Stochastic boundary molecular dynamics simulation of L-ribose in the active site of Actinoplanes missouriensis xylose isomerase and its Val135Asn mutant with improved reaction rate

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1749, Issue 1, 2005, Pages 65-73

  Santa, Harri ^a   Kammonen, Juha ^a   Lehtonen, Olli ^a   Karimäki, Johanna ^a   Pastinen, Ossi ^a   Leisola, Matti ^a   Turunen, Ossi ^a  

^a AALTO UNIVERSITY   (Finland)

Author keywords

Catalytic efficiency; L Ribose; Molecular dynamics; Site directed mutagenesis; Xylose isomerase

Indexed keywords

BACTERIAL ENZYME; GLUCOSE; OXYGEN; RIBOSE; XYLOSE ISOMERASE;

ACTINOPLANES MISSOURIENSIS; ARTICLE; BACTERIUM; CONTROLLED STUDY; HYDROGEN BOND; MOLECULAR DYNAMICS; MUTATION; NONHUMAN; PRIORITY JOURNAL; SIMULATION; STOCHASTIC MODEL;

ACTINOPLANES MISSOURIENSIS;

EID: 17444393192     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2005.02.007     Document Type: Article

References (40)

1. B. Asbóth, and G. Náray-Szabó Mechanism of action of d-xylose isomerase Curr. Protein Pept. Sci. 1 2000 237 254
2. H. Häusler, and A.E. Stütz d-xylose (d-glucose) isomerase and related enzymes in carbohydrate synthesis Top. Curr. Chem. 215 2001 77 114
3. A. Vuolanto, O. Pastinen, H.E. Schoemaker, and M. Leisola C-2 epimer formation of tetrose, pentose and hexose sugars by xylose isomerase Biocatal. Biotransform. 20 2002 235 240
4. Y.B. Tewari, and R.N. Goldberg An investigation of the equilibria between aqueous ribose, ribulose and arabinose Biophys. Chem. 22 1985 197 204
5. O. Pastinen, H.E. Schoemaker, and M. Leisola Xylose isomerase catalysed novel hexose epimerization Biocatal. Biotransform. 17 1999 393 400
6. O. Pastinen, K. Visuri, H.E. Schoemaker, and M. Leisola Novel reactions of xylose isomerase from Streptomyces rubiginosus Enzyme Microb. Technol. 25 1999 695 700
7. M. Garcia-Viloca, C. Alhambra, A.G. Truhlar, and J. Gao Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects J. Comput. Chem. 24 2003 177 190
8. T.D. Fenn, D. Ringe, and G.A. Petsko Xylose isomerase in substrate and inhibitor Michaelis states: atomic resolution studies of a metal-mediated hydride shift Biochemistry 43 2004 6464 6474
9. A.-M. Lambeir, I. Lasters, W.J. Quax, and J.M. Van der Laan Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis: 2. Site-directed mutagenesis of xylose binding site Biochemistry 31 1992 5459 5466
10. R.D. Whitaker, Y. Cho, J. Cha, H.L. Carrell, J.P. Glusker, P.A. Karplus, and C.A. Batt Probing roles of active site residues in d-xylose isomerase J. Biol. Chem. 270 1995 22895 22906
11. H. Hu, Y.Y. Shi, and C.X. Wang Exploring the interaction between d-xylose isomerase and d-xylose by free energy calculation Proteins 26 1996 157 166
12. M. Whitlow, A.J. Howard, B.C. Finzel, T.L. Poulos, E. Winborne, and G.L. Gilliland A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 Å Streptomyces rubiginosus structures with xylitol and d-xylose Proteins 9 1991 153 173
13. O. Turunen, K. Etuaho, F. Fenel, J. Vehmaanperä, X. Wu, J. Rouvinen, and M. Leisola Combination of weakly stabilizing mutations with a disulfide-bridge in the α-helix region of Trichoderma reesei endo-1,4-β-xylanase II increases the thermal stability through synergism J. Biotechnol. 88 2001 37 46
14. N. Guex, and M.C. Peitsch SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 18 1997 2714 2723
15. M.M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilising the principle of protein-dye binding Anal. Biochem. 72 1976 248 254
16. P. Kuzmic Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase Anal. Biochem. 237 1996 260 273
