Exploring the interaction between D-xylose isomerase and D-xylose by free energy calculation.
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 cut-off 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.
Hu
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Department of Biology, University of Science and Technology of China, Hefei, People's Republic of China.
Shi
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YY
Wang
C X
CX
D019747:Aldose-Ketose Isomerases; D002238:Carbohydrate Epimerases / Q000737:chemistry* / Q000235:genetics; D006860:Hydrogen Bonding; D013816:Thermodynamics; D014994:Xylose / Q000737:chemistry*
D014994:Xylose; D002238:Carbohydrate Epimerases; D019747:Aldose-Ketose Isomerases; C023298:xylose isomerase