonance]] forms that contribute some [[double-bond]] character and inhibit rotation around its axis, so that the alpha carbons are roughly [[coplanar]]. The other two [[dihedral angle]]s in the peptide bond determine the local shape assumed by the protein backbone. Due to the chemical structure of the individual amino acids, the protein chain has directionality. 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. 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 [[tertiary structure|conformation]], whereas ''peptide'' is generally reserved for a short amino acid oligomers often lacking a stable three-dimensional structure. However, the boundary between the two is not well defined and usually lies near 20&ndash;30 residues.<ref name="Lodish">Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J. (2004). ''Molecular Cell Biology'' 5th ed. WH Freeman and Company: New York, NY.</ref> ''Polypeptide'' can refer to any single linear chain of amino acids, usually regardless of length, but often implies an absence of a defined [[tertiary structure|conformation]]. == Synthesis == {{main article|Protein biosynthesis}} [[Image:Genetic code.svg|thumb|300px|left|The [[DNA]] sequence of a gene [[genetic code|encodes]] the [[amino acid]] sequence of a protein.]] Proteins are assembled from amino acids using information encoded in [[gene]]s. 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 [[codon]]s and each three-nucleotide combination stands for an amino acid, for example AUG stands 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. Genes encoded in DNA are first [[transcription (genetics)|transcribed]] into pre-[[messenger RNA]] (mRNA) by proteins such as [[RNA polymerase]]. 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]]. In [[prokaryote]]s 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]]. In contrast, [[eukaryote]]s make mRNA in the [[cell nucleus]] and then translocate it across the [[nuclear membrane]] into the [[cytoplasm]], where [[protein biosynthesis|protein synthesis]] then takes place. The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second.<ref name="Dobson">Dobson CM. (2000). The nature and significance of protein folding. In ''Mechanisms of Protein Folding'' 2nd ed. Ed. RH Pain. ''Frontiers in Molecular Biology'' series. Oxford University Press: New York, NY.</ref> The process of synthesizing a protein from an mRNA template is known as [[translation (genetics)|translation]]. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its [[base pair]]ing [[anticodon]] located on a [[transfer RNA]] molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme [[aminoacyl tRNA synthetase]] "charges" the tRNA molecules with the correct amino acids. The growing polypeptide is often termed the ''nascent chain''. Proteins are always biosynthesized from [[N-terminus]] to [[C-terminus]]. 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 unit]]s), or the derivative unit kilodalton (kDa). [[Yeast]] proteins are on average 466 amino acids long and 53 kDa in mass.<ref name="Lodish" /> The largest known proteins are the [[titin]]s, 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.<ref>{{cite journal |author=Fulton A, Isaacs W |title=Titin, a huge, elastic sarcomeric protein with a probable role in morphogenesis |journal=Bioessays |volume=13 |issue=4 |pages=157–61 |year=1991 |pmid=1859393 | doi = 10.1002/bies.950130403 <!--Retrieved from CrossRef by DOI bot-->}}</ref> ===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.<ref>{{cite journal |author=Bruckdorfer T, Marder O, Albericio F |title=From production of peptides in milligram amounts for research to multi-tons quantities for drugs of the future |journal=Curr Pharm Biotechnol |volume=5 |issue=1 |pages=29–43 |year=2004 |pmid=14965208 | doi = 10.2174/1389201043489620 <!--Retrieved from CrossRef by DOI bot-->}}</ref> 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.<ref>{{cite journal |author=Schwarzer D, Cole P |title=Protein semisynthesis and expressed protein ligation: chasing a protein's tail |journal=Curr Opin Chem Biol |volume=9 |issue=6 |pages=561–9 |year=2005 |pmid=16226484 | doi = 10.1016/j.cbpa.2005.09.018 <!--Retrieved from CrossRef by DOI bot-->}}</ref> These methods are useful in laboratory [[biochemistry]] and [[cell biology]], though generally not for commercial applications. Chemical synthesis is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native [[tertiary structure]]. Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction. == Structure of proteins == {{main|Protein structure}} [[Image:Proteinviews-1tim.png|thumb|500px|Three possible representations of the three-dimensional structure of the protein [[triose phosphate isomerase]]. Left: all-atom representation colored by atom type. Middle: simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).]] Most proteins [[protein folding|fold]] into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its [[native state]]. Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular [[Chaperone (protein)|chaperone]]s to fold into their native states. Biochemists often refer to four distinct aspects of a protein's structure: * ''[[Primary structure]]'': the [[peptide sequence|amino acid sequence]] * ''[[Secondary structure]]'': regularly repeating local structures stabilized by [[hydrogen bond]]s. The most common examples are the [[alpha helix]] and [[beta sheet]].<ref name="Branden">Branden C, Tooze J. (1999). ''Introduction to Protein Structure'' 2nd ed. Garland Publishing: New York, NY</ref> 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. Tertiary structure is generally stabilized by nonlocal interactions, most commonly the formation of a [[hydrophobic core]], but also through [[Salt bridge (protein)|salt bridge]]s, hydrogen bonds, [[disulfide bond]]s, and even [[post-translational modification]]s. The term "tertiary structure" is often used as synonymous with the term ''fold''. * ''[[Quaternary structure]]'': the shape or structure that results from the [[protein-protein interaction|interaction]] of more than one protein molecule, usually called ''[[protein subunit]]s'' in this context, which function as part of the larger assembly or [[protein complex]]. [[Image:Protein Dynamics Cytochrome C 2NEW smaller.gif|frame|NMR structures of the protein [[cytochrome c]] in solution show the constantly shifting dynamic structure of the protein. [[:Image:Protein Dynamics Cytochrome C 2NEW small.gif|Larger version]].]] Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "[[Chemical conformation|conformation]]s", and transitions between them are called ''conformational changes.'' Such changes are often induced by the binding of a [[Substrate (biochemistry)|substrate]] molecule to an enzyme's [[active site]], or the physical region of the protein that participates in chemical catalysis. In solution all proteins also undergo variation in structure through thermal vibration and the collision with other molecules, see the animation on the right. [[Image:Protein Composite.jpg|500px|thumb|Molecular surface of several proteins showing their comparative sizes. From left to right are: [[Antibody]] (IgG), [[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 protein]]s, [[fibrous protein]]s, and [[membrane protein]]s. Almost all globular proteins are [[soluble]] and many are enzymes. Fibrous proteins are often structural; membrane proteins often serve as [[receptor (biochemistry)|receptors]] or provide channels for polar or charged molecules to pass through the cell membrane. A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own [[dehydration]], are called [[dehydron]]s. === 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. Common experimental methods of structure determination include [[X-ray crystallography]] and [[protein NMR|NMR spectroscopy]], both of which can produce information at [[atom]]ic resolution. [[Cryoelectron microscopy]] is used to produce lower-resolution structural information about very large protein complexes, including assembled [[virus]]es;<ref name="Branden" /> a variant known as [[electron crystallography]] can also produce high-resolution information in some cases, especially for two-dimensional crystals of membrane proteins.<ref>Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T. (2005). Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. ''Nature'' 438(7068):633–8.</ref> 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. Many more gene sequences are known than protein structures. 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. In particular, globular proteins are comparatively easy to [[crystallize]] in preparation for X-ray crystallography. Membrane proteins, by contrast, are difficult to crystallize and are underrepresented in the PDB.<ref>Walian P, Cross TA, Jap BK. (2004). Structural genomics of membrane proteins ''Genome Biol'' 5(4): 215.</ref> [[Structural genomics]] initiatives have attempted to remedy these deficiencies by systematically solving representative structures of major fold classes. [[Protein structure prediction]] methods attempt to provide a means of generating a plausible structure for proteins whose structures have not been experimentally determined. == Cellular functions == {{Expand-section|Use of protein (especially the use in cell buffering agent)|date=March 2008}} Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes.<ref name="Lodish" /> With the exception of certain types of [[RNA]], most other biological molecules are relatively inert elements upon which proteins act. 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.<ref name="Voet">Voet D, Voet JG. (2004). ''Biochemistry'' Vol 1 3rd ed. Wiley: Hoboken, NJ.</ref> The set of proteins expressed in a particular cell or cell type is known as its [[proteome]]. [[Image:Hexokinase ball and stick model, with substrates to scale copy.png|thumb|350px|right|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, [[adenosine triphosphate|ATP]] and [[glucose]].]] The chief characteristic of proteins that allows their diverse set of functions is their ability to bind other molecules specifically and tightly. 