Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods

Carbohydrate Research

Volumn 403, Issue , 2015, Pages 38-47

  Tvaroška, Igor ^a,b  

^a INSTITUTE OF CHEMISTRY   (Slovakia)

^b The Philosopher University in Nitra Geoinformatics and Regional Development   (Slovakia)

Author keywords

Catalytic mechanism; Computational modeling; Glycosyl transfer; Glycosyltransferases; Nucleophilic substitution; QM MM methods

Indexed keywords

CATALYSIS; ELECTRONIC STRUCTURE; MECHANICS; MECHANISMS; MOLECULAR MODELING; QUANTUM THEORY;

CATALYTIC MECHANISMS; CATALYZED REACTIONS; COMPUTATIONAL MODELLING; GLYCOSYL; GLYCOSYL TRANSFER; GLYCOSYL TRANSFERASE; MOLECULAR MECHANICS METHOD; NUCLEOPHILIC SUBSTITUTIONS; QUANTUM MECHANIC/MOLECULAR MECHANIC METHOD; QUANTUM MECHANICS/MOLECULAR MECHANICS;

ENZYMES;

GLYCOSYLTRANSFERASE;

ANIMAL; ARTICLE; BIOCATALYSIS; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR MECHANICS; PRIORITY JOURNAL; QUANTUM MECHANICS; QUANTUM THEORY; REACTION ANALYSIS;

ANIMALS; BIOCATALYSIS; CHEMISTRY; GLYCOSYLTRANSFERASES; HUMANS; METABOLISM; MODELS, MOLECULAR; QUANTUM THEORY;

EID: 84963958337     PISSN: 00086215     EISSN: 1873426X     Source Type: Journal    
DOI: 10.1016/j.carres.2014.06.017     Document Type: Review

References (76)

