Comparative DFT study on the α-glycosidic bond in reactive species of galactosyl diphosphates

Chemical Papers

Volumn 63, Issue 5, 2009, Pages 598-607

  Kóňa, Juraj ^a   Tvaroška, Igor ^a  

^a INSTITUTE OF CHEMISTRY   (Slovakia)

Author keywords

B3LYP; M05 2X; Manganese ion cofactor; Oxocarbenium ion; Retaining glycosyltransferase; Sugar phosphate

Indexed keywords

EID: 70350616050     PISSN: 03666352     EISSN: 13369075     Source Type: Journal    
DOI: 10.2478/s11696-009-0060-4     Document Type: Article

References (66)

1. Adamo, C., & Barone, V. (1998). Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models. Journal of Chemical Physics, 108, 664-675. DOI: 10.1063/1.475428.
2. 2+ cation on the stereochemistry of the sugar-diphosphate linkage. Ab initio modeling on nucleotide-sugars. Journal of Physical Chemistry A, 104, 4609-4617. DOI: 10.1021/jp000028x.
3. André, I., Tvaroška, I., & Carver, J. P. (2003). On the reaction pathways and determination of transition-state structures for retaining α-galactosyltransferases. Carbohydrate Research, 338, 865-877. DOI: 10.1016/S0008-6215(03)00050-8.
4. Becke, A. D. (1993). Density-functional thermochemistry. 3. The role of exact exchange. Journal of Chemical Physics, 98, 5648-5652. DOI: 10.1063/1.464913.
5. Biarnés, X., Ardèvol, A., Planas, A., Rovira, C., Laio, A., & Parrinello, M. (2007). The conformational free energy landscape of β-d-glucopyranose. Implications for substrate preactivation in β-glucoside hydrolases. Journal of the American Chemical Society, 129, 10686-10693 DOI: 10.1021/ja068411o.
6. Biarnés, X., Nieto, J., Planas, A., & Rovira, C. (2006). Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-β-glucanase: Insight from first principles molecular dynamics simulations. Journal of Biological Chemistry, 281, 1432-1441. DOI: 10.1074/jbc.M507643200.
7. Bottoni, A., Miscione, G. P., & De Vivo, M. (2005). A theoretical DFT investigation of the lysozyme mechanism: Computational evidence for a covalent intermediate pathway. Proteins-Structure Function and Bioinformatics, 59, 118-130. DOI: 10.1002/prot.20396.
8. Brooks, S. A., Dwek, M. V., & Schumacher, U. (2002). Functional & molecular glycobiology (1st ed.) (pp. 287-327). Oxford: BIOS Scientific Publishers Ltd.
9. Coskuner, O. (2007). Preferred conformation of the glycosidic linkage of methyl β-mannose. Journal of Chemical Physics, 127, 015101. DOI: 10.1063/1.2747238.
10. Csonka, G. I. (2002). Proper basis set for quantum mechanical studies of potential energy surfaces of carbohydrates. Journal of Molecular Structure: THEOCHEM, 584, 1-4. DOI: 10.1016/S0166-1280(02)00096-9.
11. Dkhissi, A., & Blossey, R. (2007). Performance of DFT/MPWB1K for stacking and H-bonding interactions. Chemical Physics Letters, 439, 35-39. DOI: 10.1016/j.cplett.2007.03.065.
12. Fabian, W. M. F. (2007). Metal binding induced conformational interconversions in methyl β-d-xylopyranoside. Theoretical Chemistry Accounts, 117, 223-229. DOI: 10.1007/s00214-006-0130-4.
13. Fois, E. S., Penman, J. I., & Madden, P. A. (1993). Self-interaction corrected density functionals and the structure of metal clusters. Journal of Chemical Physics, 98, 6352-6360. DOI: 10.1063/1.464828.
14. Frisch, M. J., Headgordon, M., & Pople, J. A. (1990a). A direct MP2 gradient-method. Chemical Physics Letters, 166, 275-280. DOI: 10.1016/0009-2614(90)80029-D.
15. Frisch, M. J., Headgordon, M., & Pople, J. A. (1990b). Semidirect algorithms for the MP2 energy and gradient. Chemical Physics Letters, 166, 281-289. DOI: 10.1016/0009-2614(90)80030-H.
16. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Jr., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., & Pople, J. A. (2005). Gaussian 03, Revision D.02 and E.01 [computer software]. Wallingford, CT: Gaussian, Inc.
