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, DOI https://doi.org/10.1016/j.jmgm.2003.09.003.
Full text not available from this repository.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 |
|---|---|
| Funders: | UNSPECIFIED |
| 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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