What induces pocket openings on protein surface patches involved in protein–protein interactions?
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We previously showed for the proteins BCL-XL, IL-2, and MDM2 that transient pockets at their protein–protein binding interfaces can be identified by applying the PASS algorithm to molecular dynamics (MD) snapshots. We now investigated which aspects of the natural conformational dynamics of proteins induce the formation of such pockets. The pocket detection protocol was applied to three different conformational ensembles for the same proteins that were extracted from MD simulations of the inhibitor bound crystal conformation in water and the free crystal/NMR structure in water and in methanol. Additional MD simulations studied the impact of backbone mobility. The more efficient CONCOORD or normal mode analysis (NMA) techniques gave significantly smaller pockets than MD simulations, whereas tCONCOORD generated pockets comparable to those observed in MD simulations for two of the three systems. Our findings emphasize the influence of solvent polarity and backbone rearrangements on the formation of pockets on protein surfaces and should be helpful in future generation of transient pockets as putative ligand binding sites at protein–protein interfaces.
KeywordsBinding pocket CONCOORD Molecular dynamics simulation Normal mode analysis Protein–protein interaction inhibition Structure-based drug design tCONCOORD
This work was funded by a grant of the Deutsche Forschungsgemeinschaft (Center for Bioinformatics, Saarland University). We thank Jan Fuhrmann and Dirk Neumann for making available their BALLPass implementation to us.
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