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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Zou, Xiaoqin Liu, Hao-yang |
| Description | Author Affiliation: Liu HY ( Dalton Cardiovascular Research Center and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA.) |
| Abstract | An accurate and fast evaluation of the electrostatics in ligand-protein interactions is crucial for computer-aided drug design. The pairwise generalized Born (GB) model, a fast analytical method originally developed for studying the solvation of organic molecules, has been widely applied to macromolecular systems, including ligand-protein complexes. However, this model involves several empirical scaling parameters, which have been optimized for the solvation of organic molecules, peptides, and nucleic acids but not for energetics of ligand binding. Studies have shown that a good solvation energy does not guarantee a correct model of solvent-mediated interactions. Thus, in this study, we have used the Poisson-Boltzmann (PB) approach as a reference to optimize the GB model for studies of ligand-protein interactions. Specifically, we have employed the pairwise descreening approximation proposed by Hawkins et al.(1) for GB calculations and DelPhi for PB calculations. The AMBER all-atom force field parameters have been used in this work. Seventeen protein-ligand complexes have been used as a training database, and a set of atomic descreening parameters has been selected with which the pairwise GB model and the PB model yield comparable results on atomic Born radii, the electrostatic component of free energies of ligand binding, and desolvation energies of the ligands and proteins. The energetics of the 15 test complexes calculated with the GB model using this set of parameters also agrees well with the energetics calculated with the PB method. This is the first time that the GB model has been parametrized and thoroughly compared with the PB model for the electrostatics of ligand binding. |
| ISSN | 15206106 |
| e-ISSN | 15205207 |
| Journal | The Journal of Physical Chemistry B |
| Issue Number | 18 |
| Volume Number | 110 |
| Language | English |
| Publisher | American Chemical Society (United States) |
| Publisher Date | 2006-05-11 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Models, Chemical Proteins Chemistry Ligands Poisson Distribution Protein Binding Solvents Static Electricity Thermodynamics Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Physical chemistry |
| Content Type | Text |
| Resource Type | Article |
| Subject | Surfaces, Coatings and Films Materials Chemistry Medicine Physical and Theoretical Chemistry |
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