About this Journal Submit a Manuscript Table of Contents
Advances in Physical Chemistry
Volume 2012 (2012), Article ID 867409, 15 pages
http://dx.doi.org/10.1155/2012/867409
Review Article

Applications of Potential Energy Surfaces in the Study of Enzymatic Reactions

Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada N9B 3P4

Received 26 June 2011; Revised 23 August 2011; Accepted 29 August 2011

Academic Editor: Laimutis Bytautas

Copyright © 2012 Eric A. C. Bushnell et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. D. Young, Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems, Wiley-Interscience, New York, NY, USA, 2001.
  2. P. E. M. Siegbahn and F. Himo, “Recent developments of the quantum chemical cluster approach for modeling enzyme reactions,” Journal of Biological Inorganic Chemistry, vol. 14, no. 5, pp. 643–651, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. C. J. Cramer, Essentials of Computational Chemistry: Theories and Models, John Wiley & Sons, New York, NY, USA, 2002.
  4. P. E. M. Siegbahn and T. Borowski, “Modeling enzymatic reactions involving transition metals,” Accounts of Chemical Research, vol. 39, no. 10, pp. 729–738, 2006. View at Publisher · View at Google Scholar · View at Scopus
  5. F. Himo, “Quantum chemical modeling of enzyme active sites and reaction mechanisms,” Theoretical Chemistry Accounts, vol. 116, no. 1–3, pp. 232–240, 2006. View at Publisher · View at Google Scholar · View at Scopus
  6. A. D. Becke, “A new mixing of Hartree-Fock and local density-functional theories,” The Journal of Chemical Physics, vol. 98, no. 2, pp. 1372–1377, 1993. View at Scopus
  7. A. D. Becke, “Density-functional thermochemistry. III. The role of exact exchange,” The Journal of Chemical Physics, vol. 98, no. 7, pp. 5648–5652, 1993. View at Scopus
  8. C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Physical Review B, vol. 37, no. 2, pp. 785–789, 1988. View at Publisher · View at Google Scholar · View at Scopus
  9. P. E. M. Siegbahn, “The performance of hybrid DFT for mechanisms involving transition metal complexes in enzymes,” Journal of Biological Inorganic Chemistry, vol. 11, no. 6, pp. 695–701, 2006. View at Publisher · View at Google Scholar · View at Scopus
  10. B. Mennucci and J. Tomasi, “Continuum solvation models: a new approach to the problem of solute's charge distribution and cavity boundaries,” Journal of Chemical Physics, vol. 106, no. 12, pp. 5151–5158, 1997. View at Scopus
  11. J. Tomasi, B. Mennucci, and E. Cancès, “The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level,” Journal of Molecular Structure: THEOCHEM, vol. 464, no. 1–3, pp. 211–226, 1999. View at Publisher · View at Google Scholar · View at Scopus
  12. L. Hu, P. Söderhjelm, and U. Ryde, “On the convergence of QM/MM energies,” Journal of Chemical Theory and Computation, vol. 7, no. 3, pp. 761–777, 2011. View at Publisher · View at Google Scholar
  13. Y. Zhang, J. Kua, and J. A. McCammon, “Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies,” Journal of Physical Chemistry B, vol. 107, no. 18, pp. 4459–4463, 2003. View at Scopus
  14. M. Klähn, S. Braun-Sand, E. Rosta, and A. Warshel, “On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions,” Journal of Physical Chemistry B, vol. 109, no. 32, pp. 15645–15650, 2005. View at Publisher · View at Google Scholar · View at Scopus
  15. H. M. Senn and W. Thiel, “QM/MM methods for biomolecular systems,” Angewandte Chemie International Edition, vol. 48, no. 7, pp. 1198–1229, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. J. Llano and J. W. Gauld, Mechanistics of Enzyme Catalysis: From Small to Large Active-Site Models, vol. 2, Wiley-VCH, Weinheim, Germany, 2010.
  17. O. Acevedo and W. L. Jorgensen, “Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions,” Accounts of Chemical Research, vol. 43, no. 1, pp. 142–151, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. M. Dal Peraro, P. Ruggerone, S. Raugei, F. L. Gervasio, and P. Carloni, “Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations,” Current Opinion in Structural Biology, vol. 17, no. 2, pp. 149–156, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. Y. Hagiwara, M. J. Field, O. Nureki, and M. Tateno, “Editing Mechanism of Aminoacyl-tRNA synthetases operates by a hybrid ribozyme/protein catalyst,” Journal of the American Chemical Society, vol. 132, no. 8, pp. 2751–2758, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. J. Blumberger, “Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment,” Physical Chemistry Chemical Physics, vol. 10, no. 37, pp. 5651–5667, 2008. View at Publisher · View at Google Scholar · View at Scopus
  21. H. Liu, J. Llano, and J. W. Gauld, “A DFT study of nucleobase dealkylation by the DNA repair enzyme AlkB,” Journal of Physical Chemistry B, vol. 113, no. 14, pp. 4887–4898, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. S. Shaik, H. Hirao, and D. Kumar, “Reactivity of high-valent iron-oxo species in enzymes and synthetic reagents: a tale of many states,” Accounts of Chemical Research, vol. 40, no. 7, pp. 532–542, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. R. Poli and J. N. Harvey, “Spin forbidden chemical reactions of transition metal compounds. New ideas and new computational challenges,” Chemical Society Reviews, vol. 32, no. 1, pp. 1–8, 2003. View at Publisher · View at Google Scholar · View at Scopus
  24. E. A. C. Bushnell, E. Erdtman, J. Llano, L. A. Eriksson, and J. W. Gauld, “The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase,” Journal of Computational Chemistry, vol. 32, no. 5, pp. 822–834, 2011. View at Publisher · View at Google Scholar
  25. P. J. Silva and M. J. Ramos, “Density-functional study of mechanisms for the cofactor-free decarboxylation performed by uroporphyrinogen III decarboxylase,” Journal of Physical Chemistry B, vol. 109, no. 38, pp. 18195–18200, 2005. View at Publisher · View at Google Scholar · View at Scopus
  26. W. Huang, J. Llano, and J. W. Gauld, “Redox mechanism of glycosidic bond hydrolysis catalyzed by 6-phospho-α-glucosidase: a DFT study,” Journal of Physical Chemistry B, vol. 114, no. 34, pp. 11196–11206, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. R. De Bont and N. van Larebeke, “Endogenous DNA damage in humans: a review of quantitative data,” Mutagenesis, vol. 19, no. 3, pp. 169–185, 2004. View at Publisher · View at Google Scholar · View at Scopus
  28. Y. Wang, “Bulky DNA lesions induced by reactive oxygen species,” Chemical Research in Toxicology, vol. 21, no. 2, pp. 276–281, 2008. View at Publisher · View at Google Scholar · View at Scopus
  29. J. S. Taylor, “Unraveling the molecular pathway from sunlight to skin cancer,” Accounts of Chemical Research, vol. 27, no. 3, pp. 76–82, 1994. View at Scopus
  30. H. Kamiya, S. Iwai, and H. Kasai, “The (6-4) photoproduct of thymine-thymine induces targeted substitution mutations in mammalian cells,” Nucleic Acids Research, vol. 26, no. 11, pp. 2611–2617, 1998. View at Publisher · View at Google Scholar · View at Scopus
  31. M. Lysetska, A. Knoll, D. Boehringer, T. Hey, G. Krauss, and G. Krausch, “UV light-damaged DNA and its interaction with human replication protein A: an atomic force microscopy study,” Nucleic Acids Research, vol. 30, no. 12, pp. 2686–2691, 2002. View at Scopus
  32. W. L. Neeley and J. M. Essigmann, “Mechanisms of formation, genotoxicity, and mutation of guanine oxidation products,” Chemical Research in Toxicology, vol. 19, no. 4, pp. 491–505, 2006. View at Publisher · View at Google Scholar · View at Scopus
  33. E. C. Friedberg, L. D. McDaniel, and R. A. Schultz, “The role of endogenous and exogenous DNA damage and mutagenesis,” Current Opinion in Genetics and Development, vol. 14, no. 1, pp. 5–10, 2004. View at Publisher · View at Google Scholar · View at Scopus
  34. T. Lindahl, “Instability and decay of the primary structure of DNA,” Nature, vol. 362, no. 6422, pp. 709–715, 1993. View at Publisher · View at Google Scholar · View at Scopus
  35. F. Drabløs, E. Feyzi, P. A. Aas et al., “Alkylation damage in DNA and RNA—repair mechanisms and medical significance,” DNA Repair, vol. 3, no. 11, pp. 1389–1407, 2004. View at Publisher · View at Google Scholar
  36. Y. Mishina, E. M. Duguid, and C. He, “Direct reversal of DNA alkylation damage,” Chemical Reviews, vol. 106, no. 2, pp. 215–232, 2006. View at Publisher · View at Google Scholar · View at Scopus
  37. B. Sedgwick, P. A. Bates, J. Paik, S. C. Jacobs, and T. Lindahl, “Repair of alkylated DNA: recent advances,” DNA Repair, vol. 6, no. 4, pp. 429–442, 2007. View at Publisher · View at Google Scholar · View at Scopus
  38. T. Lindahl, B. Sedgwick, M. Sekiguchi, and Y. Nakabeppu, “Regulation and expression of the adaptive response to alkylating agents,” Annual Review of Biochemistry, vol. 57, pp. 133–157, 1988. View at Scopus
  39. A. K. McCullough, M. L. Dodson, and R. S. Lloyd, “Initiation of base excision repair: glycosylase mechanisms and structures,” Annual Review of Biochemistry, vol. 68, pp. 255–285, 1999. View at Publisher · View at Google Scholar · View at Scopus
  40. P. J. O'Brien and T. Ellenberger, “Human alkyladenine DNA glycosylase uses acid-base catalysis for selective excision of damaged purines,” Biochemistry, vol. 42, no. 42, pp. 12418–12429, 2003. View at Publisher · View at Google Scholar · View at Scopus
  41. S. C. Trewick, T. F. Henshaw, R. P. Hausinger, T. Lindahl, and B. Sedgwick, “Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage,” Nature, vol. 419, no. 6903, pp. 174–178, 2002. View at Publisher · View at Google Scholar · View at Scopus
  42. P. Ø. Falnes, R. F. Johansen, and E. Seeberg, “AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli,” Nature, vol. 419, no. 6903, pp. 178–182, 2002. View at Publisher · View at Google Scholar · View at Scopus
  43. T. Duncan, S. C. Trewick, P. Koivisto, P. A. Bates, T. Lindahl, and B. Sedgwick, “Reversal of DNA alkylation damage by two human dioxygenases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 26, pp. 16660–16665, 2002. View at Publisher · View at Google Scholar · View at Scopus
  44. L. Aravind and E. V. Koonin, “The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases,” Genome biology, vol. 2, no. 3, Article ID RESEARCH0007, 2001. View at Scopus
  45. B. Yu, W. C. Edstrom, J. Benach et al., “Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB,” Nature, vol. 439, no. 7078, pp. 879–884, 2006. View at Publisher · View at Google Scholar · View at Scopus
  46. Z. Zhang, J.-S. Ren, K. Harlos, C. H. McKinnon, I. J. Clifton, and C. J. Schofield, “Crystal structure of a clavaminate synthase-Fe(II)-2-oxoglutarate-substrate-NO complex: evidence for metal centred rearrangements,” FEBS Letters, vol. 517, no. 1–3, pp. 7–12, 2002. View at Publisher · View at Google Scholar
  47. R. Nakajima and I. Yamazaki, “The mechanism of oxyperoxidase formation from ferryl peroxidase and hydrogen peroxide,” Journal of Biological Chemistry, vol. 262, no. 6, pp. 2576–2581, 1987. View at Scopus
  48. G. I. Berglund, G. H. Carlsson, A. T. Smith, H. Szöke, A. Henriksen, and J. Hajdu, “The catalytic pathway of horseradish peroxidase at high resolution,” Nature, vol. 417, no. 6887, pp. 463–468, 2002. View at Publisher · View at Google Scholar · View at Scopus
  49. M. J. Frisch, G. W. Trucks, H. B. Schlegel, et al., Gaussian 03, Revision D.02, Gaussian, Inc., Wallingford, Conn, USA, 2004.
  50. Jaguar, Schrodinger, L. L. C., Portland, Ore, USA, 5.5 edition, 1991–2003.
  51. J. San Filippo Jr., L. J. Romano, C. I. Chern, and J. S. Valentine, “Cleavage of esters by superoxide,” Journal of Organic Chemistry, vol. 41, no. 3, pp. 586–588, 1976. View at Scopus
  52. J. San Filippo Jr., C. I. Chern, and J. S. Valentine, “Oxidative cleavage of α-keto, α-hydroxy, and α-halo ketones, esters, and carboxylic acids by superoxide,” Journal of Organic Chemistry, vol. 41, no. 6, pp. 1077–1078, 1976. View at Scopus
  53. Y. M. Chiou and L. Que, “Models for α-keto acid-dependent non-heme iron enzymes: structures and reactivity of [FeIICL(O2CCOPh)](ClO4) complexes,” Journal of the American Chemical Society, vol. 117, no. 14, pp. 3999–4013, 1995. View at Scopus
  54. M. P. Mehn, K. Fujisawa, E. L. Hegg, and L. Que, “Oxygen activation by nonheme iron(II) complexes: α-keto carboxylate versus carboxylate,” Journal of the American Chemical Society, vol. 125, no. 26, pp. 7828–7842, 2003. View at Publisher · View at Google Scholar · View at Scopus
  55. T. Borowski, A. Bassan, and P. E. M. Siegbahn, “Mechanism of dioxygen activation in 2-oxoglutarate-dependent enzymes: a hybrid DFT study,” Chemistry: A European Journal, vol. 10, no. 4, pp. 1031–1041, 2004. View at Scopus
  56. T. Borowski, A. Bassan, and P. E. M. Siegbahn, “A hybrid density functional study of O-O bond cleavage and phenyl ring hydroxylation for a biomimetic non-heme iron complex,” Inorganic Chemistry, vol. 43, no. 10, pp. 3277–3291, 2004. View at Publisher · View at Google Scholar · View at Scopus
  57. A. Bassan, T. Borowski, and P. E. M. Siegbahn, “Quantum chemical studies of dioxygen activation by mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad,” Dalton Transactions, no. 20, pp. 3153–3162, 2004. View at Publisher · View at Google Scholar · View at Scopus
  58. T. Borowski, A. Bassan, and P. E. M. Siegbahn, “4-hydroxyphenylpyruvate dioxygenase: a hybrid density functional study of the catalytic reaction mechanism,” Biochemistry, vol. 43, no. 38, pp. 12331–12342, 2004. View at Publisher · View at Google Scholar · View at Scopus
  59. G. F. Barnard and M. Akhtar, “Stereochemistry of porphyrinogen carboxy-lyase reaction in haem biosynthesis,” Journal of the Chemical Society, Chemical Communications, no. 13, pp. 494–496, 1975. View at Publisher · View at Google Scholar · View at Scopus
  60. G. F. Barnard and M. Akhtar, “Stereochemical and mechanistic studies on the decarboxylation of uroporphyrinogen III in haem biosynthesis,” Journal of the Chemical Society, Perkin Transactions 1, pp. 2354–2360, 1979. View at Scopus
  61. M. Akhtar, “The modification of acetate and propionate side chains during the biosynthesis of haem and chlorophylls: mechanistic and stereochemical studies,” Ciba Foundation symposium, vol. 180, pp. 131–152, 1994. View at Scopus
  62. J. Fan, Q. Liu, Q. Hao, M. Teng, and L. Niu, “Crystal structure of uroporphyrinogen decarboxylase from Bacillus subtilis,” Journal of Bacteriology, vol. 189, no. 9, pp. 3573–3580, 2007. View at Publisher · View at Google Scholar · View at Scopus
  63. I. U. Heinemann, M. Jahn, and D. Jahn, “The biochemistry of heme biosynthesis,” Archives of Biochemistry and Biophysics, vol. 474, no. 2, pp. 238–251, 2008. View at Publisher · View at Google Scholar
  64. B. M. Martins, B. Grimm, H. P. Mock, R. Huber, and A. Messerschmidt, “Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum: implications for the catalytic mechanism,” Journal of Biological Chemistry, vol. 276, no. 47, pp. 44108–44116, 2001. View at Publisher · View at Google Scholar · View at Scopus
  65. H. P. Mock, L. Trainotti, E. Kruse, and B. Grimm, “Isolation, sequencing and expression of cDNA sequences encoding uroporphyrinogen decarboxylase from tobacco and barley,” Plant Molecular Biology, vol. 28, no. 2, pp. 245–256, 1995. View at Scopus
  66. A. H. Jackson, H. A. Sancovich, A. M. Ferramola et al., “Macrocyclic intermediates in the biosynthesis of porphyrins,” Philosophical Transactions of the Royal Society of London. Series B, vol. 273, no. 924, pp. 191–206, 1976. View at Scopus
  67. J. D. Phillips, F. G. Whitby, J. P. Kushner, and C. P. Hill, “Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase,” The EMBO Journal, vol. 22, no. 23, pp. 6225–6233, 2003. View at Publisher · View at Google Scholar · View at Scopus
  68. G. Chaufan, M. C. Ríos de Molina, and L. C. San Martín de Viale, “How does hexachlorobenzene treatment affect liver uroporphyrinogen decarboxylase?” International Journal of Biochemistry and Cell Biology, vol. 33, no. 6, pp. 621–630, 2001. View at Publisher · View at Google Scholar · View at Scopus
  69. C. A. Lewis and R. Wolfenden, “Uroporphyrinogen decarboxylation as a benchmark for the catalytic proficiency of enzymes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 45, pp. 17328–17333, 2008. View at Publisher · View at Google Scholar · View at Scopus
  70. S. Billi de Catabbi, M. C. Ríos de Molina, and L. C. San Martín de Viale, “Studies on the active centre of rat liver porphyrinogen carboxylase in vivo effect of hexachlorobenzene,” International Journal of Biochemistry, vol. 23, no. 7-8, pp. 675–679, 1991.
  71. K. M. Jones and P. M. Jordan, “Purification and properties of the uroporphyrinogen decarboxylase from Rhodobacter sphaeroides,” Biochemical Journal, vol. 293, no. 3, pp. 703–712, 1993. View at Scopus
  72. M. Akhtar, New Comprehensive Biochemistry: Biosynthesis of Tetrapyrroles, vol. 19, Elsevier, London, UK, 1991.
  73. M. J. Bearpark, F. Ogliaro, T. Vreven, et al., “CASSCF calculations for excited states of large molecules: choosing when to use the RASSCF, ONIOM and MMVB approximations,” in Computation in Modern Science and Engineering, Parts A and B, T. E. Simos and G. Maroulis, Eds., vol. 2, pp. 583–585, Amer Inst Physics, Melville, NY, USA, 2007.
  74. S. Dapprich, I. Komáromi, K. S. Byun, K. Morokuma, and M. J. Frisch, “A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives,” Journal of Molecular Structure: THEOCHEM, vol. 461-462, pp. 1–21, 1999. View at Publisher · View at Google Scholar · View at Scopus
  75. S. Humbel, S. Sieber, and K. Morokuma, “The IMOMO method: integration of different levels of molecular orbital approximations for geometry optimization of large systems: test for n-butane conformation and SN2 reaction: RCl+Cl,” Journal of Chemical Physics, vol. 105, no. 5, pp. 1959–1967, 1996. View at Scopus
  76. F. Maseras and K. Morokuma, “IMOMM—a new integrated ab-initio plus molecular mechanics geometry optimization scheme of equilibrium structures and transition-states,” Journal of Computational Chemistry, vol. 16, no. 9, pp. 1170–1179, 1995.
  77. K. Morokuma, D. G. Musaev, T. Vreven, H. Basch, M. Torrent, and D. V. Khoroshun, “Model studies of the structures, reactivities, and reaction mechanisms of metalloenzymes,” IBM Journal of Research and Development, vol. 45, no. 3-4, pp. 367–395, 2001. View at Scopus
  78. M. Svensson, S. Humbel, R. D. J. Froese, T. Matsubara, S. Sieber, and K. Morokuma, “ONIOM: a multilayered integrated MO+MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)3)2+H2 oxidative addition,” Journal of Physical Chemistry, vol. 100, no. 50, pp. 19357–19363, 1996. View at Scopus
  79. T. Vreven, K. S. Byun, I. Komáromi et al., “Combining quantum mechanics methods with molecular mechanics methods in ONIOM,” Journal of Chemical Theory and Computation, vol. 2, no. 3, pp. 815–826, 2006. View at Publisher · View at Google Scholar · View at Scopus
  80. T. Vreven and K. Morokuma, “On the application of the IMOMO (integrated molecular orbital + molecular orbital) method,” Journal of Computational Chemistry, vol. 21, no. 16, pp. 1419–1432, 2000. View at Scopus
  81. T. Vreven, K. Morokuma, O. Farkas, H. B. Schlegel, and M. J. Frisch, “Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints,” Journal of Computational Chemistry, vol. 24, no. 6, pp. 760–769, 2003. View at Publisher · View at Google Scholar · View at Scopus
  82. D. A. Case, T. E. Cheatham, T. Darden et al., “The Amber biomolecular simulation programs,” Journal of Computational Chemistry, vol. 26, no. 16, pp. 1668–1688, 2005. View at Publisher · View at Google Scholar · View at Scopus
  83. H. de Verneuil, S. Sassa, and A. Kappas, “Purification and properties of uroporphyrinogen decarboxylase from human erythrocytes. A single enzyme catalyzing the four sequential decarboxylations of uroporphyrinogens I and III,” Journal of Biological Chemistry, vol. 258, no. 4, pp. 2454–2460, 1983. View at Scopus
  84. A. B. Juárez, C. Aldonatti, M. S. Vigna, and M. C. Ríos de Molina, “Studies on uroporphyrinogen decarboxylase from Chlorella kessleri (Trebouxiophyceae, Chlorophyta),” Canadian Journal of Microbiology, vol. 53, no. 2, pp. 303–312, 2007. View at Publisher · View at Google Scholar · View at Scopus
  85. R. Wolfenden, X. Lu, and G. Young, “Spontaneous hydrolysis of glycosides,” Journal of the American Chemical Society, vol. 120, no. 27, pp. 6814–6815, 1998. View at Publisher · View at Google Scholar · View at Scopus
  86. D. L. Zechel and S. G. Withers, “Glycosidase mechanisms: anatomy of a finely tuned catalyst,” Accounts of Chemical Research, vol. 33, no. 1, pp. 11–18, 2000. View at Publisher · View at Google Scholar · View at Scopus
  87. J. M. Stubbs and D. Marx, “Glycosidic bond formation in aqueous solution: on the oxocarbenium intermediate,” Journal of the American Chemical Society, vol. 125, no. 36, pp. 10960–10962, 2003. View at Publisher · View at Google Scholar · View at Scopus
  88. J. M. Stubbs and D. Marx, “Aspects of glycosidic bond formation in aqueous solution: chemical bonding and the role of water,” Chemistry: A European Journal, vol. 11, no. 9, pp. 2651–2659, 2005. View at Publisher · View at Google Scholar · View at Scopus
  89. K. Das, D. Ray, N. R. Bandyopadhyay, T. Ghosh, A. K. Mohanty, and M. Misra, “A study of the mechanical, thermal and morphological properties of microcrystalline cellulose particles prepared from cotton slivers using different acid concentrations,” Cellulose, vol. 16, no. 5, pp. 783–793, 2009. View at Publisher · View at Google Scholar · View at Scopus
  90. Q. P. Liu, G. Sulzenbacher, H. Yuan et al., “Bacterial glycosidases for the production of universal red blood cells,” Nature Biotechnology, vol. 25, no. 4, pp. 454–464, 2007. View at Publisher · View at Google Scholar · View at Scopus
  91. B. Capon, “Mechanism in carbohydrate chemistry,” Chemical Reviews, vol. 69, no. 4, pp. 407–498, 1969. View at Scopus
  92. B. Henrissat, “A classification of glycosyl hydrolases based on amino acid sequence similarities,” Biochemical Journal, vol. 280, no. 2, pp. 309–316, 1991. View at Scopus
  93. J. D. McCarter and S. G. Withers, “Mechanisms of enzymatic glycoside hydrolysis,” Current Opinion in Structural Biology, vol. 4, no. 6, pp. 885–892, 1994. View at Publisher · View at Google Scholar · View at Scopus
  94. B. Henrissat and G. Davies, “Structural and sequence-based classification of glycoside hydrolases,” Current Opinion in Structural Biology, vol. 7, no. 5, pp. 637–644, 1997. View at Publisher · View at Google Scholar · View at Scopus
  95. M. L. Sinnott, “Catalytic mechanisms of enzymic glycosyl transfer,” Chemical Reviews, vol. 90, no. 7, pp. 1171–1202, 1990. View at Scopus
  96. G. J. Davies, T. M. Gloster, and B. Henrissat, “Recent structural insights into the expanding world of carbohydrate-active enzymes,” Current Opinion in Structural Biology, vol. 15, no. 6, pp. 637–645, 2005. View at Publisher · View at Google Scholar · View at Scopus
  97. B. P. Rempel and S. G. Withers, “Covalent inhibitors of glycosidases and their applications in biochemistry and biology,” Glycobiology, vol. 18, no. 8, pp. 570–586, 2008. View at Publisher · View at Google Scholar · View at Scopus
  98. J. Thompson, C. R. Gentry-Weeks, N. Y. Nguyen, J. E. Folk, and S. A. Robrish, “Purification from Fusobacterium mortiferum ATCC 25557 of a 6-phosphoryl-O-α-D-glucopyranosyl:6-phosphoglucohydrolase that hydrolyzes maltose 6-phosphate and related phospho-α-D-glucosides,” Journal of Bacteriology, vol. 177, no. 9, pp. 2505–2512, 1995. View at Scopus
  99. A. Varrot, V. L. Y. Yip, Y. Li et al., “NAD+ and metal-ion dependent hydrolysis by family 4 glycosidases: structural insight into specificity for phospho-β-D-glucosides,” Journal of Molecular Biology, vol. 346, no. 2, pp. 423–435, 2005. View at Publisher · View at Google Scholar · View at Scopus
  100. J. Thompson, S. B. Ruvinov, D. I. Freedberg, and B. G. Hall, “Cellobiose-6-phosphate hydrolase (CelF) of Escherichia coli: characterization and assignment to the unusual family 4 of glycosylhydrolases,” Journal of Bacteriology, vol. 181, no. 23, pp. 7339–7345, 1999. View at Scopus
  101. F. Kunst, N. Ogasawara, I. Moszer et al., “The complete genome sequence of the gram-positive bacterium Bacillus subtilis,” Nature, vol. 390, no. 6657, pp. 249–256, 1997. View at Publisher · View at Google Scholar · View at Scopus
  102. J. Thompson, A. Pikis, S. B. Ruvinov, B. Henrissat, H. Yamamoto, and J. Sekiguchi, “The gene glvA of Bacillus subtilis 168 encodes a metal-requiring, NAD(H)-dependent 6-phospho-α-glucosidase. Assignment to family 4 of the glycosylhydrolase superfamily,” Journal of Biological Chemistry, vol. 273, no. 42, pp. 27347–27356, 1998. View at Publisher · View at Google Scholar · View at Scopus
  103. B. G. Hall, A. Pikis, and J. Thompson, “Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations,” Molecular Biology and Evolution, vol. 26, no. 11, pp. 2487–2497, 2009. View at Publisher · View at Google Scholar · View at Scopus
  104. B. I. Cantarel, P. M. Coutinho, C. Rancurel, T. Bernard, V. Lombard, and B. Henrissat, “The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics,” Nucleic Acids Research, vol. 37, no. 1, pp. D233–D238, 2009. View at Publisher · View at Google Scholar · View at Scopus
  105. S. S. Rajan, X. Yang, F. Collart et al., “Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+-dependent phospho-α-glucosidase from Bacillus subtilis,” Structure, vol. 12, no. 9, pp. 1619–1629, 2004. View at Publisher · View at Google Scholar · View at Scopus
  106. V. L. Y. Yip, J. Thompson, and S. G. Withers, “Mechanism of GlvA from Bacillus subtilis: a detailed kinetic analysis of a 6-phospho-α-glucosidase from glycoside hydrolase family 4,” Biochemistry, vol. 46, no. 34, pp. 9840–9852, 2007. View at Publisher · View at Google Scholar · View at Scopus
  107. V. L.Y. Yip and S. G. Withers, “Family 4 glycosidases carry out efficient hydrolysis of thioglycosides by an α,β-elimination mechanism,” Angewandte Chemie International Edition, vol. 45, no. 37, pp. 6179–6182, 2006. View at Publisher · View at Google Scholar