title: Hydrophobic Binding Hot Spots of Bcl-xL Protein-Protein Interfaces by Cosolvent Molecular Dynamics Simulation.
abstract: Identifying binding hot spots in protein-protein interfaces is important for understanding the binding specificity and for the design of nonpeptide, small molecule inhibitors. Molecular dynamics simulation in the isopropanol/water cosolvent environment and in water was employed to investigate Bcl-xL protein, which has a highly flexible, large, and primarily hydrophobic binding site. Simulations of either the apo- or holocrystal structures of the Bcl-xL in pure water fail to generate conformations found in the cocrystal structures of Bcl-xL in complex with its binding partners due to hydrophobic collapse. In contrast, simulations in cosolvent starting either from the apo- or holocrystal structure of the Bcl-xL yield binding-site conformations similar to that found in the cocrystal structures of Bcl-xL. Hydrophobic binding hot spots identified using the conformations from the cosolvent simulations are in excellent agreement with experimental structural data of known inhibitors. Importantly, cosolvent simulations revealed the highly dynamic nature of the hydrophobic binding pockets in Bcl-xL and yielded new structural insights for the design of novel Bcl-xL small-molecule inhibitors.
authors.affiliation: Comprehensive Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , 1500 East Medical Center Drive, Ann Arbor, Michigan 48109-0934, United States.
authors.forename: Chao-Yie
authors.initials: CY
authors.lastname: Yang
authors.affiliation: Comprehensive Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , 1500 East Medical Center Drive, Ann Arbor, Michigan 48109-0934, United States.
authors.forename: Shaomeng
authors.initials: S
authors.lastname: Wang
keywords: Bcl-xL protein; Protein−protein interfaces; cosolvent molecular dynamics simulation