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. 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. 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<sup>-15</sup> M) but does not bind at all to its amphibian homolog [[onconase]] (>1 M). 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]]. Proteins can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of the same molecule, they can [[oligomer]]ize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers. [[Protein-protein interaction]]s also regulate enzymatic activity, control progression through the [[cell cycle]], and allow the assembly of large [[protein complex]]es that carry out many closely related reactions with a common biological function. Proteins can also bind to, or even be integrated into, cell membranes. The ability of binding partners to induce conformational changes in proteins allows the construction of enormously complex [[cell signaling|signaling]] networks. ===Enzymes=== {{main|Enzyme}} The best-known role of proteins in the cell is their duty as [[enzyme]]s, which [[catalysis|catalyze]] chemical reactions. Enzymes are usually highly specific catalysts that accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in [[metabolism]] and [[catabolism]], as well as [[DNA replication]], [[DNA repair]], and [[RNA synthesis]]. Some enzymes act on other proteins to add or remove chemical groups in a process known as [[post-translational modification]]. About 4,000 reactions are known to be catalyzed by enzymes.<ref>{{cite journal|url=http://www.expasy.org/NAR/enz00.pdf|author= Bairoch A.|year= 2000|title= The ENZYME database in 2000 |journal=Nucleic Acids Res|volume=28|pages=304–305|pmid= 10592255 | doi = 10.1093/nar/28.1.304 <!--Retrieved from CrossRef by DOI bot-->}}</ref> The rate acceleration conferred by enzymatic catalysis is often enormous - as much as 10<sup>17</sup>-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).<ref>{{cite journal |author=Radzicka A, Wolfenden R.|year= 1995|title= A proficient enzyme |journal= Science |volume=6 |issue=267 |pages=90–3| pmid=7809611|doi= 10.1126/science.7809611}}</ref> The molecules bound and acted upon by enzymes are known as [[Substrate (biochemistry)|substrate]]s. 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 - 3-4 residues on average - that are directly involved in catalysis.<ref>[http://www.ebi.ac.uk/thornton-srv/databases/CSA/ The Catalytic Site Atlas at The European Bioinformatics Institute]</ref> The region of the enzyme that binds the substrate and contains the catalytic residues is known as the [[active site]]. This was first suggested by [[Emil Fischer]] in 1894 that both the [[enzyme]] and the [[substrate]] must be geometrically compatible for them to bind and perform a certain task. This is referred to as the [[Lock and Key Theory]]. ===Cell signaling and ligand transport=== [[Image:Mouse-cholera-antibody-1f4x.png|thumb|150px|A mouse antibody against [[cholera]] that binds a [[carbohydrate]] antigen.]] Many proteins are involved in the process of [[cell signaling]] and [[signal transduction]]. 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 [[biological tissue|tissues]]. Others are [[membrane protein]]s that act as [[receptor (biochemistry)|receptors]] whose main function is to bind a signaling molecule and induce a biochemical response in the cell. 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. [[Antibodies]] are protein components of [[adaptive immune system]] whose main function is to bind [[antigen]]s, or foreign substances in the body, and target them for destruction. Antibodies can be [[secrete]]d into the extracellular environment or anchored in the membranes of specialized [[B cell]]s known as [[plasma cell]]s. Whereas enzymes are limited in their binding affinity for their substrates by the necessity of conducting their reaction, antibodies have no such constraints. An antibody's binding affinity to its target is extraordinarily high. Many ligand transport proteins bind particular small biomolecules and transport them to other locations in the body of a multicellular organism. 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 canonical example of a ligand-binding protein is [[hemoglobin]], which transports [[oxygen]] from the [[lung]]s to other organs and tissues in all [[vertebrate]]s and has close [[Homology (biology)|homolog]]s in every biological [[kingdom (biology)|kingdom]]. [[Transmembrane protein]]s can also serve as ligand transport proteins that alter the [[Semipermeable membrane|permeability]] of the cell membrane to small molecules and ions. The membrane alone has a [[hydrophobic]] core through which [[Chemical polarity|polar]] or charged molecules cannot [[diffusion|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. ===Structural proteins=== Structural proteins confer stiffness and rigidity to otherwise-fluid biological components. Most structural proteins are [[fibrous protein]]s; for