The conformational free energy of carbohydrates

Mini-Reviews in Organic Chemistry

Volumn 8, Issue 3, 2011, Pages 256-262

  Kuttel, Michelle M ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

Carbohydrates; Dihedral angles; Free energy; Hydroxymethyl; Polysaccharides; Ring conformations

Indexed keywords

CONFORMATIONS; DIHEDRAL ANGLE; FREE ENERGY;

CARBOHYDRATES MOLECULES; CONFORMATIONAL FREE ENERGY; CONFORMATIONAL SPACE; ENERGY DETERMINATION; ENERGY STUDIES; FREE-ENERGY CALCULATIONS; HYDROXYMETHYL; METHOD AND TECHNIQUE; POSSIBLE FUTURES; RING CONFORMATIONS;

CARBOHYDRATES;

EID: 79959951675     PISSN: 1570193X     EISSN: None     Source Type: Journal    
DOI: 10.2174/157019311796197364     Document Type: Review

References (95)

1. Stenger, J.; Cowman, M.; Eggers, F.; Eyring, E. M.; Kaatze, U.; Petrucci, S. Molecular dynamics and kinetics of monosaccharides in solution. a broadband ultrasonic relaxation study. J. Phys. Chem. B 2000, 104, 4782-4790.
2. Polacek, R.; Stenger, J.; Kaatze, U. Chair-chair conformational flexibility, pseudorotation and exocyclic group isomerization of monosaccharides in water. J. Chem. Phys. 2002, 116(7), 2973-2982.
3. Haller, J.; Kaatze, U. Kinetics of conformer formation of glucose and maltose in aqueous solutions. Chem. Phys. Lett. 2008, 463(4-6), 413-417.
4. Lipkind, G. M.; Verovsky, V. E.; Kochetkov, N. K. Conformational states of maltose and cellobiose in solution: a comparison of calculated and experimental data. Carbohydr. Res. 1984, 133, 1-13.
5. Lipkind, G. M.; Shashkov, A. S.; Kochetkov, N. K. Nuclear Overhauser effect and conformational states of cellobiose in solution. Carbohydr. Res. 1985, 141, 191-197.
6. Shashkov, A. S.; Lipkind, G. M.; Kochetkov, N. K. Nuclear Overhauser effects for methyl b-maltoside and the conformational states of maltose in aqueous solution. Carbohydr. Res. 1986, 147, 175-182.
7. Cumming, D. A.; Carver, J. P. Virtual and solution conformations of oligosaccharides. Biochemistry 1987, 26, 6664-6676.
8. Lütteke, T.; von der Lieth, C.-W. pdb-care (PDB Carbohydrate Residue check): a program to support annotation of complex carbohydrate structures in PDB files. BMC Bioinformatics 2004, 5.
9. Lütteke, T.; M. F.; von der Lieth, C.-W. Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. Nucleic Acids Res. 2005, 33, D242-D246.
10. Cross, S.; Kuttel, M. M.; Stone, J. E.; Gain, J. E. Visualisation of cyclic and multi-branched molecules with VMD. J. Mol. Graph. Modell. 2009, 28, 131-139.
11. Brady, J. W.; Schmidt, R. K. The role of hydrogen bonding in carbohydrates: molecular dynamics simulations of maltose in aqueous solution. J. Phys. Chem. 1993, 97, 958-966.
12. Astley, T.; Birch, G. G.; Drew, M. G. B.; Rodger, P. M. Lifetime of a hydrogen bond in aqueous solutions of carbohydrates. J. Phys. Chem. 1999, 103, 5080-5090.
13. Engelsen, S. B.; Pérez, S. Unique similarity of the asymmetric trehalose solid-state hydration and the diluted aqueous-solution hydration. J. Phys. Chem. B 2000, 104, 9301-9311.
14. Kuttel, M. M.; Naidoo, K. J. Free energy surfaces for the a(1 4)-glycosidic linkage: Implications for polysaccharide solution structure and dynamics. J. Phys. Chem. B 2005, 109, 7468-7474.
15. Kuttel, M. M.; Naidoo, K. J. Ramachandran free-energy surfaces for disaccharides: trehalose, a case study. Carbohydr. Res. 2005, 340, 875-879.
16. Momany, F. A.; Willet, J. L. Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose configurations. J. Comput. Chem. 2000, 21(13), 1204-1219.
17. Strati, G. L.; Willet, J. L.; Momany, F. A. Ab initio computational study of bcellobiose conformers using B3LYP/6-311++G**. Carbohydr. Res. 2003, 337, 1833-1849.
18. 3, O boats and skew-boat conformations. Carbohydr. Res. 2004, 339, 537-551.
19. Schnupf, D.; Willet, J. L.; Bosma, W. B.; Momany, F. A. DFT studies of the disaccharide, a-maltose: relaxed isopotential maps. Carbohydr. Res. 2007, 342, 2270-2285.
20. 1 to skew conformations of β-D-glucopyranose. Carbohydr. Res. 2009, 344, 2266-2269.
