Protein domains

Protein domains are a part of protein structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural domains. One domain may appear in a variety of different proteins.

Overview

Protein domains serve various functions, such as binding small molecules, other proteins, or DNA. They are typically 25-500 amino acids long with specific functions, which may include enzymatic activities or binding ligands. Domains often form functional units, such as the calcium-binding domain of a larger protein.

Classification

Protein domains are classified into families based on sequence and structure similarities. The Protein Data Bank (PDB) and Pfam are two databases that classify protein domains. The PDB categorizes domains based on their tertiary structure, while Pfam categorizes them based on their sequence.

Structure

The structure of a protein domain is defined by its secondary structure elements, such as alpha helices and beta sheets. These elements are arranged to form a compact, globular structure. The structure of a domain can be determined using techniques such as X-ray crystallography or Nuclear Magnetic Resonance (NMR).

Function

The function of a protein domain is often related to its structure. For example, a domain with a pocket or groove on its surface might bind a small molecule or part of another protein. Some domains have enzymatic activity, while others are involved in protein-protein interactions or signal transduction.

Evolution

Protein domains can evolve independently of the rest of the protein. This is because they can fold and function independently, and because their coding sequences can move around in the genome. This process, known as domain shuffling, has been important in the evolution of new proteins.

See also

• Protein structure
• Protein folding
• Protein-protein interaction
• Protein Data Bank
• Pfam