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Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1
Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, UTM Skudai, 81310 Johor Bahru, Malaysia
School of Bioscience and Technology, Faculty Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
These authors contributed equally to this work.
* Author to whom correspondence should be addressed.
Received: 18 August 2012; in revised form: 16 October 2012 / Accepted: 7 November 2012 / Published: 26 November 2012
Abstract: Currently, there is no three-dimensional structure of D-specific dehalogenase (DehD) in the protein database. We modeled DehD using ab initio technique, performed molecular dynamics (MD) simulation and docking of D-2-chloropropionate (D-2CP), D-2-bromopropionate (D-2BP), monochloroacetate (MCA), monobromoacetate (MBA), 2,2-dichloropropionate (2,2-DCP), d,l-2,3-dichloropropionate (d,l-2,3-DCP), and 3-chloropropionate (3-CP) into the DehD active site. The sequences of DehD and D-2-haloacid dehalogenase (HadD) from Pseudomonas putida AJ1 have 15% sequence similarity. The model had 80% of the amino acid residues in the most favored region when compared to the crystal structure of DehI from Pseudomonas putida PP3. Docking analysis revealed that Arg107, Arg134 and Tyr135 interacted with D-2CP, and Glu20 activated the water molecule for hydrolytic dehalogenation. Single residue substitutions at 25–30 °C showed that polar residues of DehD were stable when substituted with nonpolar residues and showed a decrease in activity within the same temperature range. The molecular dynamics simulation of DehD and its variants showed that in R134A variant, Arg107 interacted with D-2CP, while in Y135A, Gln221 and Arg231 interacted with D-2CP. It is our emphatic belief that the new model will be useful for the rational design of DehDs with enhanced potentials.
Keywords: D-stereospecific dehalogenase; Rhizobium sp. RC1; DehD; interacting residues; docking; molecular dynamics simulation
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Sudi, I.Y.; Wong, E.L.; Joyce-Tan, K.H.; Shamsir, M.S.; Jamaluddin, H.; Huyop, F. Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1. Int. J. Mol. Sci. 2012, 13, 15724-15754.
Sudi IY, Wong EL, Joyce-Tan KH, Shamsir MS, Jamaluddin H, Huyop F. Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1. International Journal of Molecular Sciences. 2012; 13(12):15724-15754.
Sudi, Ismaila Y.; Wong, Ee L.; Joyce-Tan, Kwee H.; Shamsir, Mohd S.; Jamaluddin, Haryati; Huyop, Fahrul. 2012. "Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1." Int. J. Mol. Sci. 13, no. 12: 15724-15754.