title: Conformational variation of an extreme drug resistant mutant of HIV protease.
abstract: Molecular mechanisms leading to high level drug resistance have been analyzed for the clinical variant of HIV-1 protease bearing 20 mutations (PR20); which has several orders of magnitude worse affinity for tested drugs. Two crystal structures of ligand-free PR20 with the D25N mutation of the catalytic aspartate (PR20D25N) revealed three dimers with different flap conformations. The diverse conformations of PR20D25N included a dimer with one flap in a unique "tucked" conformation; directed into the active site. Analysis of molecular dynamics (MD) simulations of the ligand-free PR20 and wild-type enzymes showed that the mutations in PR20 alter the correlated interactions between two monomers in the dimer. The two flaps tend to fluctuate more independently in PR20 than in the wild type enzyme. Combining the results of structural analysis by X-ray crystallography and MD simulations; unusual flap conformations and weakly correlated inter-subunit motions may contribute to the high level resistance of PR20.
authors.affiliation: Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors.forename: Chen-Hsiang
authors.initials: CH
authors.lastname: Shen
authors.affiliation: Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors.forename: Yu-Chung
authors.initials: YC
authors.lastname: Chang
authors.affiliation: Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
authors.forename: Johnson
authors.initials: J
authors.lastname: Agniswamy
authors.affiliation: Department of Biology, Georgia State University, Atlanta, GA 30303, USA; Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Harrison
authors.affiliation: Department of Biology, Georgia State University, Atlanta, GA 30303, USA; Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA. Electronic address: iweber@gsu.edu.
authors.forename: Irene T
authors.initials: IT
authors.lastname: Weber
mesh_terms: D002219:Carbamates / Q000737:chemistry; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D024882:Drug Resistance, Viral; D016333:HIV Protease / Q000737:chemistry*; D017320:HIV Protease Inhibitors / Q000737:chemistry*; D015497:HIV-1 / Q000201:enzymology*; D056004:Molecular Dynamics Simulation; D020125:Mutation, Missense; D011485:Protein Binding; D017433:Protein Structure, Secondary; D013449:Sulfonamides / Q000737:chemistry
chemical_list: D002219:Carbamates; C540659:GRL 02031; D017320:HIV Protease Inhibitors; D013449:Sulfonamides; D016333:HIV Protease
keywords: Coordinated motions; Drug resistance mutations; Flap dynamics; HIV-1 protease; Molecular dynamics simulations; Resistance mechanisms; X-ray crystallography