Molecular Modeling and MM-PBSA Free Energy Analysis of Endo-1,4-β-Xylanase from Ruminococcus albus 8

Abstract

Endo-1,4-β-xylanase (EC 3.2.1.8) is the enzyme from Ruminococcus albus 8 (R. albus 8) (Xyn10A), and catalyzes the degradation of arabinoxylan, which is a major cell wall non-starch polysaccharide of cereals. The crystallographic structure of Xyn10A is still unknown. For this reason, we report a computer-assisted homology study conducted to build its three-dimensional structure based on the known sequence of amino acids of this enzyme. In this study, the best similarity was found with the Clostridium thermocellum (C. thermocellum) N-terminal endo-1,4-β-d-xylanase 10 b. Following the 100 ns molecular dynamics (MD) simulation, a reliable model was obtained for further studies. Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) methods were used for the substrate xylotetraose having the reactive sugar, which was bound in the −1 subsite of Xyn10A in the 4C1 (chair) and 2SO (skew boat) ground state conformations. According to the simulations and free energy analysis, Xyn10A binds the substrate with the −1 sugar in the 2SO conformation 39.27 kcal·mol−1 tighter than the substrate with the sugar in the 4C1 conformation. According to the Xyn10A-2SO Xylotetraose (X4(sb) interaction energies, the most important subsite for the substrate binding is subsite −1. The results of this study indicate that the substrate is bound in a skew boat conformation with Xyn10A and the −1 sugar subsite proceeds from the 4C1 conformation through 2SO to the transition state. MM-PBSA free energy analysis indicates that Asn187 and Trp344 in subsite −1 may an important residue for substrate binding. Our findings provide fundamental knowledge that may contribute to further enhancement of enzyme performance through molecular engineering.

Multi‐spectroscopic and molecular dynamics simulations investigation of the binding mechanism of polybrominated diphenyl ethers to hen egg white lysozyme

“…Molecular dynamics simulations lasting 50 ns were performed for each system. The last 20 ns of the dynamic simulation were selected to calculate the binding free energies of three HEWL‐PBDEs complexes by employing the MM‐PBSA approach . As shown in Table , the calculated binding free energies are −64.79 ± 3.24 kJ·mol −1 for BDE25, −12.94 ± 0.65 kJ·mol −1 for BDE47, and − 9.74 ± 0.49 kJ·mol −1 for BDE154.…”

Evaluation of peptide designing strategy against subunit reassociation in mucin 1: A steered molecular dynamics approach

“…MM-PBSA (Molecular Mechanism Poisson–Boltzmann surface area) is a method used to post process docked structures and to evaluate binding free energies of complexes [ 42 , 43 ]. The binding free energy of the complex is the sum of electrostatic, van der waals, polar and non-polar interactions between the molecules [ 44 , 45 ]. From each MD-simulated complex, about 300 frames at regular intervals were retrieved from the last 15ns of the trajectory.…”

Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

“…The MM–PBSA method was used to calculate the binding free energy: ∆ G bind = G complex − ( G receptor + G ligand ), where G complex , G receptor , and G ligand are the free energies of the complex, protein, and ligand, respectively. Each of the Δ G terms was calculated by summing the molecular mechanics free energy (Δ G MM ), solvation free energy (Δ G sol ), and vibrational entropy terms ( T Δ S ) [ 58 ]: Δ G = Δ G MM + Δ G sol − T Δ S . Δ G MM is the standard force field energy, including strain energies from covalent bonds and torsion angles as well as noncovalent van der Waals and electrostatic energies.…”