List of proteins explained

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

Proteins may be classified as to their three-dimensional structure (also known a protein fold). The two most widely used classification schemes are:^[1]

• CATH database^[2]
• Structural Classification of Proteins database (SCOP)^[3]

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.^[4] Finally other proteins appear not to adopt any stable conformation and are referred to as intrinsically disordered.^[5]

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

Proteins may also be classified based on their cellular function. A widely used classification is PANTHER (protein analysis through evolutionary relationships) classification system.^[6]

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 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

Transport protein

• Ion channel
• Solute carrier family

Immune

• Acute phase protein
• Antibody
• Chemokines and their receptors
• Cytokines and their receptors
• MHC Class I
• MHC Class II
• Pattern recognition receptors

Genetic

• DNA/RNA synthesis
• DNA repair
• replication
• transcription (Transcription factor, transcriptional coregulator)

Signal transduction

Signal transduction

Sub-cellular distribution

Proteins may also be classified by which subcellular compartment they are found.^{[7] [8]}

Nuclear

Nuclear proteins

Cytosolic

Cytosolic proteins

Cytoskeletal

Cytoskeletal proteins

Organelle

Endoplasmic reticulum

Endoplasmic reticulum resident protein

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

• Integral membrane protein
• Peripheral membrane protein

Extracellular matrix

Extracellular matrix proteins

Plasma

Blood protein

Species distribution

• Mammalian
• Vertebrate
• Plant
• Bacterial proteins
• Archaeal proteins
• Viral proteins

Notes and References

1. Csaba G, Birzele F, Zimmer R . Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis . BMC Structural Biology . 9 . 23 . April 2009 . 19374763 . 2678134 . 10.1186/1472-6807-9-23 . free .
2. 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 . 6 . CATH: increased structural coverage of functional space . Nucleic Acids Research . 49 . D1 . D266–D273 . January 2021 . 33237325 . 7778904 . 10.1093/nar/gkaa1079 .
3. Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG . SCOP2 prototype: a new approach to protein structure mining . Nucleic Acids Research . 42 . Database issue . D310–4 . January 2014 . 24293656 . 3964979 . 10.1093/nar/gkt1242 .
4. Dishman AF, Volkman BF . Design and discovery of metamorphic proteins . Current Opinion in Structural Biology . 74 . 102380 . June 2022 . 35561475 . 9664977 . 10.1016/j.sbi.2022.102380 .
5. Trivedi R, Nagarajaram HA . Intrinsically Disordered Proteins: An Overview . International Journal of Molecular Sciences . 23 . 22 . November 2022 . 14050 . 36430530 . 9693201 . 10.3390/ijms232214050 . free .
6. Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, Vandergriff JA, Doremieux O . 6 . 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 . January 2003 . 12520017 . 165562 . 10.1093/nar/gkg115 .
7. Web site: Trans J . Subcellular Compartments . Scitable . Nature Education . 2014 . en.
8. 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 . 6 . A subcellular map of the human proteome . Science . 356 . 6340 . May 2017 . 28495876 . 10.1126/science.aal3321 . 10744558 .