An independent folding unit within the tertiary structure of a protein. The domain is usually a combination of several super secondary structural units to the protein polypeptide chain Secondary structure On the basis of the above, it is further curled and folded into several relatively independent spherical assemblies. Structural Domain is another structure hierarchy between the secondary and tertiary structures. The so-called domain refers to the closely separated spherical structure region in the protein subunit structure, also known as jurisdiction. The polypeptide chain first forms a regular secondary structure from adjacent amino acid residues in some regions, and then forms a super secondary structure from the adjacent secondary structure fragments. On this basis, the polypeptide chain folds into a spherical tertiary structure. For larger protein molecules or subunits, polypeptide chains are often associated by two or more spatially distinct, relatively independent regional structures to form a tertiary structure. This relatively independent regional structure is called a domain. For smaller protein molecules or subunits, the domain and its tertiary structure often mean the same thing, that is, these proteins or subunits are single domains. The structural domain itself is tightly assembled, but the relationship between structural domains is loose. A segment of peptide chain with different length is often connected between the domain and the domain, forming the so-called hinge region. The number of domains in different protein molecules is different, and several domains in the same protein molecule are similar or very different from each other. The amino acid residues of common domains range from 100 to 400, the smallest domain has only 40 to 50 amino acid residues, and the large domain can have more than 400 amino acid residues.
In order to study the basic rules of protein molecular structure, people use different methods to classify known protein structures from different perspectives. Some are based on biological functions, some are based on the structure itself, and some are based on the combination of the two for classification research. For example, zinc metalloproteinases are a class of endopeptidases that can catalyze the hydrolysis of peptide bonds in the peptide chain. Although the overall spatial structure of each subfamily member is significantly different, the structure of the catalytic active site is very similar, so they are classified as a class of proteins.
However, it is M Levitt and C Chothia's classification of protein structure. This method considers that the combination of secondary structures constitutes the core of most domain structures, and accordingly, protein structures are divided into four categories: α Type β Type α/β Type and other types of domain structures. α Type domain structure is mainly composed of α- Spiral, such as the structure of myoglobin. β Type I domain structure is mainly composed of antiparallel kinks, usually two kinks are wrapped together, such as the structure of plastid blue. α/β Type domain structure is composed of α- Spiral wrapped in parallel β- Chain dominated; β-α-β It is composed of patterns, such as the structure of triose phosphate isomerase, glucose isomerase catalytic domain, etc. Some proteins are composed of discontinuous α- and β- The patterns are combined, and usually α- A part of the spirally wrapped domain forms a small antiparallel β- These structures can be considered to belong to the fourth category, such as the structures of some nucleases. In addition, there are some small proteins, which are rich in disulfide bonds or metal ions, forming a special kind. The structure of these proteins seems to be affected by metal ions or disulfide bridges to a large extent, so they seem to be out of order than conventional proteins.
The types are: α- Spiral type; α/β Type; whole β- Folding type; Random roll type.
Domain In essence, the domain is the combination of the secondary structure and serves as the component of the tertiary structure. Each domain represents a function.
A peptide chain of some globular proteins, or two or more peptide chains connected by covalent bonds, can be spatially distinguished into several spherical substructures, each of which is called a domain. Each domain of the same protein is linked with each other by peptide chains, and most of the links between the two domains are single stranded peptide chains. Only in very few cases will there be a few double stranded peptide chains connecting different domains. In the electron density diagram drawn by the X-ray diffraction experiment, it can be clearly seen that there are some cracks in some globular protein fields. These cracks are the links between various domains. Although the links between domains are loose, they still belong to the same peptide chain, There is an essential difference between linking by peptide chain and maintaining structure by non bond interaction between subunits of protein. The domain has proximity correlation in space, that is, the amino acid residues that are close to each other in the primary structure are also close to each other in the three-dimensional spatial structure of the domain, and the amino acid residues that are far away from each other in the primary structure are also far away from each other in the spatial structure of the domain, even belonging to different domains.
Domains are closely related to the physiological function of proteins. Sometimes several domains work together to complete a physiological function, and sometimes one domain can independently complete a physiological function, but it is impossible for an incomplete domain to produce physiological functions. Therefore, domain is the structural basis of protein physiological function, but it must be pointed out that although domain and protein function are closely related, the concepts of domain and functional domain are different.
Domain Formation: the structure between domains is relatively loose, often forming cracks or cave cracks with many non-polar amino acid residues, so it is hydrophobic, water molecules are not allowed to enter, but can accommodate the cofactor of sodium protein or the substrate molecule of enzyme.
Meaning: The active site or allosteric structure site of the protein is mostly located in the fissure. Due to the flexibility of the connection between domains, each domain can carry out a relatively large range of relative movement to open or close the cracks, facilitating the interaction between protein molecules and other molecules, so these sites are often where the active center is located, or where the allosteric compounds are bound.
Domain
