Summary
Proteins are a class of macromolecular organic compounds that are essential to life. They consist of a long polypeptide chain that usually adopts a single stable three-dimensional structure. They fulfill a wide variety of functions including providing structural stability to cells, catalyze chemical reactions that produce or store energy or synthesize other biomolecules including nucleic acids and proteins, transport essential nutrients, or serve other roles such as signal transduction. They are selectively transported to various compartments of the cell or in some cases, secreted from 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-dimensional structure (also known a protein 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 of alpha helices), all beta proteins (domains consisting of beta 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 as metamorphic proteins.[5] Finally other proteins appear not to adopt any stable conformation and are referred to as intrinsically disordered.[6]
Proteins frequently contain two or more domains, each have a different fold separated by intrinsically disordered regions. These are referred to as multi-domain proteins.
Function edit
Proteins may also be classified based on their celluar function. A widely used classification is PANTHER (protein analysis through evolutionary relationships) classification system.[7]
Structural edit
Catalytic edit
Enzymes classified according to their Enzyme Commission number (EC). Note that strictly speaking, an EC number corresponds 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
- Chemokines and their receptors
- Cytokines and 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
Cytosolic proteins
Cytoskeletal edit
Organelle edit
Endoplasmic reticulum edit
Endoplasmic reticulum resident protein
Lysosomal edit
Mitochondial edit
Mitochondrial DNA that encode mitochondial proteins (note that some mitochondial proteins are encoded by nuclear DNA)
Chloroplast edit
Chloroplast DNA that 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. PMID 9309224.
- ^ 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. PMC 2678134. PMID 19374763.
- ^ 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. PMC 7778904. PMID 33237325.
- ^ 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. PMC 3964979. PMID 24293656.
- ^ 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. PMC 9664977. PMID 35561475.
- ^ Trivedi R, Nagarajaram HA (November 2022). "Intrinsically Disordered Proteins: An Overview". International Journal of Molecular Sciences. 23 (22): 14050. doi:10.3390/ijms232214050. PMC 9693201. PMID 36430530.
- ^ a b Thomas 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. PMC 165562. PMID 12520017.
- ^ 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. PMID 27993784.
- ^ 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. PMID 28495876. S2CID 10744558.