Automatic and accurate method for analysis of proteins that undergo hinge-mediated domain and loop movements

The structures of proteins that undergo significant main-chain conformational change are reported with increasing frequency. Three-dimensional atomic models are often available for two alternative conformational states of the same molecule. Inspection has shown these states to be varied in nature, arising by mechanisms that include hinge-facilitated closure between domains and smaller-scale loop motions within domains; these movements are often induced by metal ion binding or ligand binding. Polypeptides that display flexible segments are also observed in different crystal conformations or as alternatively packed subunits. Although subjective visual inspection has been previously used to compare structures and analyze conformational changes, there is a need for an objective method.

We have developed a straightforward, robust, and objective algorithm that can locate the residues that mediate and participate in the changes between the two conformational states. Our method does not require initial superpositioning. We illustrate the method by considering several test cases. The first example is maltose binding protein, a polypeptide that exhibits rigid-body domain closure involving multiple hinges. The second is lactate dehydrogenase, which undergoes both loop and subdomain movement; we accurately describe the location and relative magnitude of these deformations. Finally, in the example of aspartate transcarbamoylase, both hinge-mediated domain movement and functionally relevant loop rearrangements are described. In the instances in which domain closure occurs, the residues that serve as hinges between the domains involved are accurately predicted. In addition, our technique successfully identifies the exact residues that undergo intra-domain loop movements, even for movements that are accompanied by larger scale inter-domain rearrangements.

Our algorithm is successful in its comprehensive analysis and description of complex hinge-mediated domain motion for all structures displaying rigid-body movement and is accurate in identifying the location of any independent intra-domain rearrangements.