Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field.
Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field.
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DOI：
10.1002/jcc.23109
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发表时间：
2013-01-30
影响因子：
3
通讯作者：
Patel, Sandeep
中科院分区：
文献类型：
--
作者：
Zhong, Yang;Patel, Sandeep
关键词：
Lysozyme is a well-studied enzyme that hydrolyzes the β-(1,4)-glycosidic linkage of N-acetyl-β-glucosamine (NAG)n oligomers. The active site of hen egg-white lysozyme (HEWL) is believed to consist of six subsites, A-F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all-atom molecular dynamics simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)3. Molecular dynamics trajectories are applied to analyze structures and conformation of the complex as well as protein-ligand interactions, including the hydrogen-bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)3 are investigated independently based on a fixed-charge model and a polarizable model. We also apply MM-GBSA methods based on molecular dynamics using both non-polarizable and polarizable force fields in order to compute binding free energies. We also study the correlation between RMSD and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed-charge models.
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