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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 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.