Adaptive Steered Molecular Dynamics Combined With Protein Structure Networks Revealing the Mechanism of Y68I/G109P Mutations That Enhance the Catalytic Activity of D-psicose 3-Epimerase From Clostridium Bolteae

Abstract

The scarcity, richness, and other important physiological functions of D-psicose make it crucial to increase the yield of D-psicose. The production of D-psicose can be accomplished by D-psicose 3-epimerase (DPEase) from Clostridium bolteae (CbDPEase) catalyzing the substrate D-fructose. Although the catalytic efficiency of the CbDPEase has been raised via using the site-directed mutagenesis (Y68I/G109P) technique, structure-activity relationship in the wild-type CbDPEase and Y68I/G109P mutant is currently poorly understood. In our study, a battery of molecular modeling methods [homology modeling, adaptive steered molecular dynamics (ASMD) simulations, and Molecular Mechanics/Generalized Born Surface Area (MM-GB/SA)], combined with protein structure networks, were employed to theoretically characterize the reasons for the differences in the abilities of the D-fructose catalyzed by the wild-type CbDPEase and Y68I/G109P mutant. Protein structure networks demonstrated that site-directed mutagenesis enhanced the connectivity between D-fructose and CbDPEase, leading to the increased catalytic efficiency mediated by the functional residues with high betweenness. During the dissociation of the D-fructose from the Y68I/G109P mutant, planes of benzene rings of F248 and W114 could be continuously parallel to the stretching direction of D-fructose. It made the tunnel have an open state and resulted in the stable donor-π interactions between D-fructose and the benzene rings around 18Å. The stronger substrate-protein interactions were detected in the Y68I/G109P mutant, instead of in the wild-type CbDPEase, which were consistent with the binding free energy and Potential Mean of Force (PMF) results. The theoretical results illustrated the reasons that Y68I/G109P mutations increased the catalytic efficiency of CbDPEase and could be provided the new clue for further DPEase engineering.

The Protection of Crocin Against Ulcerative Colitis and Colorectal Cancer via Suppression of NF-κB-Mediated Inflammation

“…Four systems (P-NF-κB, T-NF-κB, P-NF-κB + crocin, and T- NF-κB + crocin) were performed molecular dynamics simulations using Amber 16 software ( Wang et al, 2017a ; Lee et al, 2017b ). Protein network centrality analysis, which can compute weighted centrality measures among ligand binding to protein, were performed with the cytoscape plugin RINalyzer ( Doncheva et al, 2011 ; Zhu et al, 2018 ).…”

Targeting N-Terminal Human Maltase-Glucoamylase to Unravel Possible Inhibitors Using Molecular Docking, Molecular Dynamics Simulations, and Adaptive Steered Molecular Dynamics Simulations

“…In order to explore the conformational changes in the active pocket and unbinding pathway for NtMGAM, molecular dynamics (MD) simulations (Zhu et al, 2018;Zhu et al, 2019;Liu et al, 2020) and adaptive steered molecular dynamics (ASMD) simulations (Zhu et al, 2018) were performed between two inhibitors (DSK and acarbose) and NtMGAM (PDB ID: 3L4U) (Lyann et al, 2010) (workflow listed in Supplementary Figure S2). Our results may provide new ideas for the further design of α-glucosidase inhibitors.…”

Random acceleration and steered molecular dynamics simulations reveal the (un)binding tunnels in adenosine deaminase and critical residues in tunnels

“…Multiple unbinding pathways identied by RAMD simulations RAMD, which is an effective approach for identifying the possible tunnel of macromolecules containing protein, has also been successfully applied in many systems. [22][23][24][25][26]32 This study identied the unbinding pathways of two inhibitors (PRH and FRK) from ADA. For the two complexes, 300 simulations were performed to determine the trajectory and observe the unbinding pathway of the inhibitor with VMD.…”

“…21,22 RAMD is an excellent approach for determining the possible tunnels of a protein, and this technique has been applied to identify new tunnels in many systems. [22][23][24][25][26] RAMD is improved on the basis of conventional simulation and steered molecular dynamics simulation. It applies force in either direction of the ligand to see whether the ligand can be shied under the action of force.…”