The reaction pathway of the isomerization of D-xylose catalyzed by the enzyme D-xylose isomerase: A theoretical study

Proteins: Structure, Function and Genetics

Volumn 27, Issue 4, 1997, Pages 545-555

  Hu, Hao ^a   Liu, Haiyan ^a   Shi, Yunyu ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

molecular mechanics; PM3 method; quantum mechanics; reaction pathway; semi empirical

Indexed keywords

XYLOSE; XYLOSE ISOMERASE;

ARTICLE; CATALYSIS; ENZYME ACTIVE SITE; ENZYME MECHANISM; ISOMERISM; MOLECULAR DYNAMICS; PRIORITY JOURNAL; QUANTUM MECHANICS;

ALDOSE-KETOSE ISOMERASES; BINDING SITES; CARBOHYDRATE EPIMERASES; CATALYSIS; COMPUTER SIMULATION; ELECTROSTATICS; MAGNESIUM; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, THEORETICAL; STEREOISOMERISM; THERMODYNAMICS; VACUUM; XYLOSE;

EID: 0031006738     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199704)27:4<545::AID-PROT7>3.0.CO;2-9     Document Type: Article

References (34)

1. Kollman, P.A. Theory of enzyme mechanisms. Curr. Opin. Struct. Biol. 2:765-771, 1992.
2. Kollman, P.A. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 93:2395-2417, 1993.
3. Warshel, A. "Computer Modeling of Chemical Reactions in Enzymes and in Solutions." New York: John Wiley & Sons, 1991.
4. Warshel, A. Computer simulations of enzymatic reactions. Curr. Opin. Struct. Biol. 2:230-236, 1992.
5. Merz Jr., K.M. Computer simulation of enzymatic reactions. Curr. Opin. Struct. Biol. 3:234-240, 1993.
6. Alex, A., Clark, T. J. MO-studies of enzymatic reaction mechanisms. I. Model molecular orbital study of the cleavage of peptides by carboxypeptidase. Comp. Chem. 13:704-717, 1992.
7. Daggett, V., Schröder, S., Kollman, P. Catalytic pathway of serine proteases: Classical and quantum mechanical calculations. J. Am. Chem. Soc. 113:8926-8935, 1991.
8. von Onciul, A.R., Clark, T. Molecular orbital studies of enzyme mechanisms. II. Catalytic oxidation of alcohols by liver alcohol dehydrogenase. J. Comp. Chem. 14:392-400, 1993.
9. Warshel, A., Levitt, M. Theoretical studies of enzymatic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103:227, 1976.
10. Warshel, A. A microscopic model for calculations of chemical processes in aqueous solutions. Chem. Phys. Lett. 55:459, 1978.
11. Warshel, A. Calculations of chemical processes in solutions. J. Phys. Chem. 83:1640, 1979.
12. Field, M.J., Bash, P.A., Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comp. Chem. 11:700-733, 1990.
13. Field, M.J. In: "Computer Simulation in Biological Systems." van Gunsteren, W.F., Weiner, P.K., Wilkinson, A.J. (eds.). Leiden: ESCOM, 1993.
14. Gao, J. Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials. J. Phys. Chem. 96:537, 1992.
15. Liu, H.Y., Shi, Y.Y. Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution. J. Comp. Chem. 15:1311-1318, 1994.
16. Bash, P.A., Field, M.J., Davenport, R.C., Petsko, G.A., Ringe, D., Karplus, M. Computer simulation and analysis of the reaction pathway of Triosephosphate isomerase. Biochemistry 30:5826-5832, 1991.
17. Collyer, C.A., Henrick, K., Blow, D.M. Mechanism for aldose-ketose interconversion by D-xylose isomerase involving ring opening followed by a 1,2-hydride shift. J. Mol. Biol. 212:211-235, 1989.
18. Henrick, K., Collyer, C.A., Blow, D.M. Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5Å and 2.3Å resolution, respectively. J. Mol. Biol. 208:129-157, 1989.
19. Jenkins, I., Janin, J., Rey, F., Chiadmi, M., van Tilbeurgh, H., Lasters, L., De Maeyer, M., Van Belle, D., Wodak, S.J., Lauwereys, M., Stansses, P., Mrabet, N.T., Snauwaert, J., Matthyssens, G., Lambeir, A.M. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding site. Biochemistry 31:5449-5458, 1992.
20. Lambeir, A.M., Lauwereys, M., Stansses, P., Mrabet, N.T., Snauwaert, J., van Tilbeurgh, H., Matthyssens, G.H., Lasters, L., De Maeyer, D., Wodak, S.J., Jenkins, I., Chiadmi, M., Janin, J. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 2. Site-directed mutagenesis of xylose binding site. Biochemistry 31:5459-5466, 1992.
21. Whitlow, M., Hoeard, A.J., Finzel, B.C., Pouos, T.L., Winborne, E., Gilliland, G.L. A metal-mediated hydride shift mechanism for xylose isomerase based on the 1. 6Å Streptomyces rubiginosus structures with xylitol and D-xylose. Proteins 9:153-173, 1991.
22. van Tilbeurgh, H., Jenkins, J., Chiadmi, M., Janin, J., Wodak, S., Mrabet, N.T., Lambeir, A.-M. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 3. Changing metal specificity and the PH profile by site-directed mutagenesis. Biochemistry 31:5467-5471, 1992.
23. Allen, K.N., Lavie, A., Farber, G.K, Glasfeld, A., Petsko, G.A., Ringe, D. Isotopic exchange plus substrate and inhibition kinetics of D-xylose isomerase do not support a proton-transfer mechanism. Biochemistry 1481-1487, 1994.
24. Lavie, A., Allen, K.N., Petsko, G.A., Ringe, D. X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis. Biochemistry 33:5469-5480, 1994.
25. Smart, O.S., Akins, J., Blow, B.M. Molecular mechanics simulations of a conformational rearrangement of D-xylose in the active site of D-xylose isomerase. Proteins 13:100-111, 1992.
26. Zheng, Y.J., Merz, Jr. K.M., Farber, G.K. Theoretical examination of the mechanism of aldose-ketose isomerization. Protein Eng. 6:479-484, 1993.
27. Stewart, J.J.P. Optimization of parameters for semiempirical methods. J. Comp. Chem. 10:209-220, 1989.
28. Stewart, J.J.P. Quantum Chemistry Program Exchange 455.
29. van Gunsteren, W.F., Berendsen, H.J.C. Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, Nijenborgh 16, 9747. Groningen, The Netherlands, 1987.
30. Liu, H.Y., Shi, Y.Y. Combination of molecular dynamic simulation program GROMOS with semi-empirical quantum chemistry method AM1. Chin. Sci. Bull. 38:2023-2024, 1993.
31. Besler, B.H., Merz, K.M. Jr., Kollman, P.A. Atomic charges derived from semiempirical methods. J. Comp. Chem. 11:431-439, 1990.
32. Kemp, D.S., Vellaccio, F. "Organic Chemistry." New York: Worth Publishers, 1980.
33. Morrison, R.T., Boyd, R.N. "Organic Chemistry." Allyn and Bacon, 1983.
34. Chen, W.P. Glucose isomerase. Process Biochem. 15:36-41, 1980.