Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation.

ABSTRACT: A method is proposed to study protein-ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first-encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide-protein complex. The peptide adop

SUBMITTER: Cardone A 

PROVIDER: S-EPMC4409547 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature