Prediction of solvation sites at the interface of Src SH2 domain complexes using molecular dynamics simulations.

摘要: Src Homology 2 (SH2) domains are approximately 100 amino acid that mediate recognition of tyrosine-phosphorylated sites by signalling proteins. Structures SH2 with bound ligands indicate a potentially important role water in influencing the binding thermodynamics. In this study, we used molecular dynamics (MD) simulation methods to evaluate solvation at interface domain. We designed software, WaRP (Water Residency Potential), compute positions hydration from coordinates data MD simulations and studied impact computed on prediction thermodynamics domain phosphorylated peptides using method based accessible surface area buried upon association. Two dually one monophosphorylated ligand were studied. showed software predicted between 70% 85% crystallographic molecules depending complexes. Comparison structures both unbound partners led thorough evaluation behaviour during reaction. also all ligand-SH2 investigated may be derive entropy change provided heat capacity is known. This study first examine structure around contributes our understanding domains.