17. Gibson, R. P., Tarling, C. A., Roberts, S., Withers, S. G., & Davies, G. J. (2004). The donor subsite of trehalose-6-phosphate synthase: Binary complexes with UDP-glucose and UDP-2-deoxy-2-fluoro-glucose at 2 Å resolution. Journal of Biological Chemistry, 279, 1950-1955. DOI: 10.1074/jbc.M307643200.
18. Hohenstein, E. G., Chill, S. T., & Sherrill, C. D. (2008). Assessment of the performance of the M05-2X and M06-2X exchange-correlation functionals for noncovalent interactions in biomolecules. Journal of Chemical Theory and Computation, 4, 1996-2000. DOI: 10.1021/ct800308k.
19. Hricovíni, M., Scholtzová, E., & Bízik, F. (2007). B3LYP/6-311++G** study of structure and spin-spin coupling constant in heparin disaccharide. Carbohydrate Research, 342, 1350-1356. DOI: 10.1016/j.carres.2007.03.020.
20. Ikeda, Y., & Takahashi, M. (2007). Glycosyltransferases and glycosidases: Enzyme mechanisms. In J. P. Kamerling, G. J. Boons, Y. C. Lee, A. Suzuki, N. Taniguchi, & A. G. J. Voragen (Eds.), Comprehensive glycosciense (Vol. 3, pp. 115-127). Oxford: Elsevier.
21. Ionescu, A. R., Whitfield, D. M., Zgierski, M. Z., & Nukada, T. (2006). Investigations into the role of oxocarbenium ions in glycosylation reactions by ab initio molecular dynamics. Carbohydrate Research, 341, 2912-2920. DOI: 10.1016/j.carres.2006.09.027.
22. Johnson, B. G., Gonzales, C. A., Gill, P. M. W., & Pople, J. A. (1994). A density-functional study of the simplest hydrogen abstraction reaction. Effect of self-interaction correction. Chemical Physics Letters, 221, 100-108. DOI: 10.1016/0009-2614(94)87024-1.
23. Jones, P. G., & Kirby, A. J. (1979). Linear relationship between bond length and reactivity. Journal of Chemical Society, Chemical Communications, 1979, 288-289. DOI: 10.1039/C39790000288.
24. Jones, P. G., & Kirby, J. (1982). Evidence from crystal structures for an incipient fragmentation reaction. Journal of Chemical Society, Chemical Communications, 1982, 1365-1366. DOI: 10.1039/C39820001365.
25. 3,O boat forms. Journal of Physical Chemistry A, 110, 7477-7484. DOI: 10.1021/jp061024g.
26. Kozmon, S., & Tvaroška, I. (2006). Catalytic mechanism of glycosyltransferases: Hybrid quantum mechanical/molecular mechanical study of inverting N-acetylglucosaminyltransferase I. Journal of American Chemical Society, 128, 16921-16927. DOI: 10.1021/ja065944o.
27. Lairson, L. L., Chiu, C. P. C., Ly, H. D., He, S. M., Wakarchuk, W. W., Strynadka, N. C. J., & Withers, S. G. (2004). Intermediate trapping on a mutant retaining α-galactosyltransferase identifies an unexpected aspartate residue. Journal of Biological Chemistry, 279 28339-28344. DOI: 10.1074/jbc.M400451200.
28. Lairson, L. L., Henrissat, B., Davies, G. J., & Withers, S. G. (2008). Glycosyltransferases: Structures, functions, and mechanism. Annual Reviews of Biochemistry, 77, 521-555. DOI: 10.1146/annurev.biochem.76.061005.092322.
29. Lee, C. T., Yang, W. T., & Parr, R. G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density. Physical Review B, 37, 785-789. DOI: 10.1103/PhysRevB.37.785.
30. Lii, J. H., Ma, B. Y., & Allinger, N. L. (1999). Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates. Journal of Computational Chemistry, 20, 1593-1603. DOI: 10.1002/(SICI)1096-987X(19991130)20:15〈1593::AID-JCC1〉3.0.CO;2-A.
31. Lynch, B. J., Fast, P. L., Harris, M., & Truhlar, D. G. (2000). Adiabatic connection for kinetics. Journal of Physical Chemistry A, 104, 4811-4815. DOI: 10.1021/jp000497z.
32. Miehlich, B., Savin, A., Stoll, H., & Preuss, H. (1989). Results obtained with the correlation-energy density functionals of Becke and Lee, Yang and Parr. Chemical Physics Letters, 157, 200-206. DOI: 10.1016/0009-2614(89)87234-3.
33. Mohr, M., Bryce, R. A., & Hillier, I. H. (2001). Quantum chemical studies of carbohydrate reactivity: Acid catalyzed ring opening reactions. Journal of Physical Chemistry A, 105, 8216-8222. DOI: 10.1021/jp010901+.
