title: [Conformational changes in HIV-1 proteinase: effect of protonation of the active center on conformation of HIV-1 proteinase in water].
abstract: At weak acidic pH, where HIV-1 proteinase is most stable and active, its catalytic Asp 25/25' dyad shares one proton. At a physiological pH the dyad is deprotonated, however, 2 ns molecular dynamics simulations of the HIV-1 protease with monoprotonated and deprotonated Asp25/25' dyad is performed, in order to investigate the influence of Asp25/25' protonation state on the proteinase dynamics. For net charge neutralization the 4 Cl- ions were included. In case of deprotonated active site the significant tertiary structure deviation of HIV-1 PR structure from crystal structure is observed, while in the monoprotonated one the tertiary structure fluctuates near starting structure. Possible mechanism of the influence of the Asp25/25' protonation state on proteinase dynamics is discussed.
authors.affiliation: Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv. dikov@imbg.org.ua
authors.forename: D B
authors.initials: DB
authors.lastname: Koval'skiĭ
authors.forename: D S
authors.initials: DS
authors.lastname: Kanibolotskiĭ
authors.forename: V N
authors.initials: VN
authors.lastname: Dubina
authors.forename: A I
authors.initials: AI
authors.lastname: Korneliuk
mesh_terms: D001224:Aspartic Acid / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002384:Catalysis; D002712:Chlorides / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D016333:HIV Protease / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008962:Models, Theoretical; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011522:Protons; D014867:Water / Q000737:chemistry*
chemical_list: D002712:Chlorides; D011522:Protons; D014867:Water; D001224:Aspartic Acid; D016333:HIV Protease