example, [[actin]] and [[tubulin]] are globular and soluble as monomers, but [[polymer]]ize to form long, stiff fibers that comprise the [[cytoskeleton]], which allows the cell to maintain its shape and size. [[Collagen]] and [[elastin]] are critical components of [[connective tissue]] such as [[cartilage]], and [[keratin]] is found in hard or filamentous structures such as [[hair]], [[nail (anatomy)|nails]], [[feather]]s, [[hoof|hooves]], and some [[animal shell]]s. Other proteins that serve structural functions are [[motor protein]]s such as [[myosin]], [[kinesin]], and [[dynein]], which are capable of generating mechanical forces. These proteins are crucial for cellular [[motility]] of single celled organisms and the [[spermatozoon|sperm]] of many sexually reproducing multicellular organisms. They also generate the forces exerted by contracting [[muscle]]s. == Methods of study == {{main|Protein methods}} As some of the most commonly studied biological molecules, the activities and structures of proteins are examined both ''[[in vitro]]'' and ''[[in vivo]]''. ''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 [[reaction mechanism|chemical mechanism]] of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules. 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. ===Protein purification=== {{main|Protein purification}} In order to perform ''[[in vitro]]'' analysis, a protein must be purified away from other cellular components. This process usually begins with [[cytolysis|cell lysis]], in which a cell's membrane is disrupted and its internal contents released into a solution known as a [[crude lysate]]. The resulting mixture can be purified using [[ultracentrifugation]], which fractionates the various cellular components into fractions containing soluble proteins; membrane [[lipid]]s and proteins; cellular [[organelle]]s, and [[nucleic acid]]s. [[Precipitation (chemistry)|Precipitation]] by a method known as [[salting out]] can concentrate the proteins from this lysate. 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 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 assay]]s if the protein has enzymatic activity. Additionally, proteins can be isolated according their charge<ref>[http://isoelectric.ovh.org Calculating protein charge (isoelectric point)]</ref> using [[electrofocusing]]. For natural proteins, a series of purification steps may be necessary to obtain protein sufficiently pure for laboratory applications. 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. 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. 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. ===Cellular localization=== [[Image:Localisations02eng.jpg|thumb|300px|right|Proteins in different [[cellular compartment]]s 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. 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 [[protein targeting|targeted]] to specific organelles or cellular structures is often unclear. A useful technique for assessing cellular localization uses genetic engineering to express in a cell a [[fusion protein]] or [[chimera (protein)|chimera]] consisting of the natural protein of interest linked to a "[[reporter gene|reporter]]" such as [[green fluorescent protein]] (GFP). The fused protein's position within the cell can be cleanly and efficiently visualized using [[microscopy]], as shown in the figure opposite. In these cases, additional fluorescent chimeric proteins are generally required to prove the inferred localization. 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. 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. 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. 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. Another applicable technique is cofractionation in sucrose (or other material) gradients using [[isopycnic centrifugation]]. 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. 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. 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. 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, which can be followed ''in vivo'' by GFP tagging or ''in vitro'' by [[enzyme kinetics]] and binding studies. ===Proteomics and bioinformatics=== {{main|Proteomics|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]]. Key experimental techniques in proteomics include [[Two-dimensional gel electrophoresis|2D electrophoresis]], which allows the separation of a large number of proteins, [[mass spectrometry]], which allows rapid high-throughput identification of proteins and sequencing of peptides (most often after [[in-gel digestion]]), [[protein microarray]]s, 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 interaction]]s. The total complement of biologically possible such interactions is known as the [[interactome]]. A systematic attempt to determine the structures of proteins representing every possible fold is known as [[structural genomics]]. The large amount of genomic and proteomic data available for a variety of organisms, including the [[human