Paper Citing NAMD - Abstract
Chinnasamy, Sathishkumar; Nagamani, Selvaraman; Muthusamy, Karthikeyan
Zn2+ ion of the snake venom metalloproteinase (SVMP) plays a critical role in ligand binding: a molecular dynamics simulation study
RSC ADVANCES, 5:70566-70576, 2015
Snake venom metalloproteinase (SVMP) is one of the major components of snake venom and it is a root causative agent for edema, local tissue damage, inflammation, blood coagulation and hemorrhage during the snake bite. The catalytic activity of SVMP is regulated by metal ions (Zn2+ and Ca2+). In this study, the three dimensional structure of SVMP was modeled with Zn2+ and Ca2+ ions. Molecular docking, prime/MM-GBSA (Delta G(Bind) calculations), quantum polarized ligand docking (QPLD), QM-MM interaction energy analysis and molecular dynamics simulation were performed for the compound Clerodane diterpenoid with the SVMP in the presence and absence of metal ions (Zn2+ and Ca2+). The result shows that the metal ions are present in the ligand binding domain are critical for the SVMP protein to function, particularly the Zn2+ ion. Further, we observed that both the ions have a significant effect on ligand binding.
