Issue 86, 2015

Zn2+ ion of the snake venom metalloproteinase (SVMP) plays a critical role in ligand binding: a molecular dynamics simulation study

Abstract

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 (ΔGBind 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.

Graphical abstract: Zn2+ ion of the snake venom metalloproteinase (SVMP) plays a critical role in ligand binding: a molecular dynamics simulation study

Supplementary files

Article information

Article type
Paper
Submitted
24 Jul 2015
Accepted
11 Aug 2015
First published
18 Aug 2015

RSC Adv., 2015,5, 70566-70576

Author version available

Zn2+ ion of the snake venom metalloproteinase (SVMP) plays a critical role in ligand binding: a molecular dynamics simulation study

S. Chinnasamy, S. Nagamani and K. Muthusamy, RSC Adv., 2015, 5, 70566 DOI: 10.1039/C5RA14693C

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