genome]], allows researchers to efficiently identify [[homology (biology)|homologous]] proteins in distantly related organisms by [[sequence alignment]]. [[Sequence profiling tool]]s can perform more specific sequence manipulations such as [[restriction enzyme]] maps, [[open reading frame]] analyses for [[nucleotide]] sequences, and [[secondary structure]] prediction. From this data [[phylogenetic tree]]s can be constructed and [[evolution]]ary hypotheses developed using special software like [[ClustalW]] regarding the ancestry of modern organisms and the genes they express. The field of [[bioinformatics]] seeks to assemble, annotate, and analyze genomic and proteomic data, applying [[computer science|computational]] techniques to biological problems such as [[gene finding]] and [[cladistics]]. ===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. 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. 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.<ref name="Zhang">Zhang Y, Skolnick J. (2005). The protein structure prediction problem could be solved using the current PDB library. ''Proc Natl Acad Sci USA'' 102(4):1029–34.</ref> Many structure prediction methods have served to inform the emerging field of [[protein engineering]], in which novel protein folds have already been designed.<ref name="Kuhlman">Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. (2003). Design of a novel globular protein fold with atomic-level accuracy. ''Science'' 302(5649):1364–8.</ref> A more complex computational problem is the prediction of intermolecular interactions, such as in [[docking (molecular)|molecular docking]] and [[protein-protein interaction prediction]]. The processes of protein folding and binding can be simulated using techniques derived from [[molecular dynamics]], which increasingly take advantage of [[distributed computing]] as in the [[Folding@Home]] project. The folding of small alpha-helical protein domains such as the [[villin]] headpiece<ref name="Zagrovic">Zagrovic B, Snow CD, Shirts MR, Pande VS. (2002). Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. ''J Mol Biol'' 323(5):927–37.</ref> and the [[HIV]] accessory protein<ref name="Herges">Herges T, Wenzel W. (2005). In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field. ''Phys Rev Let'' 94(1):018101.</ref> 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 [[rhodopsin]]s.<ref name="Hoffmann">Hoffmann M, Wanko M, Strodel P, Konig PH, Frauenheim T, Schulten K, Thiel W, Tajkhorshid E, Elstner M. (2006). Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. ''J Am Chem Soc'' 128(33):10808-18. </ref> ==Nutrition== {{further|[[Protein in nutrition]]}} Most [[microorganism]]s and plants can biosynthesize all 20 standard [[amino acids]], while animals, (including humans) must obtain some of the amino acids from the [[diet (nutrition)|diet]].<ref name="Voet" /> Key enzymes in the biosynthetic pathways that synthesize certain amino acids - such as [[aspartokinase]], which catalyzes the first step in the synthesis of [[lysine]], [[methionine]], and [[threonine]] from [[aspartate]] - are not present in animals. The amino acids that an organism cannot synthesize on its own are referred to as [[essential amino acids]]. 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. In animals, amino acids are obtained through the consumption of foods containing protein. Ingested proteins are broken down through [[digestion]], which typically involves [[Denaturation (biochemistry)|denaturation]] of the protein through exposure to [[acid]] and [[hydrolysis]] by enzymes called [[protease]]s. Some ingested amino acids are used for protein biosynthesis, while others are converted to [[glucose]] through [[gluconeogenesis]], or fed into the [[citric acid cycle]]. 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]].<ref>{{cite journal |author=Brosnan J |title=Interorgan amino acid transport and its regulation |url=http://jn.nutrition.org/cgi/content/full/133/6/2068S |journal=J Nutr |volume=133 |issue=6 Suppl 1 |pages=2068S–72S |year=2003 |pmid=12771367}}</ref> Amino acids are also an important dietary source of [[nitrogen]]. == History == {{further|[[History of molecular biology]]}} Proteins were recognized as a distinct class of biological molecules in the eighteenth century by [[Antoine François, comte de Fourcroy|Antoine Fourcroy]] and others, distinguished by the molecules' ability to [[coagulate]] or [[flocculation|flocculate]] under treatments with heat or acid. Noted examples at the time included albumin from [[egg white]]s, [[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]]. The term "protein" to describe these molecules was proposed in 1838 by Mulder's associate [[Jöns Jakob Berzelius]]. 