Can current force fields reproduce ring puckering in 2-O-sulfo-α-l-iduronic acid? A molecular dynamics simulation study

Carbohydrate Research

Volumn 345, Issue 5, 2010, Pages 689-695

  Gandhi, Neha S ^a   Mancera, Ricardo L ^a,b  

^a CURTIN UNIVERSITY   (Australia)

^b CURTIN UNIVERSITY   (Australia)

Author keywords

GLYCAM; GROMOS; Iduronic acid; Molecular dynamics; Puckering

Indexed keywords

AQUEOUS SOLUTIONS; CONFORMATIONAL EQUILIBRIUM; CONFORMATIONAL FLEXIBILITY; CONFORMATIONAL TRANSITIONS; CURRENT FORCES; EQUILIBRIUM FLUCTUATION; FORCE FIELDS; GLYCAM; GLYCOSAMINOGLYCANS; GROMOS96; IDURONIC ACID; MOLECULAR DYNAMICS SIMULATIONS; PROTON NMR; RING-PUCKERING; ROTAMERS; SPC/E WATER; WATER POTENTIAL;

ACIDS; CARBOHYDRATES; DYNAMICS; GLUCOSE; MOLECULAR DYNAMICS; MOLECULAR MECHANICS;

BOATS;

2 O SULFO ALPHA IDURONIC ACID; IDURONIC ACID; UNCLASSIFIED DRUG;

AQUEOUS SOLUTION; ARTICLE; CARBOHYDRATE ANALYSIS; CHEMICAL BOND; CONFORMATIONAL TRANSITION; FORCE; MECHANICAL TORSION; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PREDICTION; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; SIMULATION; STRUCTURE ANALYSIS;

ELECTROMAGNETIC FIELDS; IDURONIC ACID; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; THERMODYNAMICS;

EID: 77649155701     PISSN: 00086215     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.carres.2009.12.020     Document Type: Article

References (57)

1. Varki A., Cummings R.D., Esko J.D., Freeze H.H., Hart G.W., and Etzler M.E. Essentials of Glycobiology. 2nd ed. (2009), CSHL Press, New York p. 784
2. Ferro D.R., Provasoli A., Ragazzi M., Casu B., Torri G., Bossennec V., Perly B., Sinay P., Petitou M., and Choay J. Carbohydr. Res. 195 (1990) 157-167
3. Mulloy B., Forster M.J., Jones C., and Davies D.B. Biochem. J. 293 (1993) 849-858
4. Ferro D.R., Provasoli A., Ragazzi M., Torri G., Casu B., Gatti G., Jacquinet J.C., Sinay P., Petitou M., and Choay J. J. Am. Chem. Soc. 108 (1986) 6773-6778
5. Ernst S., Venkataraman G., Sasisekharan V., Langer R., Cooney C.L., and Sasisekharan R. J. Am. Chem. Soc. 120 (1998) 2099-2107
6. Cremer D., and Pople J.A. J. Am. Chem. Soc. 97 (1975) 1354-1358
7. Massimo R., Dino R.F., and Augusto P. J. Comput. Chem. 7 (1986) 105-112
8. Jin L., Barran P.E., Deakin J.A., Lyon M., and Uhrin D. Phys. Chem. Chem. Phys. 7 (2005) 3464-3471
9. Zhang Z., McCallum S.A., Xie J., Nieto L., Corzana F., Jiménez-Barbero J.S., Chen M., Liu J., and Linhardt R.J. J. Am. Chem. Soc. 130 (2008) 12998-13007
10. Verli H., and Guimarães J.A. Carbohydr. Res. 339 (2004) 281-290
11. Becker C.F., Guimarães J.A., and Verli H. Carbohydr. Res. 340 (2005) 1499
12. Mikhailov D., Mayo K.H., Vlahov I.R., Toida T., Pervin A., and Linhardt R.J. Biochem. J. 318 (1996) 93-102
13. Angulo J., Nieto P.M., and Martín-Lomas M. Chem. Commun. (2003) 1512-1513
14. Mikhailov D., Linhardt R.J., and Mayo K.H. Biochem. J. 328 (1997) 51-61
15. Forster M.J., and Mulloy B. Biopolymers 33 (1993) 575-588
16. Murphy K.J., McLay N., and Pye D.A. J. Am. Chem. Soc. 130 (2008) 12435-12444
17. Pol-Fachin L., and Verli H. Carbohydr. Res. 343 (2008) 1435-1445
18. Woods R.J., Dwek R.A., Edge C.J., and Fraser-Reid B. J. Phys. Chem. 99 (1995) 3832-3846
19. van Gunsteren, W.; Billeter, S.; Eising, A.; Hünenberger, P.; Krüger, P.; Mark, A.; Scott, W.; Tironi, I. Biomolecular Simulations: the GROMOS96 Manual and User Guide, 1996.
20. Pieter, M. S. H.; Francisco, C.; Stefaan, D.; Dirk, A. T.; Koen, A.; José, C. M. J. Comput. Chem., in press.
21. 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
22. Berendsen H.J.C., Grigera J.R., and Straatsma T.P. J. Phys. Chem. 91 (1987) 6269-6271
23. William L.J., Jayaraman C., Jeffry D.M., Roger W.I., and Michael L.K. J. Chem. Phys. 79 (1983) 926-935
24. Gatti G., Casu B., Hamer G.K., and Perlin A.S. Macromolecules 12 (2002) 1001-1007
25. Lins R.D., and Hünenberger P.H. J. Comput. Chem. 26 (2005) 1400-1412
26. Ott K.-H., and Meyer B. J. Comput. Chem. 17 (1996) 1068-1084
27. Mulloy B., and Forster M.J. Glycobiology 10 (2000) 1147-1156
28. Seo M., Castillo N., Ganzynkowicz R., Daniels C.R., Woods R.J., Lowary T.L., and Roy P.-N. J. Chem. Theory Comput. 4 (2008) 184-191
29. Taha H.A., Castillo N., Roy P.-N., and Lowary T.L. J. Chem. Theory Comput. 5 (2009) 430-438
30. Basma M., Sundara S., Çalgan D., Vernali T., and Woods R.J. J. Comput. Chem. 22 (2001) 1125-1137
31. Jin, L. Ph.D. Thesis, University of Edinburgh, 2007.
32. Jin L., Hricovini M., Deakin J.A., Lyon M., and Uhrin D. Glycobiology (2009) cwp105
33. Wolfe S. Acc. Chem. Res. 5 (2002) 102-111
34. Kirschner K.N., and Woods R.J. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 10541-10545
35. Yongye A.B., Gonzalez-Outeiriño J., Glushka J., Schultheis V., and Woods R.J. Biochemistry 47 (2008) 12493-12514
36. Biarnes X., Ardevol A., Planas A., Rovira C., Laio A., and Parrinello M. J. Am. Chem. Soc. 129 (2007) 10686-10693
37. Sega M., Autieri E., and Pederiva F. J. Chem. Phys. 130 (2009) 225102
38. Spiwok V., and Tvaroska I. Carbohydr. Res. 344 (2009) 1575-1581
39. Hill A.D., and Reilly P.J. J. Chem. Inf. Model. 47 (2007) 1031-1035
40. Bérces A., Whitfield D.M., and Nukada T. Tetrahedron 57 (2001) 477-491
41. Tvaroska I., Hricovíni M., and Petráková E. Carbohydr. Res. 189 (1989) 359-362
42. Hricovíni M. Carbohydr. Res. 341 (2006) 2575-2580
43. Hricovíni M., and Bízik F. Carbohydr. Res. 342 (2007) 779-783
44. Schüttelkopf A.W., and Van Aalten D.M.F. Acta Crystallogr., Sect. D 60 (2004) 1355-1363
45. van der Spoel, D.; Lindahl, E.; Hess, B.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A.; Feenstra, K. A.; van Drunen, R. gromacs User Manual, 3.3; Department of Biophysical Chemistry, University of Groningen: Groningen, The Netherlands, 2006.
46. Case, D. A.; Darden, T. A.; Cheatham I, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. amber 9, University of California, San Francisco, 2006.
47. Tom D., Darrin Y., and Lee P. J. Chem. Phys. 98 (1993) 10089-10092
48. Berendsen H.J.C., Postma J.P.M., Gunsteren W.F.v., DiNola A., and Haak J.R. J. Chem. Phys. 81 (1984) 3684-3690
49. Huige C.J.M., and Altona C. J. Comput. Chem. 16 (1995) 56-79
50. Yongye, A.; Tessier, M.; Kawatkar, S.; Kirschner, K. N.; Tschampel, S.; Woods, R. J. Glycam_0f.dat: Woods Group (2005-2009). GLYCAM Web. Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 2008.
51. Bayly C.I., Cieplak P., Cornell W.D., and Kollman P.A. J. Phys. Chem. 97 (1993) 10269-10280
52. Pigache, A.; Cieplak, P.; Dupradeau, F. Y. In Automatic and Highly Reproducible RESP and ESP Charge Derivation: Application to the Development of Programs red and xred, 227th ACS National Meeting, Anaheim, CA, USA, Mar 28-Apr 1; Anaheim, CA, USA, 2004.
53. Woods R.J., and Chappelle R. J. Mol. Struct.: THEOCHEM 527 (2000) 149-156
54. Frisch, M. J. T. G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A. Jr.; 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.; 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, 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. gaussian 03, Revision C. 02, Gaussian, Gaussian, Inc.: Pittsburgh, PA, 2004.
55. Jeffrey G.A., and Yates J.H. Carbohydr. Res. 74 (1979) 319-322
56. Forster, M. J. mdxvu-Molecular Dynamics X11 Viewer. 0.95, 2005.
57. Haasnoot C.A.G., de Leeuw F.A.A.M., and Altona C. Tetrahedron 36 (1980) 2783-2792