proteindomain

A protein domain is a discrete unit within a protein that can evolve, function, and exist independently of other parts of the protein. Domains often fold into stable three-dimensional structures and are typically a few tens to a few hundred amino acids long. A protein may contain one domain or multiple domains in a single polypeptide, sometimes arranged in a modular fashion with flexible linkers between them.

Domains provide specific functions such as catalysis, binding to other molecules, or mediating interactions with proteins, nucleic acids, or membranes. Many domains retain their structure and function when transferred to different proteins, supporting the modular nature of proteins.

Evolutionarily, domains are units of modularity that can be duplicated, inserted, or shuffled between genes, contributing to functional diversity. The arrangement of domains, known as domain architecture, influences how a protein behaves, including substrate specificity, regulation, and localization.

Domain identification employs sequence similarity, multiple sequence alignments, and structural analyses. Profile hidden Markov models capture conserved patterns across families. Major resources catalog domains and provide annotations, including Pfam, InterPro, SMART, CATH, and SCOP.

Applications include functional annotation of genomes, understanding disease mutations that affect a domain, and engineering proteins by swapping domains to create novel functions.

Examples of common domains include kinase catalytic domains, SH2 and SH3 domains (signal transduction), PDZ domains (scaffolding), and immunoglobulin-like domains (cell adhesion).