List of proteins

Schematic representation of structural classes of protein according to the CATH classification scheme.

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, transporting essential nutrients, or serving 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

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

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

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
• Complement System

Genetic

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

Signal transduction

Signal transduction

Sub-cellular distribution

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

Proteins may also be classified by which subcellular compartment they are found.

Nuclear

Nuclear proteins

Cytosolic

Cytosolic proteins

Cytoskeletal

Cytoskeletal proteins

Organelle

Endoplasmic reticulum

Endoplasmic reticulum resident protein

Mitochondrial

Mitochondrial DNA that encode mitochondrial proteins (note that some mitochondrial 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 proteins
• Vertebrate proteins
• Plant proteins
• Bacterial proteins
• Archaeal proteins
• Viral proteins