Molecular dynamics study of HIV-1 protease-substrate complex: Roles of thewater molecules at the loop structures of the active site

Several molecular dynamics (MD) simulations of HIV-1 protease (HIV-1 PR)-su bstrate complex were performed. The initial structure of the enzyme-substra te (ES) complex was constructed based on the X-ray crystallographic structu re of the HIV-1 PR-inhibitor (JG-365) complex. First, we investigate which of Asp25 and Asp25' at the catalytic site (two catalytic Asp residues) is p rotonated in the ES complex. These MD simulations have revealed that the pr otein hydrolysis mechanism is initiated from the ES complex in which Asp25' is protonated. This protein hydrolysis mechanism was already studied using quantum chemical calculations, which suggested that the specific conformat ion of the ES complex was essential for enzymatic activity. Next, we invest igate the mechanism for the maintenance of specific conformation of the ES complex. The MD simulations suggest that two water molecules at the loop st ructures of the active site have a substantial role in maintaining the spec ific conformation for initiation of the enzyme reaction. This indicates tha t the enzymatic activity of HIV-1 PR cannot be induced by only the protease encoded by the RNA gene of HIV-1, but this also requires the incorporation of water molecules into the active site.