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Analysis of chloride ion-proline interaction of dehalogenase enzymes bymolecular dynamics simulation

Raghunath Satpathy, Rasmiranjan Behera, BiswajitNayak

This work reports the preference of chloride ion -Proline amino acid interaction among the dehalogenase enzyme. We retrieved 22 dehalogenase and non dehalogenase enzyme available crystallographic structure (from PDB) that contains chloride ion in the structure. Further 3.5 angstrom proximity amino acid residues from the chloride ion was computed for all the selected proteins by an in house built software. The result indicates, in case of the dehalogenase enzymes contains proline residues proximity to chloride ion was uniquely identified. Again a case study was performed to identify the dynamics of the proline residue with respect to the Cl- ion, by considering the protein having PDB ID 1EDB. The dynamics study during 5 nanosecond MD simulation by GROMACS 4.0.5 reveals that both 223 proline and 226 Val interact with the Cl- ion more frequently and PRO CA- CL atomic distance is little fluctuated (fluctuation range within 0.5 angstrom). Then to check the structure, function relationship, 3 different substitution mutations were performed on Proline position according to the comparable molecular weight. Then the mutant structures were subjected to 1 nano second molecular dynamics simulation. The result indicates Proline present proximity to chloride ions is important for the dehalogenase enzyme activity.