1. T.A. Beyer, J.E. Sadler, J.I. Rearick, J.C. Paulson, and R.L. Hill Adv. Enzymol. 52 1981 23 175
2. H. Schachter Curr. Opin. Struct. Biol. 1 1991 755 765
3. R. Kleene, and E.G. Berger Biochim. Biophys. Acta 1154 1993 283 325
4. J. Montreuil, J.F.G. Vliegenthart, and H. Schachter New Comprehensive Biochemistry, Glycoproteins Vol. 29a 1995 Elsevier Science B.V. Amsterdam
5. M.L. Sinnott Chem. Rev. 90 1990 1171 1202
6. D.L. Zechel, and S.G. Withers C.D. Poulter, Compr. Nat. Prod. Chem 1999 Elsevier New York 279 314
7. G. Davies, M.L. Sinnott, and S.G. Withers M.L. Sinott, Comprehensive Biological Catalysis 1998 Academic Press Limited New York 119 208
8. D.L. Zechel, and S.G. Withers Acc. Chem. Res. 33 2000 11 18
9. C. Breton, J. Mucha, and C. Jeanneau Biochimie 83 2001 713 718
10. I. Tvaroška TIGG 17 2005 177 190
11. I. Tvaroška ACS Symp. Ser. 930 2006 285 301
12. C. Breton, L. Snajdrova, C. Jeanneau, J. Koča, and A. Imberty Glycobiology 16 2006 29r 37r
13. L.L. Lairson, and S.G. Withers Chem. Commun. 2004 2243 2248
14. I.B.H. Wilson, C. Breton, A. Imberty, and I. Tvaroška B.O. Fraser-Reid, K. Tatsuta, J. Thiem, G.L. Cote, S. Flitsch, Y. Ito, H. Kondo, S.-I. Nishimura, B. Yu, Glycoscience Chemistry and Chemical Biology 2008 Springer-Verlag Berlin Heidelberg 2267 2323
15. B. Henrissat, G. Sulzenbacher, and Y. Bourne Curr. Opin. Struct. Biol. 18 2008 527 533
16. R. Zhang, V.L.Y. Yip, S.G. Withers Comprehensive Natural Products II - Chemistry and Biology L. Mander, and H.-W. Liu Enzymes and Enzyme Mechanisms Vol. 8 2010 Elsevier Ltd 385 422
17. Perez, S.; Tvaroška, I. Adv. Carbohydr. Chem. Biochem. 2014, 71, in press.
18. L.L. Lairson, B. Henrissat, G.J. Davies, and S.G. Withers Annu. Rev. Biochem. 77 2008 521 555
19. I. Tvaroška Mini-Rev. Org. Chem. 8 2011 263 269
20. I. Tvaroška, I. Andre, and J.P. Carver J. Am. Chem. Soc. 122 2000 8762 8776
21. I. Tvaroška, I. Andre, and J.P. Carver Glycobiology 13 2003 559 566
22. I. Tvaroška Carbohydr. Res. 339 2004 1007 1014
23. I. Andre, I. Tvaroška, and J.P. Carver Carbohydr. Res. 338 2003 865 877
24. P.E.M. Siegbahn, and F. Himo Wires Comput. Mol. Sci. 1 2011 323 336
25. S. Kozmon, and I. Tvaroška J. Am. Chem. Soc. 128 2006 16921 16927
26. M. Krupicka, and I. Tvaroška J. Phys. Chem. B 113 2009 11314 11319
27. U.M. Unligil, and J.M. Rini Curr. Opin. Struct. Biol. 10 2000 510 517
28. B.W. Murray, V. Wittmann, M.D. Burkart, S.C. Hung, and C.H. Wong Biochemistry 36 1997 823 831
29. S.C. Kim, A.N. Singh, and F.M. Raushel Arch. Biochem. Biophys. 267 1988 54 59
30. P.K. Qasba, B. Ramakrishnan, and E. Boeggeman Trends Biochem. Sci. 30 2005 53 62
31. B. Ramakrishnan, and P. Qasba J. Mol. Biol. 310 2001 205 218
32. B. Ramakrishan, P.V. Balaji, and P.K. Qasba J. Mol. Biol. 318 2002 491 502
33. H. Schachter, F. Reck, and H. Paulsen Methods Enzymol. 363 2003 459 475
34. I. Tvaroška, S. Kozmon, M. Wimmerova, and J. Koča J. Am. Chem. Soc. 134 2012 5563 15571
35. I. Tvaroška, S. Kozmon, M. Wimmerova, and J. Koča Chem. Eur. J. 19 2013 8153 8162
36. G.W. Hart, M.P. Housley, and C. Slawson Nature 446 2007 1017 1022
37. G.W. Hart, and R.J. Copeland Cell 143 2010 672 676
38. M.B. Lazarus, Y.S. Nam, J.Y. Jiang, P. Sliz, and S. Walker Nature 469 2011 564 568
39. M.S. Macauley, G.E. Whitworth, A.W. Debowski, D. Chin, and D.J. Vocadlo J. Biol. Chem. 280 2005 25313 25322
40. M. Schimpl, X.W. Zheng, V.S. Borodkin, D.E. Blair, A.T. Ferenbach, A.W. Schuttelkopf, I. Navratilova, T. Aristotelous, O. Albarbarawi, D.A. Robinson, M.A. Macnaughtan, and D.M.F. van Aalten Nat. Chem. Biol. 8 2012 969 974
