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CRK is a signal transducing adaptor protein, which mediates proteinprotein interactions in signaling pathways. CRK has several proteinbinding modules named SH2 and SH3 domains. Our goal is the design of high-affinity peptides binding to CRK SH2. First, we developed original GPU docking program using MM potential energy and the generalized born (GB) solvent as scoring functions. After pose predictions, MM-PBSA rescoring were conducted. In rescoring, we compared several radii sets which determines the boundary between solute and solvent. Furthermore, we performed additional conformational search of peptides in the unbound states to take account of ligand’s reorganization effects. Our methods showed high performances in discrimination of known binding sequences.

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1P043 Computational design of short peptide inhibitors of protein-protein interactions in intracellular signaling mediated by CRK-SH2(01B. Protein:Structure &amp; Function,Poster)