(Logo) Domains in Proteins

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This section is largely based on the excellent review by Gerstein et al. (1994). Mark Gerstein is also largely responsible for The Protein Motions Database

Protein flexibility is demonstrated by large relative movements of domains, for example, in aspartic proteinases the two lobes have large relative shifts as identified by Sali et al., (1992). Such motions are important for functions like catalysis, ligand binding, regulation of activity, formation of protein assemblies and transport of metabolites. Often the domains constitute a binding site at the interface wherein closed conformations of domains correspond to inactive form of the enzyme while open conformations of domains correspond to the active form of the enzyme, illustrating induced fit in recognition (Koshland, 1958).

Mechansisms of domain movements -

  1. Intrinsic flexibility -
    Several small movements in secondary structures which has a cummulative effect. This may be further classified into two types:

  2. Hinged domain movements -
    In order that each subunit in the tobacco bushy stunt virus fits into the icosahedral symmetry, the S and P domains undergo displacements mainly by the change in conformation of the peptide that forms a linker between the two (Olsen et al., 1983). On the other hand in the transport proteins like lactoferrin, the open and closed forms of the two domains involve a 53 degree rotation which is achieved by two strands that connect two domains (Anderson et al., 1990). More complex hinge motions take place in protein kinase (Knighton et al., 1991) and in adenylate kinases (Berry et al., 1994).

  3. Ball-and-socket motion -
    The variable (light and heavy chain) domains of antibodies rotate about 50 degrees with respect to the heavy (light and heavy chain) by means of a combination of hinge and shear motions (Lesk and Chothia, 1988).

R. Sowdhamini 1995
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Last updated 11th Jun '96