A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding.

ABSTRACT: Cyanovirin-N (CVN), a cyanobacterial lectin, exemplifies a class of antiviral agents that inhibit HIV by binding to the highly glycosylated envelope protein gp120. Here, we investigate the energetics of glycan recognition using a computationally inexpensive flexible docking approach, backbone perturbation docking (BP-Dock). We benchmarked our method using two mutants of CVN: P51G-m4-CVN, which binds dimannose with high affinity through domain B, and CVN((mutDB)), in which binding to domain B has been abolished through mutation of five polar residues to small nonpolar side chains. We investigated the energetic contribution of these polar residues along with the additional position 53 by docking dimannose to single-point CVN mutant models. Analysis of the docking simulations indicated that t

SUBMITTER: Bolia A 

PROVIDER: S-EPMC4026791 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature