AUTOMATIC AND ACCURATE METHOD FOR ANALYSIS OF PROTEINS THAT UNDERGO HINGE-MEDIATED DOMAIN AND LOOP MOVEMENTS

Background: The structures of proteins that undergo significant main-c hain conformational change are reported with increasing frequency. Thr ee-dimensional atomic models are often available for two alternative c onformational states of the same molecule. Inspection has shown these states to be varied in nature, arising by mechanisms that include hing e-facilitated closure between domains and smaller-scale loop motions w ithin domains; these movements are often induced by metal ion binding or ligand binding. Polypeptides that display flexible segments are als o observed in different crystal conformations or as alternatively pack ed subunits. Although subjective visual inspection has been previously used to compare structures and analyze conformational changes, there is a need for an objective method. Results: We have developed a straig htforward, robust, and objective algorithm that can locate the residue s that mediate and participate in the changes between the two conforma tional states. Our method does not require initial superpositioning. W e illustrate the method by considering several test cases. The first e xhibits rigid-body domain closure involving multiple hinges. The secon d is lactate dehydrogenase, which undergoes both loop and subdomain mo vement; we accurately describe the location and relative magnitude of these deformations. Finally, in the example of aspartate transcarbamoy lase, both hinge-mediated domain movement and functionally relevant lo op rearrangements are described. In the instances in which domain clos ure occurs, the residues that serve as hinges between the domains invo lved are accurately predicted. In addition, our technique successfully identifies the exact residues that undergo intra-domain loop movement s, even for movements that are accompanied by larger scale inter-domai n rearrangements. Conclusions: Our algorithm is successful in its comp rehensive analysis and description of complex hinge-mediated domain mo tion for all structures displaying rigid-body movement and is accurate in identifying the location of any independent intradomain rearrangem ents.