Insight towards the conserved water mediated recognition of catalytic and structural Zn+2 ions in human Matrix Metalloproteinase-8 enzyme: A study by MD-simulation methods

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Title	Insight towards the conserved water mediated recognition of catalytic and structural Zn+2 ions in human Matrix Metalloproteinase-8 enzyme: A study by MD-simulation methods
Authors	Bornali Chakrabarti¹, Hridoy R Bairagya¹, Deepak Kr Mishra¹, Pradip Kumar Chatterjee² & Bishnu P Mukhopadhyay¹*
Affiliation	¹Department of Chemistry, National Institute of Technology, Durgapur – 713 209, W.B. India; ²Thermal Engineering Department, Central Mechanical Engineering Research Institute, Durgapur – 713209,W.B, India.
Email	bpmk2@yahoo.com; *Corresponding author
Article Type	Hypothesis
Date	Received January 07, 2013; Accepted January 10, 2013; Published February 06, 2013
Abstract	Human matrix metalloproteinase-8 (hMMP-8) plays a important role in the progression of colorectal cancer, metastasis, multiple sclerosis and rheumetoid arthritis. Extensive MD-simulation of the PDB and solvated structures of hMMP-8 has revealed the presence of few conserved water molecules around the catalytic and structural zinc (ZnC and ZnS) ions. The coordination of two conserved water molecules (W and WS) to ZnS and the H-bonding interaction of WS to S151 have indicated the plausible involvement of that metal ion in the catalytic process. Beside this the coupling of ZnC and ZnS metal ions (ZnC – WH (W1)…..W2 ….H162 - ZnS) through two conserved hydrophilic centers (occupied by water molecules) may also provide some rational on the recognition of two zinc ions which were separated by ~13 Å in their X-ray structures. This unique recognition of both the Zn+2 ions in the enzyme through conserved water molecules may be implemented/ exploited for the design of antiproteolytic agent using water mimic drug design protocol.
Keywords	Matrix Metalloproteinase, MD simulation, Zn ions, Catalytic mechanism.
Citation	*Chakrabarti et al.* Bioinformation 9(3): 126-133 (2013)
Edited by	P Kangueane
ISSN	0973-2063
Publisher	Biomedical Informatics
License	This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.