17. QUANTA, Accelrys Incorporation, San Diego, CA, USA.
18. J. Jenkins, J. Janin, F. Rey, M. Chiadmi, H. van Tilbeurgh, I. Lasters, M. De Maeyer, D. Van Belle, S.J. Wodak, M. Lauwereys, P. Stanssens, N.T. Mrabet, J. Snauwaert, G. Matthyssens, and A.-M. Lambeir Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis: 1. Crystallography and site-directed mutagenesis of metal binding sites Biochemistry 31 1992 5449 5458
19. C.L. Brooks, and M. Karplus Deformable stochastic boundaries in molecular dynamics J. Chem. Phys. 79 1983 6312 6325
20. E.Y. Lau, and T.C. Bruice Active site dynamics of the HhaI methyltransferase: insights from computer simulation J. Mol. Biol. 293 1999 9 18
21. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, D. Swaminathan, and M. Karplus CHARMM: a program for macromolecular energy, minimization and dynamics calculations J. Comp. Chem. 4 1983 187 217
22. F.A. Momany, and R. Rone Validation of the general purpose Quanta 3.2/CHARMm force field J. Comp. Chem. 13 1992 888 900
23. A.T. Brünger, and M. Karplus Polar hydrogen positions in proteins: empirical energy placements and neutron diffraction comparison Proteins 4 1988 148 156
24. W.L. Jorgensen, J. Chandrasekhar, J. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 97 1983 926 935
25. J.-P. Ryckaert, G. Cicotti, and H.J.C. Berendsen Numerical integration of the cartesian equations of motion for a system with constraints: molecular dynamics on n-alkanes J. Comp. Physiol. 23 1977 327 341
26. P.J. Steinbach, and B.R. Brooks New spherical-cutoff methods for long-range forces in macromolecular simulation J. Comp. Chem. 15 1994 667 683
27. http://comp.chem.umn.edu..
28. A. Warshel, and M. Levitt Theroretical studies of enzymic reactions: dielectric, electrostatic, and steric stabilization of the carbonium ion in the reaction of lysozyme J. Mol. Biol. 103 1976 227 249
29. J.J.P. Stewart Optimization of parameters for semiempirical methods J. Comp. Chem. 10 1989 209 220
30. R.S. Mulliken Electronic population analysis on LCAO-MO molecular wave function J. Chem. Phys. 23 1955 1833 1840
31. G. Vriend WHAT IF: a molecular modeling and drug design program J. Mol. Graph. 8 1990 52 56
32. J. Nielsen, and G. Vriend Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pKa calculations Proteins: Struct., Funct., Genet. 43 2001 403 412
33. J. Karimäki, T. Parkkinen, H. Santa, O. Pastinen, M. Leisola, J. Rouvinen, and O. Turunen Engineering the substrate specificity of xylose isomerase Protein Eng. Des. Sel. 17 2004 861 869
34. A.D. Becke Density-functional exchange-energy approximation with correct asymptotic-behavior Phys. Rev., A 38 1988 3098 3100
35. C. Lee, W. Yang, and R.G. Parr Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density Phys. Rev., B 37 1998 785 789
36. R. Ahlrichs, M. Bär, M. Häser, H. Horn, and C. Kölmel Electronic-structure calculations on workstation computers-the program system TURBOMOLE Chem. Phys. Lett. 162 1989 165 169
37. K. Eichkorn, O. Treutler, H. Öhm, M. Häser, and R. Ahlrichs Auxiliary basis-sets to approximate coulomb potentials Chem. Phys. Lett. 242 1995 652 660
38. R.T. Sanderson An interpretation of bond lengths and a classification of bonds Science 114 1951 670 672
39. M. Meng, C. Lee, M. Bagdasarian, and J.G. Zeikus Switching substrate preference of thermophilic xylose isomerase from d-xylose to d-glucose by redesigning the substrate binding pocket Proc. Natl. Acad. Sci. U. S. A. 88 1991 4015 4019
40. A.-M. Lambeir, I. Lasters, W.J. Quax, J.M. Van den Laar, Glucose isomerases having altered substrate specificity. US Patent 5,310,665 (1994).