Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding

Center for Bioinformatics, The University of Kansas, Lawrence, Kansas 66047, USA.
Proteins Structure Function and Bioinformatics (Impact Factor: 2.63). 08/2012; 80(8):2089-98. DOI: 10.1002/prot.24103
Source: PubMed


Conformational changes in the side chains are essential for protein-protein binding. Rotameric states and unbound- to-bound conformational changes in the surface residues were systematically studied on a representative set of protein complexes. The side-chain conformations were mapped onto dihedral angles space. The variable threshold algorithm was developed to cluster the dihedral angle distributions and to derive rotamers, defined as the most probable conformation in a cluster. Six rotamer libraries were generated: full surface, surface noninterface, and surface interface-each for bound and unbound states. The libraries were used to calculate the probabilities of the rotamer transitions upon binding. The stability of amino acids was quantified based on the transition maps. The noninterface residues' stability was higher than that of the interface. Long side chains with three or four dihedral angles were less stable than the shorter ones. The transitions between the rotamers at the interface occurred more frequently than on the noninterface surface. Most side chains changed conformation within the same rotamer or moved to an adjacent rotamer. The highest percentage of the transitions was observed primarily between the two most occupied rotamers. The probability of the transition between rotamers increased with the decrease of the rotamer stability. The analysis revealed characteristics of the surface side-chain conformational transitions that can be utilized in flexible docking protocols.

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    • "The two-fold difference in the critical grid spacing indicates larger changes at the interface than on the rest of the surface. While the earlier studies [18,24,25] observed this trend for the side-chain rotamers, this study validates it by a more general approach based on the DADFs. "
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