An insight to conserved water molecular dynamics of catalytic and structural zn+2 ions in Matrix Metalloproteinase 13 of Human

Bornali Chakrabarti, Hridoy R. Bairagya, Payel Mallik, Bishnu P. Mukhopadhyay, Asim K. Bera

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8 Scopus citations


Matrix Metalloproteinase (MMP) −13 or Collagenase -3 plays a significant role in the formation and remodeling of bone, tumor invasion and causes osteoarthritis. Water molecular dynamic studies of the five (1XUC, 1XUD, 1XUR, 456C, 830C) PDB and solvated structures of MMP-13 in human have been carried out upto 5 ns on assigning the differential charges (+2, +1, +0.5 e) to both the Zinc ions. The MM and MD-studies have revealed the coordination of three water molecules (WH, WI and WS) to Znc and one water to Zns. The transition of geometry around the Znc from tetrahedral to octahedral via trigonal bipyramidal, and for Zns from tetrahedral to trigonal bipyramidal are seem interesting. Recognition of two zinc ions through water molecular bridging (Znc -WH (W1)…W2…. W3…. H187 -Zns) and the stabilization of variable coordination geometries around metal ions may indicate the possible involvement of Znc …Zns coupled mechanism in the catalytic process. So the hydrophilic topology and stereochemistry of water mediated coupling between Zn-ions may provide some plausible hope towards the design of some bidentate/polydentate bridging ligands or inhibitors for MMP-13.

Original languageEnglish (US)
Pages (from-to)503-516
Number of pages14
JournalJournal of Biomolecular Structure and Dynamics
Issue number4
StatePublished - Feb 2011


  • Conserved Water Molecules
  • Dynamics
  • Matrix Metalloproteinase
  • Mechanism
  • Zn ions


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