Including ligand-induced protein flexibility into protein tunnel prediction.

ABSTRACT: In proteins with buried active sites, understanding how ligands migrate through the tunnels that connect the exterior of the protein to the active site can shed light on substrate specificity and enzyme function. A growing body of evidence highlights the importance of protein flexibility in the binding site on ligand binding; however, the influence of protein flexibility throughout the body of the protein during ligand entry and egress is much less characterized. We have developed a novel tunnel prediction and evaluation method named IterTunnel, which includes the influence of ligand-induced protein flexibility, guarantees ligand egress, and provides detailed free energy information as the ligand proceeds along the egress route. IterTunnel combines geometric tunnel prediction with steered

SUBMITTER: Kingsley LJ 

PROVIDER: S-EPMC4122613 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature