Modelling of β-d-glucopyranose ring distortion in different force fields: a metadynamics study

Carbohydrate Research

Volumn 345, Issue 4, 2010, Pages 530-537

  Spiwok, Vojtěch ^a,b   Králová, Blanka ^a   Tvaroška, Igor ^b  

^a INSTITUTE OF CHEMICAL TECHNOLOGY   (Czech Republic)

^b Institute of Chemistry   (Slovakia)

Author keywords

Force field; Free energy; Metadynamics; Molecular dynamics simulation; Pyranose ring distortion

Indexed keywords

FORCE FIELD; FORCE FIELDS; METADYNAMICS; MOLECULAR DYNAMICS SIMULATIONS; PYRANOSE;

CARBOHYDRATES; CONFORMATIONS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; VACUUM;

FREE ENERGY;

ARTICLE; CALCULATION; CARBOHYDRATE ANALYSIS; CONFORMATION; CONTROLLED STUDY; ENERGY; FORCE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION; VACUUM;

CARBOHYDRATE CONFORMATION; GLUCOSIDES; MOLECULAR DYNAMICS SIMULATION; THERMODYNAMICS; WATER;

EID: 75149117767     PISSN: 00086215     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.carres.2009.12.011     Document Type: Article

References (57)

1. DeMarco M.L., and Woods R.J. Glycobiology 18 (2008) 426-440
2. Davies G.J., Ducros V.M., Varrot A., and Zechel D.L. Biochem. Soc. Trans. 31 (2003) 523-527
3. Hricovíni M. Carbohydr. Res. 341 (2006) 2575-2580
4. Marszalek P.E., Oberhauser A.F., Pang Y.-P., and Fernandez J.M. Nature 396 (1998) 661-664
5. Zhang Q., and Marszalek P.E. J. Am. Chem. Soc. 128 (2006) 5596-5597
6. Cremer D., and Pople J. J. Am. Chem. Soc. 97 (1975) 1354-1358
7. Cremer D., and Pople J. J. Am. Chem. Soc. 97 (1975) 1358-1367
8. Jeffrey G.A., and Yates J.H. Carbohydr. Res. 74 (1979) 319-322
9. Pérez S., Imberty A., Engelsen S.B., Gruza J., Mazeau K., Jiménez-Barbero J., Poveda A., Espinosa J.-F., van Eyck B.P., Johnson G., French A.D., Kouwijzer M.L.C.E., Grootenuis P.D.J., Bernardi A., Raimondi L., Senderowitz H., Durier V., Vergoten G., and Rasmussen K. Carbohydr. Res. 314 (1998) 141-155
10. Stortz C.A., Johnson G.P., French A.D., and Csonka G.I. Carbohydr. Res. 344 (2009) 2217-2228
11. Kirschner K.N., Yongye A.B., Tschampel S.M., González-Outeiriño J., Daniels C.R., Foley B.L., and Woods R.J. J. Comput. Chem. 29 (2008) 622-655
12. Kouwijzer M.L.C.E., and Grootenhuis P.D.J. J. Phys. Chem. 99 (1995) 13426-13436
13. Lins R.D., and Hünenberger P.H. J. Comput. Chem. 26 (2005) 1400-1412
14. Damm W., Frontera A., Tirado-Rives J., and Jorgensen W.L. J. Comput. Chem. 18 (1998) 1955
15. Hemmingsen L., Madsen D.E., Esbensen A.L., Olsen L., and Engelsen S.B. Carbohydr. Res. 339 (2004) 937-948
16. Barrows S.E., Dulles F.J., Cramer C.J., French A.F., and Truhlar D.G. Carbohydr. Res. 276 (1995) 219-251
17. Kräutler V., Müller M., and Hünenberger P.H. Carbohydr. Res. 342 (2007) 2097-2124
18. Pol-Fachin L., and Verli H. Carbohydr. Res. 343 (2008) 1435-1445
19. Jorgensen W.L. Acc. Chem. Res. 22 (1989) 184-189
20. Kollman P. Chem. Rev. 93 (1993) 2395-2417
21. Rodinger T., and Pomès R. Curr. Opin. Struct. Biol. 15 (2005) 164-170
22. Laio A., and Parrinello M. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 12562-12566
23. Iannuzzi M., Laio A., and Parrinello M. Phys. Rev. Lett. 90 (2003) 238302
24. Laio A., and Gervasio F.L. Rep. Prog. Phys. 71 (2008) 126601
25. Valdes H., Spiwok V., Řezáč J., Řeha D., Abo-Riziq A.G., de Vries M.S., and Hobza P. Chem. Eur. J. 14 (2008) 4886-4898
26. Spiwok V., Lipovová P., and Králová B. J. Phys. Chem. B 111 (2007) 3073-3076
27. Pfaendtner J., Branduardi D., Parrinello M., Pollard T.D., and Voth G.A. Proc. Natl. Acad. Sci. U.S.A. 106 (2009) 12723-12728
28. Sun J., Klug D.D., and Martoňák R. J. Chem. Phys. 130 (2009) 194512
29. Leone V., Lattanzi G., Molteni C., and Carloni P. PLoS Comput. Biol. 5 (2009) e1000309
30. Vargiu A.V., Ruggerone P., Magistrato A., and Carloni P. Nucleic Acids. Res. 36 (2008) 5910-5921
31. Min D., Josephine H.R., Li H., Lakner C., MacPherson I.S., Naylor G.J., Swofford D., Hedstrom L., and Yang W. PLoS Biol. 6 (2008) e206
32. Quigley D., Rodger P.M., Freeman C.L., Harding J.H., and Duffy D.M. J. Chem. Phys. 131 (2009) 094703
33. Barducci A., Chelli R., Procacci P., Schettino V., Gervasio F.L., and Parrinello M. J. Am. Chem. Soc. 128 (2006) 2705-2710
34. Biarnés X., Ardèvol A., Planas A., Rovira C., Laio A., and Parrinello M. J. Am. Chem. Soc. 129 (2007) 10686-10693
35. Spiwok V., and Tvaroška I. J. Phys. Chem. B 113 (2009) 9589-9594
36. Sega M., Autieri E., and Pederiva F. J. Chem. Phys. 130 (2009) 225102
37. Camilloni C., Provasi D., Tiana G., and Broglia R.A. Proteins 71 (2008) 1647-1654
38. Van Der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., and Berendsen H.J. J. Comput. Chem. 26 (2005) 1701-1718
39. glycam.ccrc.uga.edu.
40. Sorin E.J., and Pande V.S. Biophys. J. 88 (2005) 2472-2493
41. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., and Hermans J. Interaction Models for Water in Relation to Protein Hydration. In: Pullman B. (Ed). Intermolecular Forces (1981), D. Reidel Publishing, Dordrecht 331-342
42. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. J. Chem. Phys. 79 (1983) 926-935
43. Kirschner K.N., and Woods R.J. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 10541-10545
44. Spiwok V., and Tvaroška I. Carbohydr. Res. 344 (2009) 1575-1581
45. Lütteke T., Frank M., and von der Lieth C.W. Nucleic Acids Res. 33 (2005) D242-246
46. Guérin D.M.A., Lascombe M.-B., Costabel M., Souchon H., Lamzin V., Béguin P., and Alzari P.M. J. Mol. Biol. 316 (2002) 1061-1069
47. Money V.A., Smith N.L., Scaffidi A., Stick R.V., Gilbert H.J., and Davies G.J. Angew. Chem., Int. Ed. 45 (2006) 5136-5140
48. Kitago Y., Karita S., Watanabe N., Kamiya M., Aizawa T., Sakka K., and Tanaka Y. J. Biol. Chem. 282 (2007) 35703-35711
49. Varrot A., Frandsen T., Driguez H., and Davies G.J. Acta Crystallogr., Sect. D 58 (2002) 2201-2204
50. Zou J., Kleywegt G.J., Ståhlberg J., Driguez H., Nerinckx W., Claeyssens M., Koivula A., Teeri T.T., and Jones T.A. Structure 7 (1999) 1035-1045
51. Vandermarliere E., Bourgois T.M., Winn M.D., van Campenhout S., Volckaert G., Delcour J.A., Strelkov S.V., Rabijns A., and Courtin C.M. Biochem. J. 418 (2009) 39-47
52. Verdoucq L., Moriniére J., Bevan D.R., Esen A., Vasella A., Henrissat B., and Czjzek M. J. Biol. Chem. 279 (2004) 31796-31803
53. Mirza O., Skov L.K., Sprogøe D., van den Broek L.A.M., Beldman G., Kastrup J.S., and Gajhede M. J. Biol. Chem. 281 (2009) 35576-35584
54. van den Akker F., Feil I.K., Roach C., Platas A.A., Merritt E.A., and Hol W.G. Protein Sci. 6 (1997) 2644-2649
55. Kurihara Y., and Ueda K. Carbohydr. Res. 344 (2009) 2265-2269
56. Hansen H.S., and Hünenberger P.H. J. Comput. Chem. 31 (2009) 1-23
57. Suzuki T. Phys. Chem. Chem. Phys. 10 (2008) 96-105