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Exploring the interaction between D‐xylose isomerase and D‐xylose by free energy calculation
Author(s) -
Hu H.,
Shi Y.Y.,
Wang C.X.
Publication year - 1996
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199610)26:2<157::aid-prot5>3.0.co;2-d
Subject(s) - xylose isomerase , xylose , isomerase , chemistry , enzyme , intramolecular force , thermodynamic integration , thermodynamics , computational chemistry , stereochemistry , biochemistry , molecular dynamics , physics , fermentation
The numerical quadrature thermodynamic integration method is used to investigate enzyme‐substrate interaction of D‐xylose 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 ± 1.2 kJ/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. © Wiley‐Liss, Inc.