List of proteins
Proteinsare a class ofmacromolecularorganic compounds that are essential to life. They consist of a longpolypeptidechain that usually adopts a single stablethree-dimensional structure.They fulfill a wide variety offunctionsincluding providingstructuralstability to cells, catalyze chemical reactions that produce or store energy or synthesize otherbiomoleculesincludingnucleic acidsand proteins, transport essential nutrients, or serve other roles such assignal transduction.They are selectivelytransportedto various compartments of the cell or in some cases,secretedfrom the cell.
This list aims to organize information on how proteins are most often classified: by structure, by function, or by location.
Structure[edit]
Proteins may be classified as to their three-dimensionalstructure(also known aprotein fold). The two most widely used classification schemes are:[2]
Both classification schemes are based on a hierarchy of fold types. At the top level are all alpha proteins (domains consisting ofalpha helices), all beta proteins (domains consisting ofbeta sheets), 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 asmetamorphic proteins.[5]Finally other proteins appear not to adopt any stable conformation and are referred to asintrinsically disordered.[6]
Proteins frequently contain two or moredomains,each have a different fold separated by intrinsically disordered regions. These are referred to asmulti-domain proteins.
Function[edit]
Proteins may also be classified based on theircelluar function.A widely used classification isPANTHER(protein analysis through evolutionary relationships) classification system.[7]
Structural[edit]
Catalytic[edit]
Enzymes classified according to theirEnzyme Commission number(EC). Note that strictly speaking, anEC numbercorresponds to the reaction the enzyme catalyzes, not the protein per se. However each EC number has been mapped to one or more specific proteins.
- List of enzymes
- EC 1:Oxidoreductases
- EC 2:Transferases
- EC 3:Hydrolases
- EC 4:Lyases
- EC 5:Isomerases
- EC 6:Ligases
- EC 7:Translocases
Transport[edit]
Immune[edit]
- Antibody
- Chemokinesand their receptors
- Cytokinesand their receptors
- Pattern recognition receptors
Genetic[edit]
- DNA/RNA synthesis
- DNA repair
- replication
- transcription (Transcription factor,transcriptional coregulator)
Signal transduction[edit]
Sub-cellular distribution[edit]
Proteins may also be classified by which subcellular compartment they are found.[9][10]
Nuclear[edit]
Cytosolic[edit]
Cytoskeletal[edit]
Organelle[edit]
Endoplasmic reticulum[edit]
Endoplasmic reticulum resident protein
Lysosomal[edit]
Mitochondial[edit]
Mitochondrial DNAthat encode mitochondial proteins (note that some mitochondial proteins are encoded by nuclear DNA)
Chloroplast[edit]
Chloroplast DNAthat encode chloroplast proteins
Cell membrane[edit]
Extracellular matrix[edit]
Plasma[edit]
Species distribution[edit]
- Mammalian
- Vertebrate
- Plant
- Bacterial proteins
- Archaeal proteins
- Viral proteins
References[edit]
- ^Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM (August 1997)."CATH--a hierarchic classification of protein domain structures".Structure.5(8). London, England: 1093–108.doi:10.1016/s0969-2126(97)00260-8.PMID9309224.
- ^Csaba G, Birzele F, Zimmer R (April 2009)."Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis".BMC Structural Biology.9:23.doi:10.1186/1472-6807-9-23.PMC2678134.PMID19374763.
- ^Sillitoe I, Bordin N, Dawson N, Waman VP, Ashford P, Scholes HM, et al. (January 2021)."CATH: increased structural coverage of functional space".Nucleic Acids Research.49(D1): D266–D273.doi:10.1093/nar/gkaa1079.PMC7778904.PMID33237325.
- ^Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG (January 2014)."SCOP2 prototype: a new approach to protein structure mining".Nucleic Acids Research.42(Database issue): D310–4.doi:10.1093/nar/gkt1242.PMC3964979.PMID24293656.
- ^Dishman AF, Volkman BF (June 2022)."Design and discovery of metamorphic proteins".Current Opinion in Structural Biology.74:102380.doi:10.1016/j.sbi.2022.102380.PMC9664977.PMID35561475.
- ^Trivedi R, Nagarajaram HA (November 2022)."Intrinsically Disordered Proteins: An Overview".International Journal of Molecular Sciences.23(22): 14050.doi:10.3390/ijms232214050.PMC9693201.PMID36430530.
- ^abThomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, et al. (January 2003)."PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification".Nucleic Acids Research.31(1): 334–341.doi:10.1093/nar/gkg115.PMC165562.PMID12520017.
- ^Zhou H, Yang Y, Shen HB (March 2017)."Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features".Bioinformatics.33(6): 843–853.doi:10.1093/bioinformatics/btw723.PMID27993784.
- ^Trans J (2014)."Subcellular Compartments".Scitable.Nature Education.
- ^Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, et al. (May 2017). "A subcellular map of the human proteome".Science.356(6340).doi:10.1126/science.aal3321.PMID28495876.S2CID10744558.