Exploring the interaction between D-xylose isomerase and D-xylose by free energy calculation

✍ Scribed by Hu, H.; Shi, Y.Y.; Wang, C.X.

• Book ID: 102648399
• Publisher: John Wiley and Sons
• Year: 1996
• Tongue: English
• Weight: 847 KB
• Volume: 26
• Category: Article
• ISSN: 0887-3585
• DOI: 10.1002/(sici)1097-0134(199610)26:2<157::aid-prot5>3.0.co;2-d

✦ Synopsis

The numerical quadrature thermodynamic integration method is used to investigate enzyme-substrate interaction of Dxylose isomerase. A screening function for the coulombic interaction is introduced into the simulation to correct the effect of finite cutoff radius for the non-bonded interaction. The binding free energy difference for D-xylose with D-xylose isomerase and its N184D mutant has been calculated, and the result 3.9 2 1.2 kJ1 mol agrees well with experimental data of 4.38 kJ/mol. In addition, the structure and dynamics of enzyme-substrate complex were simulated for mutant and wild-type enzyme, respectively. Analysis of the structures and intramolecular interactions of the complexes were found to be valuable for understanding the reaction mechanism of the enzyme D-xylose isomerase.