Page Edited and Updated by: Christopher Fucile
Domain-domain interfaces exist between separate domains contained in the same chain. A domain is defined as a region of a protein containing a globular structure with a distinct self-stabilizing motif that has the ability to fold independently of the protein. Domain sequences are not unique to individual proteins; thus the structural and sequential alignment of a binding domain is often used to determine the biological function and significance of the protein. The Protein Data Bank can be used in tangent with SCOP and the NIH’s Cn3D to visualize the domain binding in proteins.
Intra-domain interfaces have a single structural domain and the surface interfacing occurs most often through disulfide bonding between the N-terminus of the protein to DNA binding C-domain.
Hetero-oligomers create an interface between permanently interacting protein chains of in different chain sequences in oligomeric enzymes. When hetero-oligomer binding occurs, the ligand on one subunit interacts both positively and cooperatively with the same type of ligand bound on adjacent subunits.
Hetero-complexes contain interfaces between different transiently interacting protein chains. Examples of hetero-complexes include signal transduction proteins, protease complexes, enzymes, antibody-antigen, and G- coupled proteins.
A common theme contained in domain-domain, intra-domain, and hetero interfaces are the presence of hydrophobic, hydrophilic interactions, and cysteine and salt bridges, which are not found in the homo structures discussed below.
Homo-oligomer surfaces are permanent interfaces between intermingling identical chains. Oligomeric enzymes bind in this way; the binding of a ligand on one subunit interacts in such a way that the same ligand interacts positively and cooperatively on the same type of ligand bound on adjacent subunits.
Homo-complexes exist between transitorily interacting interfaces that contain indistinguishable protein chains. Homo-dimer interfaces mimic the appearance of the protein interior. They incorporate non-covalent interactions and These interactions at the quaternary structural level that allow for the numerous regulatory roles including ligand binding or modification. Enzymes, transport proteins and transcriptional factors all contain homo-dimeric interactions. These types of interactions are unique in that the presence of hydrophobic or hydrophilic interfaces are rare, nor are salt bridges, which will be discussed later in the chapter. Homo-complexes prefer to form bonds between amino acids which are identical.
References (Open Access)Edit
1.^ "RCSB Protein Data Bank" RCSB Protein Data Bank. 30 March 2008. <http://www.rcsb.org/pdb/Welcome.do;jsessionid=jWiH9khbFqKgmPsIahLOxA>
3.^ "Structure Home" NCBI. 30 March 2008. <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure&itool=toolbar>