21. Ha, S. N.; Madsen, L. J.; Brady, J. W. Conformational analysis and molecular dynamics simulations of maltose. Biopolymers 1988, 27, 1927-1952.
22. Brady, J.W. Molecular dynamics simulations of β-D-glucose in aqueous solution. J. Am. Chem. Soc. 1989, 111, 5155-5165.
23. French, A. D. Comparisons of rigid and relaxed conformational maps of maltose and cellobiose. Carbohydr. Res. 1989, 188, 206-211.
24. Dowd, M. K.; French, A. D.; Reilly, P. J. Conformational analysis of the anomeric forms of sophorose, laminarabiose and cellobiose using MM3. Carbohydr. Res. 1992, 233, 15-34.
25. Hardy, B.; Sarko, A. Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers. J. Comput. Chem. 1993, 14 (7), 831-847.
26. Glennon, T. M.; Zheng, Y.; le Grand, S. M.; Shutzberg, B. A.; Merz, K. M. J. A Force field for monosaccharides and (1AA4) linked polysaccharides. J. Comput. Chem. 1994, 15(9), 1019-1040.
27. Naidoo, K. J.; Brady, J. W. The application of simulated annealing to the conformational analysis of disaccharides. Chem. Phys. 1997, 224, 261-273.
28. Naidoo, K. J.; Kuttel, M. Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations. J. Comput. Chem. 2001, 22(4), 445-456.
29. Best, R. B.; Jackson, G. E.; Naidoo, K. J. Molecular dynamics and NMR study of the a(1ss4) and a(1446) glycosidic linkages: maltose and isomaltose. J. Phys. Chem. B 2001, 105, 4742-4751.
30. Ueda, K.; Iwama, K.; Nakayama, H. Molecular dynamics simulation of neocarrabiose 2,4 '-bis(sulfate) and carrabiose 4',2-bis(sulfate) as building blocks of l-carrageenan in water. Bull. Chem. Soc. Jpn. 2001, 74(12), 2269-2277.
31. Corzana, F.; Motawia, M. S.; Penhoat, C. H. D.; Pérez, S.; Tschampel, S. M.; Woods, R. J.; Engelsen, S. B. A hydration study of (1→4) and (1→6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR. J. Comput. Chem. 2004, 25(4), 573-586.
32. Venter, G. A.; Matthews, R. P.; Naidoo, K. J. Conformational flexibility of sulphur linked saccharides a possible key to their glycosidase inhibitor activity. Mol. Simulat. 2008, 34(4), 391-401.
33. Kuttel, M.; Brady, J. W.; Naidoo, K. J. Carbohydrate solution simulations: producing a force field with experimentally consistent hydroxyl rotational frequencies. J. Comput. Chem. 2002, 23(13), 1236-1243.
34. Banavali, N. K.; Alexander D. MacKerell, J. Characterizing structural transitions using localized free energy landscape analysis. Plos One 2009, 4(5), e5525.
35. Autieri, E.; Sega, M.; Pederiva, F. Puckering free energy of pyranoses using a combined metadynamics-umbrella aampling approach. ArXiv e-prints 2010.
36. Landstrom, J.; Widmalm, G. Glycan flexibility: insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect. Carbohydr. Res. 2010, 345, 330-333.
37. Leach, A. R. Molecular modelling. Principles and applications. Addison Wesley Longman Limited, 1996.
38. Kollman, P. Free energy calculations: applications to chemical and biological phenomena. Chem. Rev. 1993, 93, 2395-2417.
39. Park, S.; Khalili-Araghi, F.; Tajkhorshid, E.; Schulten, K. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. J. Chem. Phys. 2003, 119, 3559-3566.
40. Green, D. F. Optimized parameters for continuum solvation calculations with carbohydrates. J. Phys. Chem. B 2008, 112, 5238-5249.
41. DeMarco, M. L.; Woods, R. J. Structural glycobiology: A game of snakes and ladders. Glycobiology 2008, 18(6), 426-440.
42. Hansen, H. S.; Hünenberger, P. H. Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free fnergies and interconversion barriers of glucopyranose ring conformers in water. J. Comput. Chem. 2009, 31(1), 1-23.
43. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The weighted histogram analysis method for free energy calculations on biomolecules. I. The method. J. Comput. Chem. 1992, 13(8); 1011-1021.
44. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. Multidimensional free-energy calculations using the weighted histogram analysis method. J. Comput. Chem. 1995, 16(11), 1339-1350.
45. Kumar, S.; Payne, P.W.; Vasquez, M. Method for free-energy calculations using iterative techniques. J. Comput. Chem. 1996, 17(10), 1269-1275.
