Binding structures of tri‐N‐acetyl‐β‐glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

Abstract

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.

Structural, Functional and Phylogenetic Analysis of Sperm Lysozyme-Like Proteins

“…Our results implied that binding of (NAG) 3 with LYZL proteins in B-C-D mode could be energetically more favorable, which is consistent with HEWL-(NAG) 3 showing higher binding energy in B-C-D mode [83]. These results implied that a dynamic equilibrium between population of A-B-C and B-C-D subsites occupied LYZL proteins might be existing as observed in the crystal structures of Trp62 and Asp101 mutants of HEWL [43].…”

“…This could be because of constraints placed by crystallization conditions or crystal formation that A-B-C subsites are preferred, since NMR [84] and enzymatic studies [85] suggested the occupancy of D subsite with (NAG) 3 . HEWL Tyr62→His mutant showed enhanced catalysis of (NAG) 3 [86], which implied that (NAG) 3 might be binding deeper inside the pocket to enable breakdown of (NAG) 3 between subsites D and E. Powder diffraction [87] and MD simulation studies [83] also suggested binding of (NAG) 3 in B-C-D mode to be energetically more favorable. Powder diffraction showed occupancy of A-B-C and B-C-D subsites existing in a ratio of 35:65, implying that B-C-D mode might be favorable.…”

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

“…28–32 While polarizable MD simulations using these, as well as other models, 33, 34 have been presented they are typically short in duration, being a few nanoseconds or less, such that the models have yet to be rigorously evaluated as well as used in application studies. A recent exception is a study on lysozyme using the fluctuating charge model implemented in CHARMM, 35 where simulations of up to 14 ns displayed RMS differences larger than those from the additive CHARMM22 force field. 3 More recently, an updated AMEOBA force field for proteins has been presented.…”

CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides

“…44–47 For example, in condensed-phase simulations where the high dielectric medium polarizes the molecular charge distribution changes in the geometry and conformational energetics of molecules can occur. 44, 48 Thus, a number of polarizable FFs are being developed, 44–45 based on various models including inducible point dipoles, 49–51 fluctuating charges (FQ) or electronegativity equalization, 52–56 inducible point dipole with fluctuating and fixed charges, 57 Gaussian polarization model, 58 and classical Drude oscillators. 46, 59 …”