Molecular Dynamics Simulation of HIV-1 Integrase Dimer Complexed with Viral DNA

作者：Hu Jianping^*; Wang Cunxin

来源：Chinese Journal of Chemistry, 2010, 28(1): 33-40.

• HIV-1 integrase
• viral DNA
• molecular dynamics simulation
• dynamical cross-correlation map
• principal component analysis

The biological function of HIV-1 integrase (IN) is to integrate viral DNA into the host cell chromosome. and the specific binding of IN with viral DNA is a precondition for IN to function correctly. Beforehand, the binding mode of IN dimer (IN(2)) with the 27 bp segment of viral DNA before 3' processing (3'-P) was obtained via a molecular docking method. Based on the binding mode, the aim of this article was to explore the changes of motive mode and correlative motion for the IN(2) and DNA systems after their binding through dynamical cross-correlation map (DCCM) and principal component analysis (PCA). Finally, solvent effect during the association was analyzed briefly. The results show that there is a significantly increased positive correlation in the interface region between IN(2) and viral DNA, and some obvious motive mode changes of the two systems (IN(2) and DNA) were also observed after their binding. It was found that water molecules played an important role in the recognition between IN(2) and viral DNA through analyzing the water-mediated hydrogen bonds.

• 出版日期2010-1
• 单位乐山师范学院; 北京工业大学