title: 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 molecular dynamics in an iterative process to identify tunnels that open as a result of ligand migration and calculates the potential of mean force of ligand egress through a given tunnel. Applying this new method to cytochrome P450 2B6, we demonstrate the influence of protein flexibility on the shape and accessibility of tunnels. More importantly, we demonstrate that the ligand itself, while traversing through a tunnel, can reshape tunnels due to its interaction with the protein. This process results in the exposure of new tunnels and the closure of preexisting tunnels as the ligand migrates from the active site.
authors.affiliation: Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, Indiana, 47907.
authors.forename: Laura J
authors.initials: LJ
authors.lastname: Kingsley
authors.forename: Markus A
authors.initials: MA
authors.lastname: Lill
mesh_terms: D000465:Algorithms; D020134:Catalytic Domain; D065702:Cytochrome P-450 CYP2B6 / Q000737:chemistry*; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D007093:Imidazoles / Q000737:chemistry*; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: C525744:1-(4-chlorophenyl)imidazole; D007093:Imidazoles; D008024:Ligands; C585599:CYP2B6 protein, human; D065702:Cytochrome P-450 CYP2B6
keywords: conformational ensemble; cytochrome P450 2B6; induced fit; potential of mean force; protein flexibility; steered molecular dynamics; tunnel prediction; umbrella sampling