Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1
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), mon...
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my.utm.475482019-03-05T02:08:53Z http://eprints.utm.my/id/eprint/47548/ Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1 Sudi, Ismaila Yada Wong, Ee Lin Tan, Kwee Hong Joyce Shamsir, Mohd. Shahir Jamaluddin, Haryati Huyop, Fahrul QD Chemistry 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. MDPI 2012 Article PeerReviewed application/pdf en http://eprints.utm.my/id/eprint/47548/1/IsmailaYadaSudi2012_StructurePredictionMolecularDynamicsSimulation.pdf Sudi, Ismaila Yada and Wong, Ee Lin and Tan, Kwee Hong Joyce and Shamsir, Mohd. Shahir and Jamaluddin, Haryati and Huyop, Fahrul (2012) Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1. International Journal of Molecular Sciences, 13 (12). pp. 15724-15754. ISSN 1661-6596 http://dx.doi.org/10.3390/ijms131215724 DOI:10.3390/ijms131215724 |
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QD Chemistry Sudi, Ismaila Yada Wong, Ee Lin Tan, Kwee Hong Joyce Shamsir, Mohd. Shahir Jamaluddin, Haryati Huyop, Fahrul Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1 |
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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. |
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Article |
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Sudi, Ismaila Yada Wong, Ee Lin Tan, Kwee Hong Joyce Shamsir, Mohd. Shahir Jamaluddin, Haryati Huyop, Fahrul |
author_facet |
Sudi, Ismaila Yada Wong, Ee Lin Tan, Kwee Hong Joyce Shamsir, Mohd. Shahir Jamaluddin, Haryati Huyop, Fahrul |
author_sort |
Sudi, Ismaila Yada |
title |
Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1 |
title_short |
Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1 |
title_full |
Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1 |
title_fullStr |
Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1 |
title_full_unstemmed |
Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1 |
title_sort |
structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. rc1 |
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MDPI |
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2012 |
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http://eprints.utm.my/id/eprint/47548/1/IsmailaYadaSudi2012_StructurePredictionMolecularDynamicsSimulation.pdf http://eprints.utm.my/id/eprint/47548/ http://dx.doi.org/10.3390/ijms131215724 |
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13.160551 |