Gutteridge A, Thornton JM (November 2005). "Understanding nature's catalytic toolkit". Trends in Biochemical Sciences. 30 (11): 622–29. doi: 10.1016/j.tibs.2005.09.006. PMID 16214343.

Fernández A, Scott R (September 2003). "Dehydron: a structurally encoded signal for protein interaction". Biophysical Journal. 85 (3): 1914–28. Bibcode: 2003BpJ....85.1914F. doi: 10.1016/S0006-3495(03)74619-0. PMC 1303363. PMID 12944304. Many proteins are composed of several protein domains, i.e. segments of a protein that fold into distinct structural units. Domains usually also have specific functions, such as enzymatic activities (e.g. kinase) or they serve as binding modules (e.g. the SH3 domain binds to proline-rich sequences in other proteins). Brosnan JT (June 2003). "Interorgan amino acid transport and its regulation". The Journal of Nutrition. 133 (6 Suppl 1): 2068S–72S. doi: 10.1093/jn/133.6.2068S. PMID 12771367.Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes. [28] 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. [44] The set of proteins expressed in a particular cell or cell type is known as its proteome. Zagrovic B, Snow CD, Shirts MR, Pande VS (November 2002). "Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing". Journal of Molecular Biology. 323 (5): 927–37. CiteSeerX 10.1.1.142.8664. doi: 10.1016/S0022-2836(02)00997-X. PMID 12417204. Sleator RD (2012). "Prediction of Protein Functions". Functional Genomics. Methods in Molecular Biology. Vol.815. pp.15–24. doi: 10.1007/978-1-61779-424-7_2. ISBN 978-1-61779-423-0. PMID 22130980. Mulder NJ (2007-09-28). "Protein Family Databases". eLS. Chichester, UK: John Wiley & Sons, Ltd. pp.a0003058.pub2. doi: 10.1002/9780470015902.a0003058.pub2. ISBN 978-0-470-01617-6.

Pauling L, Corey RB (May 1951). "Atomic coordinates and structure factors for two helical configurations of polypeptide chains" (PDF). Proceedings of the National Academy of Sciences of the United States of America. 37 (5): 235–40. Bibcode: 1951PNAS...37..235P. doi: 10.1073/pnas.37.5.235. PMC 1063348. PMID 14834145. Archived (PDF) from the original on 2012-11-28 . Retrieved 2009-04-14. Beyond classical molecular dynamics, quantum dynamics methods allow the simulation of proteins in atomistic detail with an accurate description of quantum mechanical effects. Examples include the multi-layer multi-configuration time-dependent Hartree (MCTDH) method and the hierarchical equations of motion (HEOM) approach, which have been applied to plant cryptochromes [85] and bacteria light-harvesting complexes, [86] respectively. Both quantum and classical mechanical simulations of biological-scale systems are extremely computationally demanding, so distributed computing initiatives (for example, the Folding@home project [87]) facilitate the molecular modeling by exploiting advances in GPU parallel processing and Monte Carlo techniques.Plewczyński D, Ginalski K (2009). "The interactome: predicting the protein-protein interactions in cells". Cellular & Molecular Biology Letters. 14 (1): 1–22. doi: 10.2478/s11658-008-0024-7. PMC 6275871. PMID 18839074. a b c Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J (2004). Molecular Cell Biology (5thed.). New York, New York: WH Freeman and Company. Stepanenko OV, Verkhusha VV, Kuznetsova IM, Uversky VN, Turoverov KK (August 2008). "Fluorescent proteins as biomarkers and biosensors: throwing color lights on molecular and cellular processes". Current Protein & Peptide Science. 9 (4): 338–69. doi: 10.2174/138920308785132668. PMC 2904242. PMID 18691124. Strümpfer J, Schulten K (2012). "Open Quantum Dynamics Calculations with the Hierarchy Equations of Motion on Parallel Computers". J. Chem. Theory Comput. 8 (8): 2808–2816. doi: 10.1021/ct3003833. PMC 3480185. PMID 23105920. Keskin O, Tuncbag N, Gursoy A (April 2008). "Characterization and prediction of protein interfaces to infer protein-protein interaction networks". Current Pharmaceutical Biotechnology. 9 (2): 67–76. doi: 10.2174/138920108783955191. hdl: 11511/32640. PMID 18393863.

Other possibilities exist, as well. For example, immunohistochemistry usually uses 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. [62] 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. Koegl M, Uetz P (December 2007). "Improving yeast two-hybrid screening systems". Briefings in Functional Genomics & Proteomics. 6 (4): 302–12. doi: 10.1093/bfgp/elm035. PMID 18218650. Archived from the original on 2017-09-11 . Retrieved 2017-07-23. 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 also work together to achieve a particular function, and they often associate to form stable protein complexes.

Amino acids

Samarin S, Nusrat A (January 2009). "Regulation of epithelial apical junctional complex by Rho family GTPases". Frontiers in Bioscience. 14 (14): 1129–42. doi: 10.2741/3298. PMID 19273120. Roohi, Bano K, Kuddus M, Zaheer MR, Zia Q, Khan MF, Ashraf GM, Gupta A, Aliev G (2017). "Microbial Enzymatic Degradation of Biodegradable Plastics". Current Pharmaceutical Biotechnology. 18 (5): 429–440. doi: 10.2174/1389201018666170523165742. PMID 28545359. Schwarzer D, Cole PA (December 2005). "Protein semisynthesis and expressed protein ligation: chasing a protein's tail". Current Opinion in Chemical Biology. 9 (6): 561–69. doi: 10.1016/j.cbpa.2005.09.018. PMID 16226484.

As of 2017 [update], the Protein Data Bank has over 126,060 atomic-resolution structures of proteins. [23] Number of proteins encoded in genomes Quinary structure: the signatures of protein surface that organize the crowded cellular interior. Quinary structure is dependent on transient, yet essential, macromolecular interactions that occur inside living cells. Ekman, Diana; Björklund, Åsa K.; Frey-Skött, Johannes; Elofsson, Arne (April 2005). "Multi-domain Proteins in the Three Kingdoms of Life: Orphan Domains and Other Unassigned Regions". Journal of Molecular Biology. 348 (1): 231–243. doi: 10.1016/j.jmb.2005.02.007. Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, etal. (September 2014). "Comparative analysis of pseudogenes across three phyla". Proceedings of the National Academy of Sciences of the United States of America. 111 (37): 13361–6. Bibcode: 2014PNAS..11113361S. doi: 10.1073/pnas.1407293111. PMC 4169933. PMID 25157146.

Types and functions of proteins

This article is about a class of molecules. For protein as a nutrient, see Protein (nutrient). For other uses, see Protein (disambiguation). Bischoff TL, Voit C (1860). Die Gesetze der Ernaehrung des Pflanzenfressers durch neue Untersuchungen festgestellt (in German). Leipzig, Heidelberg. {{ cite book}}: CS1 maint: location missing publisher ( link) With the development of X-ray crystallography, it became possible to sequence protein structures. [18] The first protein structures to be solved were hemoglobin by Max Perutz and myoglobin by John Kendrew, in 1958. [19] [20] The use of computers and increasing computing power also supported the sequencing of complex proteins. In 1999, Roger Kornberg succeeded in sequencing the highly complex structure of RNA polymerase using high intensity X-rays from synchrotrons. [18] Dobson CM (2000). "The nature and significance of protein folding". In Pain RH (ed.). Mechanisms of Protein Folding. Oxford, Oxfordshire: Oxford University Press. pp.1–28. ISBN 978-0-19-963789-8.