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{{Short description|none}}
[[Image:CATH hierarchy.png|thumb|400px|Schematic representation of structural classes of protein according to the [[CATH database|CATH]] classification scheme.<ref name="Orengo_1997">{{cite journal | vauthors = Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM | title = CATH--a hierarchic classification of protein domain structures | journal = Structure | location = London, England | volume = 5 | issue = 8 | pages = 1093–108 | date = August 1997 | pmid = 9309224 | doi = 10.1016/s0969-2126(97)00260-8 | doi-access = free }}</ref>]]
[[Protein]]s are a class of [[macromolecular]] organic compounds that are essential to life.
This list aims to organize information on how proteins are most often classified: by structure, by function,
== Structure ==
Proteins may be classified as to their three-dimensional [[Protein structure#Structural classifications of proteins|structure]] (also known a [[protein fold]]). The two most widely used classification schemes are:<ref name="Csaba_2009">{{cite journal | vauthors = Csaba G, Birzele F, Zimmer R | title = Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis | journal = BMC Structural Biology | volume = 9 | issue = | pages = 23 | date = April 2009 | pmid = 19374763 | pmc = 2678134 | doi = 10.1186/1472-6807-9-23 | doi-access = free }}</ref>
* [[CATH database]]<ref name="Sillitoe_2021">{{cite journal | vauthors = Sillitoe I, Bordin N, Dawson N, Waman VP, Ashford P, Scholes HM, Pang CS, Woodridge L, Rauer C, Sen N, Abbasian M, Le Cornu S, Lam SD, Berka K, Varekova IH, Svobodova R, Lees J, Orengo CA | display-authors = 6 | title = CATH: increased structural coverage of functional space | journal = Nucleic Acids Research | volume = 49 | issue = D1 | pages =
* [[Structural Classification of Proteins database]] (SCOP)<ref name="Andreeva_2014">{{cite journal | vauthors = Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG | title = SCOP2 prototype: a new approach to protein structure mining | journal = Nucleic Acids Research | volume = 42 | issue = Database issue | pages = D310–4 | date = January 2014 | pmid = 24293656 | pmc = 3964979 | doi = 10.1093/nar/gkt1242 | url = }}</ref>
▲* [[CATH database]]<ref name="Sillitoe_2021">{{cite journal | vauthors = Sillitoe I, Bordin N, Dawson N, Waman VP, Ashford P, Scholes HM, Pang CS, Woodridge L, Rauer C, Sen N, Abbasian M, Le Cornu S, Lam SD, Berka K, Varekova IH, Svobodova R, Lees J, Orengo CA | display-authors = 6 | title = CATH: increased structural coverage of functional space | journal = Nucleic Acids Research | volume = 49 | issue = D1 | pages = D266-D273 | date = January 2021 | pmid = 33237325 | pmc = 7778904 | doi = 10.1093/nar/gkaa1079 }}</ref>
Both classification schemes are based on a hierarchy of fold types. At the top level are all alpha proteins (domains consisting of [[alpha helix|alpha helices]]), all beta proteins (domains consisting of [[beta sheet]]s), and mixed alpha helix/beta sheet proteins.
While most proteins adopt a single stable fold, a few proteins can rapidly interconvert between one or more folds. These are referred to as [[metamorphic protein]]s.<ref name="Dishman_2022">{{cite journal | vauthors = Dishman AF, Volkman BF | title = Design and discovery of metamorphic proteins | journal = Current Opinion in Structural Biology | volume = 74 | issue = | pages = 102380 | date = June 2022 | pmid = 35561475 | pmc = 9664977 | doi = 10.1016/j.sbi.2022.102380 }}</ref> Finally other proteins appear not to adopt any stable conformation and are referred to as [[Intrinsically disordered proteins|intrinsically disordered]].<ref name="Trivedi_2022">{{cite journal | vauthors = Trivedi R, Nagarajaram HA | title = Intrinsically Disordered Proteins: An Overview | journal = International Journal of Molecular Sciences | volume = 23 | issue = 22 | date = November 2022 | page = 14050 | pmid = 36430530 | pmc = 9693201 | doi = 10.3390/ijms232214050 | url = | doi-access = free }}</ref>
Proteins frequently contain two or more [[protein domain|domains]], each have a different fold separated by intrinsically disordered regions. These are referred to as [[Protein domain#Multidomain proteins|multi-domain protein]]s.
{{clear}}
== Function ==
Proteins may also be classified based on their [[Protein#
[[Protein#
Enzymes classified according to their [[Enzyme Commission number]] (EC). Note that strictly speaking, an [[Enzyme Commission number|EC number]] corresponds to the reaction
* [[List of enzymes]]
* [[List of EC numbers (EC 1)|EC 1]]: [[Oxidoreductase]]s
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=== Immune ===
* [[Acute-phase protein|Acute phase protein]]
* [[Antibody]]
* [[Chemokine]]s and their receptors
* [[Cytokine]]s and their receptors
* [[MHC class I|MHC Class I]]
* [[MHC class II|MHC Class II]]
* [[Pattern recognition receptor]]s
=== Genetic ===
* [[DNA synthesis|DNA/RNA synthesis]]
* [[DNA repair]]▼
* transcription ([[Transcription factor]])▼
* [[DNA replication#DNA replication proteins|replication]]
▲* DNA repair
▲* transcription ([[Transcription factor]], [[Coactivator (genetics)|transcriptional coregulator]])
=== Signal transduction ===
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== Sub-cellular distribution ==
Proteins may also be classified by which subcellular compartment they are found.<ref>{{cite web |last1=Trans J |title=Subcellular Compartments |url=https://www.nature.com/scitable/topic/subcellular-compartments-14122679/ | work = Scitable | publisher = Nature Education | date = 2014 |language=en}}</ref><ref name="Thul_2017">{{cite journal | vauthors = Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, Alm T, Asplund A, Björk L, Breckels LM, Bäckström A, Danielsson F, Fagerberg L, Fall J, Gatto L, Gnann C, Hober S, Hjelmare M, Johansson F, Lee S, Lindskog C, Mulder J, Mulvey CM, Nilsson P, Oksvold P, Rockberg J, Schutten R, Schwenk JM, Sivertsson Å, Sjöstedt E, Skogs M, Stadler C, Sullivan DP, Tegel H, Winsnes C, Zhang C, Zwahlen M, Mardinoglu A, Pontén F, von Feilitzen K, Lilley KS, Uhlén M, Lundberg E | display-authors = 6 | title = A subcellular map of the human proteome | journal = Science | volume = 356 | issue = 6340 | date = May 2017 | pmid = 28495876 | doi = 10.1126/science.aal3321 | s2cid = 10744558 }}</ref>
=== Nuclear ===
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=== Cytoskeletal ===
[[Cytoskeletal proteins]]
=== Organelle ===
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=== Extracellular matrix ===
[[Extracellular matrix proteins]]
=== Plasma===
[[Blood protein]]
== Species distribution ==
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* Plant
* [[Bacterial protein]]s
* [[
* [[Viral protein]]s
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====[[Transcription factor|Transcription & Regulation]]====
*[[CI protein]]
''Transcription regulatory proteins that are receptors are in the receptors section.''
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===[[Chaperone (protein)|Chaperone proteins]]===
*[[GroEL]]
===[[Enzyme]]s===
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*[[NPW]]
*[[PEGylation]]
*[[Protein design]]
*[[Protein family]]
*[[Structural domain]] -->
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