34. Møller, C., & Plesset, M. S. (1934). Note on an approximation treatment for many-electron systems. Physical Review, 46, 618-622. DOI: 10.1103/PhysRev.46.618.
35. Momany, F. A., Appell, M., Willett, J. L., Schnupf, U., & Bosma, W. B. (2006). DFT study of α- and β-d-galactopyranose at the B3LYP/6-311++G** level of theory. Carbohydrate Research, 341, 525-537. DOI: 10.1016/j.carres.2005.12.006.
36. Momany, F. A., Schnupf, U., Willett, J. L., & Bosma, W. B. (2007). DFT study of α-maltose: Influence of hydroxyl orientations on the glycosidic bond. Structural Chemistry, 18, 611-632. DOI: 10.1007/s11224-007-9191-9.
37. 1d-glucuronic acid. Journal of Physical Chemistry A, 109, 892-897. DOI: 10.1021/jp047451g.
38. Perdew, J. P., Burke, K., & Wang, Y. (1996). Generalized gradient approximation for the exchange-correlation hole of a many-electron system. Physical Review B, 54, 16533-16539. DOI: 10.1103/PhysRevB.54.16533.
39. Perdew, J. P., Chevary, J. A., Vosko, S. H., Jackson, K. A., Pederson, M. R., Singh, D. J., & Fiolhais, C. (1992). Atoms, molecules, solids, and surfaces - applications of the generalized gradient approximation for exchange and correlation. Physical Review B, 46, 6671-6687. DOI: 10.1103/Phys-RevB.46.6671.
40. Persson, K., Ly, H. D., Dieckelmann, M., Wakarchuk, W. W., Withers, S. G., & Strynadka, N. C. J. (2001). Crystal structure of the retaining galactosyltransferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs. Nature Structural Biology, 8, 166-175. DOI: 10.1038/84168.
41. Petrova, P., Koča, J., & Imberty, A. (1999). Potential energy hypersurfaces of nucleotide sugars: Ab initio calculations, force-field parametrization, and exploration of the flexibility. Journal of the American Chemical Society, 121, 5535-5547. DOI: 10.1021/ja983854g.
42. Raab, M., Kozmon, S., & Tvaroška, I. (2005). Potential transition-state analogs for glycosyltransferases. Design and DFT calculations of conformational behavior. Carbohydrate Research, 340, 1051-1057. DOI: 10.1016/j.carres.2005.01.041.
43. Roothaan, C. C. J. (1951). New developments in molecular orbital theory. Reviews of Modern Physics, 23, 69-76. DOI: 10.1103/RevModPhys.23.69.
44. Salzner, U., & von Ragué Schleyer, P. (1994). Ab initio examination of anomeric effects in tetrahydropyrans, 1,3-dioxanes, and glucose. Journal of Organic Chemistry, 59, 2138-2155. DOI: 10.1021/jo00087a035.
45. Sarkar, M., & Schachter, H. (2001). Cloning and expression of Drosophila melanogaster UDP-GlcNAc:α-3-d-mannoside β1,2-N-acetylglucosaminyltransferase I. Biological Chemistry, 382, 209-217. DOI: 10.1515/BC.2001.028.
46. Schneider, B., Kabelac, M., & Hobza, P. (1996). Geometry of the phosphate group and its interactions with metal cations in crystals and ab initio calculations. Journal of the American Chemical Society, 118, 12207-12217. DOI: 10.1021/ja9621152.
47. Schultz, N. E., Zhao, Y., & Truhlar, D. G. (2008). Benchmarking approximate density functional theory for s/d excitation energies in 3d transition metal cations. Journal of Computational Chemistry, 29, 185-189. DOI: 10.1002/jcc.20717.
48. Stubbs, J. M., & Marx, D. (2003). Glycosidic bond formation in aqueous solution: On the oxocarbenium intermediate. Journal of the American Chemical Society, 125, 10960-10962. DOI: 10.1021/ja035600n.
49. 2O (monoclinic form). Acta Crystallographica Section C, 40, 389-393. DOI: 10.1107/S010827018400425X.
50. Tvaroška, I. (2005). Structural insights into the catalytic mechanism and transition state of glycosyltransferases using ab initio molecular modeling. Trends in Glycoscience and Glycotechnology, 17, 177-190.
51. Tvaroška, I., André, I., & Carver, J. P. (1999). Ab initio molecular orbital study of the conformational behavior of the sugar-phosphate linkage. Toward an understanding of the catalytic mechanism of glycosyltransferases. Journal of Physical Chemistry B, 103, 2560-2569. DOI: 10.1021/jp984226o.
