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

✍ Scribed by Jianping Hu; Cunxin Wang

• Publisher: John Wiley and Sons
• Year: 2010
• Tongue: English
• Weight: 403 KB
• Volume: 28
• Category: Article
• ISSN: 0256-7660
• DOI: 10.1002/cjoc.201090032

✦ Synopsis

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.