41. M.B. Lazarus, J.Y. Jiang, T.M. Gloster, W.F. Zandberg, G.E. Whitworth, D.J. Vocadlo, and S. Walker Nat. Chem. Biol. 8 2012 966 968
42. D. Adlercreutz, K. Mannerstedt, W. Wakarchuk, N. Dovichi, O. Hindsgaul, and M.M. Palcic Glycobiology 20 2010 1517
43. J.E. Pak, P. Arnoux, S.H. Zhou, P. Sivarajah, M. Satkunarajah, X.K. Xing, and J.M. Rini J. Biol. Chem. 281 2006 26693 26701
44. J.E. Pak, M. Satkunarajah, J. Seetharaman, and J.M. Rini J. Mol. Biol. 414 2011 798 811
45. A. Monegal, and A. Planas J. Am. Chem. Soc. 128 2006 16030 16031
46. N. Soya, Y. Fang, M.M. Palcic, and J.S. Klassen Glycobiology 21 2011 547 552
47. K. Persson, H.D. Ly, M. Dieckelmann, W.W. Wakarchuk, S.G. Withers, and N.C.J. Strynadka Nat. Struct. Biol. 8 2001 166 175
48. E. Boix, Y. Zhang, G.J. Swaminathan, and K. Brew J. Biol. Chem. 277 2002 28310 28318
49. L.N. Gastinel, C. Bignon, A.K. Misra, O. Hindsgaul, J.H. Shaper, and D.H. Joziasse EMBO J. 20 2001 638 649
50. H. Jamaluddin, P. Tumbale, S.G. Withers, K.R. Acharya, and K. Brew J. Mol. Biol. 369 2007 1270 1281
51. H. Gómez, J.M. Lluch, and L. Masgrau Carbohydr. Res. 356 2012 204 208
52. H. Gómez, J.M. Lluch, and L. Masgrau J. Am. Chem. Soc. 135 2013 7053 7063
53. V. Rojas-Cervellera, A. Ardevol, M. Boero, A. Planas, and C. Rovira Chem. Eur. J. 19 2013 14018 14023
54. L. Snajdrova, P. Kulhanek, A. Imberty, and J. Koča Carbohydr. Res. 339 2004 995 1006
55. H. Gómez, I. Polyak, W. Thiel, J.M. Lluch, and L. Masgrau J. Am. Chem. Soc. 134 2012 4743 4752
56. J.C. Errey, S.S. Lee, R.P. Gibson, C.M. Fleites, C.S. Barry, P.M.J. Jung, A.C. O'Sullivan, B.G. Davis, and G.J. Davies Angew. Chem., Int. Ed. 49 2010 1234 1237
57. S.S. Lee, S.Y. Hong, J.C. Errey, A. Izumi, G.J. Davies, and B.G. Davis Nat. Chem. Biol. 7 2011 631 638
58. H.D. Ly, B. Lougheed, W.W. Wakarchuk, and S.G. Withers Biochemistry 41 2002 5075 5085
59. A. Ardevol, and C. Rovira Angew. Chem., Int. Ed. 50 2011 10897 10901
60. H. Gómez, R. Rojas, D. Patel, L.A. Tabak, J.M. Lluch, and L. Masgrau Org. Biomol. Chem. 12 2014 2645 2655
61. Trnka, T.; Kozmon, S.; Tvaroška, I.; Koča, J. unpublished results.
62. Y.D. Lobsanov, P.A. Romero, B. Sleno, B.M. Yu, P. Yip, A. Herscovics, and P.L. Howell J. Biol. Chem. 279 2004 17921 17931
63. A. Bobovská, J. Kóňa, and I. Tvaroška Org. Biomol. Chem. 12 2014 4201 4210
64. L.M. Thomson, S. Bates, S. Yamazaki, M. Arisawa, Y. Aoki, and N.A.R. Gow J. Biol. Chem. 275 2000 18933 18938
65. J. Kóňa, and I. Tvaroška Chem. Pap. 63 2009 598 607
66. Bobovská, A.; Kóňa, J.; Tvaroška, I. unpublished results.
67. S.C. Kim, A.N. Singh, and F.M. Raushel J. Biol. Chem. 263 1988 10151 10154
68. I. Solt, P. Kulhanek, I. Simon, S. Winfield, M.C. Payne, G. Csanyi, and M. Fuxreiter J. Phys. Chem. B 113 2009 5728 5735
69. L.H. Hu, P. Soderhjelm, and U. Ryde J. Chem. Theory Comput. 7 2011 761 777
70. C.V. Sumowski, and C. Ochsenfeld J. Phys. Chem. A 113 2009 11734 11741
71. L.H. Hu, J. Eliasson, J. Heimdal, and U. Ryde J. Phys. Chem. A 113 2009 11793 11800
72. D.G. Truhlar, and Y. Zhao Acc. Chem. Res. 41 2008 157 167
73. X.F. Xu, I.M. Alecu, and D.G. Truhlar J. Chem. Theory Comput. 7 2011 1667 1676
74. D. Doron, A. Kohen, K. Nam, and D.T. Major J. Chem. Theory Comput. 2014
75. R. Jorgensen, T. Pesnot, H.J. Lee, M.M. Palcic, and G.K. Wagner J. Biol. Chem. 288 2013 26201 26208
76. T. Pesnot, R. Jorgensen, M.M. Palcic, and G.K. Wagner Nat. Chem. Biol. 6 2010 321 323