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, 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:
 * CATH database
 * Structural Classification of Proteins database (SCOP)

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. Finally other proteins appear not to adopt any stable conformation and are referred to as intrinsically disordered.

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 celluar function. A widely used classification is PANTHER (protein analysis through evolutionary relationships) classification system.

Structural
Protein

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

 * Antibody
 * Chemokines and their receptors
 * Cytokines and their receptors
 * 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.

Nuclear
Nuclear proteins

Cytosolic
Cytosolic proteins

Cytoskeletal
Cytoskeletal proteins

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