52. Tvaroška, I., André, I., & Carver, J. P. (2000). Ab initio molecular orbital study of the catalytic mechanism of glycosyltransferases: Description of reaction pathways and determination of transition-state structures for inverting N-acetylglucosaminyltransferases. Journal of the American Chemical Society, 122, 8762-8776. DOI: 10.1021/ja001525u.
53. Tvaroška, I., & Carver, J. P. (1994a). Ab-initio molecular-orbital calculation of carbohydrate model compounds. 2. Conformational analysis of axial and equatorial 2-methoxytetrahydropyrans. Journal of Physical Chemistry, 98, 9477-9485. DOI: 10.1021/j100089a020.
54. Tvaroška, I., & Carver, J. P. (1994b). Ab-initio molecular-orbital calculation on carbohydrate model compounds. 1. The anomeric effect in fluoro and chloro derivatives of tetrahydropyran. Journal of Physical Chemistry, 98, 6452-6458. DOI: 10.1021/j100077a006.
55. Tvaroška, I., & Carver, J. P. (1998). The anomeric and exoanomeric effects of a hydroxyl group and the stereochemistry of the hemiacetal linkage. Carbohydrate Research, 309, 1-9. DOI: 10.1016/S0008-6215(98)00114-1.
56. Tvaroška, I., Taravel, F. R., Utille, J. P., & Carver, J. P. (2002). Quantum mechanical and NMR spectroscopy studies on the conformations of the hydroxymethyl and methoxymethyl groups in aldohexosides. Carbohydrate Research, 337, 353-367. DOI: 10.1016/S0008-6215(01)00315-9.
57. Whitfield, D. M. (2007). DFT studies of the ionization of alpha and beta glycopyranosyl donors. Carbohydrate Research, 342, 1726-1740. DOI: 10.1016/j.carres.2007.05.012.
58. Withers, S. G., Rupitz, K., Street, I. P. (1988). 2-Deoxy-2-fluoro-d-glycosyl fluorides. A new class of specific mechanismbased glysosidase inhibitors. Journal of Biological Chemistry, 263, 7929-7932.
59. Zea, C. J., Camci-Unal, G., & Pohl, N. L. (2008). Thermodynamics of binding of divalent magnesium and manganese to uridine phosphates: Implications for diabetes-related hypomagnesaemia and carbohydrate biocatalysis. Chemistry Central Journal, 2, 15. DOI: 10.1186/1752-153X-2-15.
60. Zhang, Y., & Yang, W. (1998). A challenge for density functionals: Self-interaction error increases for systems with a noninteger number of electrons. Journal of Chemical Physics, 109, 2604-2608. DOI: 10.1063/1.476859.
61. Zhao, Y., Schultz, N. E., & Truhlar, D. G. (2005). Exchange-correlation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions. Journal of Chemical Physics, 123, 161103. DOI: 10.1063/1.2126975.
62. Zhao, Y., Schultz, N. E., & Truhlar, D. G. (2006). Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. Journal of Chemical Theory and Computation, 2, 364-382. DOI: 10.1021/ct0502763.
63. Zhao, Y., & Truhlar, D. G. (2004). Hybrid meta density functional theory methods for thermochemistry, thermochemical kinetics, and noncovalent interactions: The MPW1B95 and MPWB1K models and comparative assessments for hydrogen bonding and van der Waals interactions. Journal of Physical Chemistry A, 108 6908-6918. DOI: 10.1021/jp048147q.
64. Zhao, Y., & Truhlar, D. G. (2008a). Density functionals with broad applicability in chemistry. Accounts of Chemical Research, 41, 157-167. DOI: 10.1021/ar700111a.
65. Zhao, Y., & Truhlar, D. G. (2008b). Exploring the limit of accuracy of the global hybrid meta density functional for main-group thermochemistry, kinetics, and noncovalent interactions. Journal of Chemical Theory and Computation, 4, 1849-1868. DOI: 10.1021/ct800246v.
66. Zheng, J., Zhao, Y., & Truhlar, D. G. (2007). Representative benchmark suites for barrier heights of diverse reaction types and assessment of electronic structure methods for thermochemical kinetics. Journal of Chemical Theory and Computation, 3, 569-582. DOI: 10.1021/ct600281g.