Reengineering the Oligosaccharide Specificity of CVN with BP_Dock

Abstract

Cyanovirin-N (CV-N) is a cyanobacterial lectin with potent anti-HIV activity, mediated by binding to Man(1,2)Man with high affinity and specificity. These sugar-binding sites are located in two quasi-symmetric domains (A and B) of the CV-N protein. We explore the sequence space of CV-N and reengineered CV-N mutants with different binding affinity for the oligo-mannosides, through integrated computational and experimental strategies. using the sequences of two engineered CV-N,1,2 we model various CV-N mutants, and obtain these variants in complex with di-mannose sugar with a fast and flexible docking method called BP-Dock. BP-Dock can integrate both backbone and side chain conformational changes in a protein through a multi-scale approach. It mimics the nature of binding induced events by perturbation of the binding site residues through small Brownian kicks as a first order approximation of an approaching ligand. Then it computes the response fluctuation profile of the chains using the perturbation response scanning method. The response fluctuation profiles are then used to generate binding induced multiple receptor conformations of CV-N mutants for ensemble docking. The results from docking simulation are then validated with NMR experiments. Overall, this study helps us to explore the sugar binding properties of CV-N mutants and provides a better insight about the binding site of CV-N.