Insight into the Function of the Key Residues in the Binding Clefts of the Substrate with CBM4-2 of Xylanase Xyn10A by Molecular Modeling and Free Energy Calculation

In this work, it is revealed that the residues of Asn31, Trp69, Glu72, Phe110, Arg115, His117 and Arg142 play the key role in the stabilization of the binding of xylopentaose with carbohydrate binding modules (CBM4-2) of xylanase Xyn10A, which is similar with the result of the previous report. The results were compared with that of mutant type protein, X-2, with xylopentaose. Interestingly, due to the residue mutation of X-2, xylopentaose was deviated from the normal binding site of CBM4-2, indicating that the appropriate combination of substrate with the hydrolysis site residues was realized by the residues of subsite 4 and 5 in the binding clefts of CBM4-2. Furthermore, the same process molecular simulation was performed for the wild type protein and R115A mutant with xylotetraose complex systems. During the dynamics simulation process, the substrate can automatically slide to the subsites 1-4 in the wild type protein, which could not be realized in R115A mutant system. It was indicated that the substrate can be towed to the proper site (subsites 2-3) by the residues of subsite 1 and 2 in the binding clefts. Overall, in this study, the specific function of the residues in the subsites 1-5 was shown. (C) 2017 Published by Elsevier B.V.