ofbiomoleculesusingMDsimulations.Asanextensively studiedDroteinbothinexperimentsandsimulations[25-29] , lysozymewasusedasamodelprotein.MDsimulation wasperformedontwosystems,i.e.,lysozyme—water (LW)systemandlysozyme—watercluster(LWC)sys· tern.Theconformationalchangesoflysozyme,hydrogen ...
Long time equilibrium molecular dynamics (MD) simulations were performed to study the behavior of water and ions in the nanopores of lysozyme protein crystals. Pore size profile along different axes showed that the main pores lie along the z-axis consisting of an anisotropic structure. The ...
The influence and effects that the amino acids L-alanine, glycine and L-proline have on the structure, stability and hydration of lysozyme were analyzed using molecular dynamics (MD) with the CHARMM force field as implemented in the NAMD simulation package. The solution properties of lysozyme in...
Colloidal model of lysozyme aqueous solutions: A computer simulation and theoretical study. J. Phys. Chem. B 116, 2114–2120 (2012). 47. Vondrásek, J., Mason, P. E., Heyda, J., Collins, K. D. & Jungwirth, P. The molecular origin of like-charge arginine-arginine pairing in water...
Analysis of the MD trajectory showed a higher degree of backbone flexibility of the active site residues throughout the simulation time, particularly for SDS molecules. Conformational flexibility has been shown to correlate strongly with bioactivity, which for lysozyme may also relate to increased ...
A two-stage direct denaturation mechanism has been proposed based on micro-second Molecular Dynamics (MD) simulations on lysozyme in 8 M urea. The driving force in the first stage of this mechanism is the favourable protein-urea van der Waals interactions compared to protein-water interactions...
In this study, we systematically examined the interaction between lysozyme and RTN by employing various advanced spectroscopic techniques. In addition, state-of-the-art molecular modeling (molecular docking and MD simulation) approaches were implemented to theoretically scrutinize the molecular interaction ...
Highly porous cross-linked protein crystals are a novel class of nanoporous materials with vast applications in biocatalysis and selective separation membranes. Long time equilibrium molecular dynamics (MD) simulations were performed to study the behavior of water and ions in the nanop...
A molecular-dynamics simulation study predicted that the unfolding of α-helices in lysozyme molecules would involve progressive hydration by inserting water molecules in their hydrogen-bond network [42]. Insertion of water into the helix structure could facilitate the isotopic exchange in this protein ...
The protein molecular structure, interfacial adsorption behavior, and macroscopic foaming properties based on pH-induced OVA-LYS complexes at the air-water interface were reported in this study. It was shown that the binding of LYS to OVA promoted surface hydrophobic groups exposure and altered ...