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, excreted from the cell.
This list aims to organize information on how proteins are most often classified: by structure, by function, or by location.
Structure
Proteins may be classified as to their three-dimensional structure (also known a protein fold). The two most widely used classification schemes are:
While most proteins adopt a single stable fold, a few proteins can rapidly interconvert between one or more folds. These are refered to as metamorphic proteins.[3] Finally other proteins appear not to adopt any stable conformation and are referred to as intrinsically disordered.[4]
Function
Proteins may also be classified based on their celluar function. A widely used classification is PANTHER (protein analysis through evolutionary relationships) classification system.[5]
Structural
Catalytic
Enzymes classified according to their Enzyme Commission number (EC). Note that strictly speaking, an EC number corresponds to the reaction it 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
Immune
- Antibody
- Chemokines and their receptors
- Cytokines and their receptors
- Pattern recognition receptors
Genetic
- replication
- transcription (Transcription factor)
- DNA repair
Signal transduction
Sub-cellular distribution
Proteins may also be classified by which subcellular compartment they are found.[7][8]
Nuclear
Cytosolic
Cytoskeletal
Organelle
Endoplasmic reticulum
Endoplasmic reticulum resident protein
Lysosomal
Mitochondial
Mitochondrial DNA that encode mitochondial proteins (note that some mitochondial proteins are encoded by nuclear DNA)
Chloroplast
Chloroplast DNA that encode chloroplast proteins
Cell membrane
Extracellular matrix
Plasma
Species distribution
- Mammalian
- Vertebrate
- Plant
- Bacterial proteins
- Archaeal proteins
- Viral proteins
References
- ^ 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.
- ^ 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.
- ^ 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). doi:10.3390/ijms232214050. PMC 9693201. PMID 36430530.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ 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 (Oxford, England). 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.