List of proteins

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, catalyzing chemical reactions that produce or store energy or synthesize other biomolecules including nucleic acids and proteins, and signal transduction.

This list aims to organize information on how proteins are classified: by structure, function, and 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:

Function

The human genome, categorized by function of each gene product, given both as number of genes and as percentage of all genes.^[3]

Protein#Cellular_functions
PANTHER (protein analysis through evolutionary relationships) classification system^[3]

Structural

Protein#Structural_proteins

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 has been mapped to one or more specific proteins.

Signal transduction

Sub-cellular distribution

The human genome, categorized by the predicted subcellular location distribution of each gene product.^[4]

Protein#Cellular_localization

Nuclear

Nuclear proteins

Cytosolic

Cytosolic proteins

Cytoskeletal

Cytoskeletal proteins

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

Membrane protein

Extracellular matrix

Extracellular matrix proteins

Plasma

Blood protein

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.
^ ^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.

[Andreeva_2014-1] 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_2021-2] 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.

[Thomas_2003-3] 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_2017-4] 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.

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