[Conformational changes in HIV-1 proteinase: effect of protonation of the active center on conformation of HIV-1 proteinase in water]
[Article in Russian]
Institute of Molecular Biology and Genetics, NAS of Ukraine, Kyiv. dikov@imbg.org.ua
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.
PMID: 12924029 [PubMed - indexed for MEDLINE]