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 [[atomic mass unit|Da]]. The difficulty in purifying proteins in large quantities made them very difficult for early protein biochemists to study. Hence, early studies focused on proteins that could be purified in large quantities, e.g., those of [[blood]], [[egg white]], various [[toxin]]s, and digestive/metabolic enzymes obtained from [[slaughterhouse]]s. In the late 1950s, the [[Armour and Company|Armour Hot Dog Co.]] purified 1 kg (= one million milligrams) of pure bovine pancreatic [[ribonuclease A]] and made it freely available to scientists around the world. [[Linus Pauling]] is credited with the successful prediction of regular protein [[secondary structure]]s based on [[hydrogen bonding]], an idea first put forth by [[William Astbury]] in 1933. Later work by [[Walter Kauzmann]] on [[Denaturation (biochemistry)|denaturation]], based partly on previous studies by [[Kaj Ulrik Linderstrøm-Lang|Kaj Linderstrøm-Lang]], contributed an understanding of [[protein folding]] and structure mediated by [[hydrophobic core|hydrophobic interactions]]. 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, [[colloid]]s, or [[cyclol]]s. The first atomic-resolution structures of proteins were solved by [[X-ray crystallography]] in the 1960s and by [[Protein nuclear magnetic resonance spectroscopy|NMR]] in the 1980s. As of 2006, the [[Protein Data Bank]] has nearly 40,000 atomic-resolution structures of proteins. In more recent times, [[cryo-electron microscopy]] of large macromolecular assemblies and computational [[protein structure prediction]] of small protein [[structural domain|domains]] are two methods approaching atomic resolution. == See also == <div style="-moz-column-count:4; column-count:4;"> * [[Amino acid]] * [[Essential amino acid]] * [[Protein design]] * [[Isoelectric point]] * [[Intein]] * [[List of recombinant proteins]] * [[List of proteins]] * [[Prion]] * [[Edible protein per unit area of land]] * [[Expression cloning]] * [[Proteopathy]] * [[Software for molecular mechanics modeling|Software for protein modeling]] * [[Proteopedia]] </div> ==References== {{reflist|2}} == External links == * [http://www3.interscience.wiley.com/cgi-bin/jhome/36176?CRETRY=1&SRETRY=0 Proteins (the journal)], also called "Proteins: Structure, Function, and Bioinformatics" and previously "Proteins: Structure, Function, and Genetics" (1986–1995). ===Databases and projects=== * [http://harvester.fzk.de Bioinformatic Harvester] A Meta search engine (29 databases) for gene and protein information. * [http://www.rcsb.org The Protein Databank] (see also [http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html PDB Molecule of the Month], presenting short accounts on selected proteins from the PDB) * [http://www.proteopedia.org Proteopedia - Life in 3D]: rotatable, zoomable 3D model with wiki annotations for every known protein molecular structure. * [http://www.expasy.uniprot.org UniProt the Universal Protein Resource] * [http://www.proteinatlas.org Human Protein Atlas] * [http://www.ihop-net.org/UniPub/iHOP/ iHOP - Information Hyperlinked over Proteins] * [http://web.mit.edu/lms/www/ MIT's Laboratory for Protein Molecular Self-Assembly] * [http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein NCBI Entrez Protein database] * [http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure NCBI Protein Structure database] * [http://www.hprd.org/ Human Protein Reference Database] * [http://www.humanproteinpedia.org/ Human Proteinpedia] * [http://folding.stanford.edu/ Folding@Home (Stanford University)] ===Tutorials and educational websites=== * [http://www.biochemweb.org/proteins.shtml Proteins: Biogenesis to Degradation - The Virtual Library of Biochemistry and Cell Biology] * [http://web.indstate.edu/thcme/mwking/amino-acid-metabolism.html Amino acid metabolism] * [http://www.ecosci.jp/ec.html Data Book of Molecules] - Home Page for Learning Environmental Chemistry {{Protein topics}} {{Protein methods}} {{Enzymes}} {{Cytoskeletal Proteins}} {{Coagulation}} {{Complement system}} {{Carrier proteins}} {{Food chemistry}} {{Protein metabolism}} [[Category:Molecular biology]] [[Category:Nutrition]] [[Category:Proteins]] [[Category:Proteomics]] {{Link FA|ru}} {{Link FA|uk}} [[af:Proteïen]] [[ar:بروتين]] [[az:Zülal]] [[bn:প্রোটিন]] [[zh-min-nan:Nn̄g-pe̍h-chit]] [[bs:Bjelančevine]] [[bg:Белтък]] [[ca:Proteïna]] [[cs:Bílkovina]] [[da:Protein]] [[de:Protein]] [[et:Valgud]] [[el:Πρωτεΐνη]] [[es:Proteína]] [[eo:Proteino]] [[eu:Proteina]] [[fa:پروتئین]] [[fo:Protein]] [[fr:Protéine]] [[gl:Proteína]] [[ko:단백질]] [[hr:Bjelančevine]] [[io:Proteino]] [[id:Protein]] [[is:Prótín]] [[it:Proteina]] [[he:חלבון]] [[pam:Protina]] [[ka:ცილები]] [[la:Proteinum]] [[lv:Olbaltumvielas]] [[lb:Protein]] [[lt:Baltymas]] [[hu:Fehérje]] [[mk:Протеин]] [[ml:മാംസ്യം]] [[nl:Proteïne]] [[ja:タンパク質]] [[no:Protein]] [[nn:Protein]] [[nov:Proteine]] [[oc:Proteïna]] [[om:Protein]] [[ps:پروټين]] [[pl:Białka]] [[pt:Proteína]] [[ro:Proteină]] [[qu:Prutina]] [[ru:Белки]] [[sq:Proteina]] [[simple:Protein]] [[sk:Bielkovina]] [[sl:Beljakovina]] [[sr:Протеин]] [[sh:Protein]] [[su:Protéin]] [[fi:Proteiini]] [[sv:Protein]] [[ta:புரதம்]] [[te:మాంసకృత్తులు]] [[th:โปรตีน]] [[vi:Protein]] [[tr:Protein]] [[uk:Білки]] [[ur:لحمیات]] [[vls:Proteïne]] [[yi:פראטין]] [[zh:蛋白质]]