application of the linear interaction energy method (LIE) to estimate the binding free energy values of escherichia coli wild-type and mutant arginine repressor c-terminal domain (ARGRC)-l-arginine and argrc-l-citrulline protein-ligand complexes

Asi, A.M. and Rahman, N.A. and Merican, Amir Feisal (2004) application of the linear interaction energy method (LIE) to estimate the binding free energy values of escherichia coli wild-type and mutant arginine repressor c-terminal domain (ARGRC)-l-arginine and argrc-l-citrulline protein-ligand complexes. Journal of Molecular Graphics and Modelling, 22 (4). pp. 249-262. ISSN 1093-3263

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Abstract

Protein-ligand binding free energy values of wild-type and mutant C-terminal domain of Escherichia coli arginine repressor (ArgRc) protein systems bound to L-arginine or L-citrulline molecules were calculated using the linear interaction energy (LIE) method by molecular dynamics (MD) simulation. The binding behaviour predicted by the dissociation constant (K-d) calculations from the binding free energy values showed preferences for binding Of L-arginine to the wild-type ArgRc but not to the mutant ArgRc(D128N). On the other hand, L-citrulline do not favour binding to wild-type ArgRc but prefer binding to mutant ArgRc(D128N). The dissociation constant for the wild-type ArgRc-L-arginine complex obtained in this study is in agreement with reported experimental results [J. Mol. Biol. 235 (1994) 221-230]. Our results also support the experimental data for the binding Of L-citrulline to the mutant ArgRc(D128N) [J. Mol. Biol. 279 (1998) 753-760]. These showed that LIE method for protein-ligand binding free energy calculation could be applied to the wild-type and the mutant E. coli ArgRc-L-arginine and ArgRc-L-citrulline protein-ligand complexes and possibly to other transcriptional repressor-co-repressor systems as well. (C) 2003 Elsevier Inc. All rights reserved.

Item Type: Article
Additional Information: Institute of Biological Sciences, Faculty of Science Building, University of Malaya, 50603 Kuala Lumpur, MALAYSIA
Uncontrolled Keywords: Protein-ligand binding free energy, protein-ligand binding affinity, force field based simulation, molecular modelling, arginine repressor, protein, Escherichia coli K-12, range electrostatic interactions, molecular-dynamics, dna-binding, bacillus-subtilis, simulations, prediction, affinity, inhibitors, gene, sequence
Subjects: Q Science > QH Natural history > QH301 Biology
Depositing User: Miss Malisa Diana
Date Deposited: 04 Mar 2013 01:29
Last Modified: 13 Jan 2020 07:53
URI: http://eprints.um.edu.my/id/eprint/4943

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