Ab initio MD studies of HIV-1 Protease：HIV-1蛋白酶的从头计算分子动力学研究.ppt

Ab initio MD studies of HIV-1 Protease Candidate: Stefano Piana Agostinetti Supervisor: Paolo Carloni Outline Biochemistry of the enzyme HIV-1 protease (HIV-1 PR) Results The Active site conformational flexibility in the free enzyme NMR signal calculations in the HIV-1 PR/Pepstatin adduct Interplay between global protein motions and the reaction mechanism of HIV-1 PR Conclusions The HIV-1 Protease HIV-PR is required for viral maturation HIV-1 PR cleaves polypeptide chains The HIV-1 Protease cleavage site The Asp Dyad protonation state Minimal modeling of the Asp dyad Adding the Thr26-Gly27 H-bond The peptide bond dipole moment The HIV-1 PR/Pepstatin complex 13C NMR of aspartic acids 13C NMR of the Asp dyad in the HIV-1 PR/Pepstatin complex Ab initio calculations of the 13C NMR chemical shift of the Asp dyad Ab initio calculations of the 13C NMR chemical shift of the Asp dyad Resonance stabilization Model system calculations Resonance de/stabilizing contributions The reaction mechanism CMD simulation - the system HIV-1 PR/Substrate complex flexibility HIV-1 PR/Substrate complex flexibility HIV-1 PR/Substrate complex flexibility Substrate displacements Model complexes to study the reaction profile Transition states Reaction Intermediate Flap Flap Fulcrum Fulcrum Cantilever Cantilever Immature non-infective viral particles HIV-1 PR Infective Viruses Polypeptide chain (Substrate) Flap Flap Active site Asp25 Asp25’ Gly27 Gly27’ Thr26 Thr26’ Asp25 Asp25’ Asp25 Asp25’ Asp25 Asp25’ Unstable 0.0 kcal/Mol 2.0 kcal/Mol H O O O O - 180 ppm 175 ppm D 0.15 ppm H O O O O - 178 ppm 172 ppm Isotopic substitution 176 ppm 179 ppm 175 ppm 175 ppm 180 ppm MBO ratio: 1.00 MBO ratio: 1.68 50 kcal/Mol 20 kcal/Mol 50 kcal/Mol 50 kcal/Mol Single proton transfer 20 kcal/Mol Concerted double proton transfer * *