46. Darve, E.; Pohorille, A. Calculating free energies using average force. J. Chem. Phys. 2001, 115, 9169.
47. Biarnés, X.; Ardèvol, A.; Planas, A.; Rovira, C.; Laio, A.; Parrinello, M. The conformational free energy landscape of β-D-glucopyranose. Implications for substrate preactivation in b-glucoside hydrolases. J. Am. Chem. Soc. 2007, 129, 10686-10693.
48. Spiwok, V.; Tvaroška, I. Conformational free energy surface of a-N-acetylneuraminic acid: An interplay between hydrogen bonding and solvation. J. Phys. Chem. B 2009, 113, 9589-9594.
49. Spiwok, V.; Králová, B.; Tvaroška, I. Modelling of β-D-glucopyranose ring distortion in diff erent force fields: A metadynamics study. Carbohydr. Res. 2010, 345, 530-537.
50. Dickson, B. M.; Legoll, F.; Lelièvre, T.; Stoltz, G.; Fleurat-Lessard, P. Free energy calculations: An efficient adaptive biasing potential method. J. Phys. Chem. B 2010, 114(17); 5823-5830.
51. Hénin J, Fiorin, G.; Chipot, C.; Klein, M. L. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables. J. Chem. Theory Comput. 2010, 6, 35-47.
52. Sega, M.; Autieri, E.; Pederiva, F. On the calculation of puckering free energy surfaces. J. Chem. Phys. 2009, 130, 225102-2.
53. Spiwok, V.; Lipovová, P.; Králová, B. Metadynamics in essential coordinates: Free energy simulation of conformational changes. J. Phys. Chem. B 2007, 111(12), 3073-3076.
54. Spiwok, V.; Králová, B.; Tvaroška, I. Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes. J. Mol. Model. 2008, 14, 995-1002.
55. Kirschner, K.; Yongye, A.; Tschampel, S.; Gonzalez-Outeirino, J.; Daniels, C.; Foley, B.; Woods, R. GLYCAM06: A generalizable biomolecular force field for carbohydrates. J. Comput. Chem. 2008, 29, 622-655.
56. Kony, D.; Damm, W.; Stoll, S.; van Gunsteren, W. F. An improved OPLSAA force field for carbohydrates. J. Comput. Chem. 2002, 23(15), 1416-1429.
57. Lins, R. D.; Hünenberger, P. H. A new GROMOS force field for hexopyranose-based carbohydrates. J. Comput. Chem. 2005, 26(13), 1400-1412.
58. Guvench, O.; Greene, S. N.; Kamath, G.; Brady, J. W.; Venable, R. M.; Pastor, R. W.; MacKerell, A. D. Additive empirical force field for hexopyranose monosaccharides. J. Comput. Chem. 2008, 29(15), 2543-2564.
59. Hatcher, E.; Guvench, O.; MacKerell, Jr., A. D. CHARMM additive all-atom force field for acyclic polyalcohols, acyclic carbohydrates, and inositol. J. Chem. Theory Comput. 2009, 5(5), 1315-1327.
60. Hatcher, E.; Guvench, O.; MacKerell, Jr., A. D. CHARMM Additive allatom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J. Phys. Chem. B 2009, 113(37), 12466-12476.
61. Guvench, O.; Hatcher, E.; Venable, R. M.; Pastor, R. W.; Alexander D. MacKerell, J. CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses. J. Chem. Theory Comput. 2009, 5(9), 2353-2370.
62. Tschampel, S. M.; Kirschner, K. N.; Woods, R. J. Incorporation of carbohydrates into macromolecular force fields: Development and validation. 2006.
63. Stortz C. A.; Johnson, G. P.; French, A. D.; Csonka, G. I. Comparison of different force fields for the study of disaccharides. Carbohydr. Res. 2009, 344, 2217-2228.
64. López, C. A.; Rzepiela, A. J.; de Vries, A. H.; Dijkhuizen, L.; Hunenberger, P. H.; Marrink, S. J. Martini coarse-grained force field: Extension to carbohydrates. J. Chem. Theory Comput. 2009, 5(12); 3195-3210.
65. Coskuner, O.; Bergeron, D. E.; Rincon, L.; Hudgens, J. W.; Gonzalez, C. A. Glycosidic linkage conformation of methyl-a-mannopyranoside. J. Chem. Phys. 2008, 129(4), 045102.
66. Coskuner, O. Preferred conformation of the glycosidic linkage of methyl-bmannose. J. Chem. Phys. 2007, 127(1), 015101.
67. Marszalek, P. E.; Oberhauser, A. F.; Pang, Y.-P.; Fernandez, J. M. Polysaccharide elasticity governed by chair-boat transitions of the glucopyranose ring. Nature 1998, 396, 661-664.
68. Zhang, Q.; Lee, G.; Marszalek, P. E. Atomic cranks and levers control sugar ring conformations. J. Phys.:Condens. Matter 2005, 17, S1427-S1442.
69. Kuttel, M.; Naidoo, K. J. Glycosidic linkage rotations determine amylose stretching mechanism. J. Am. Chem. Soc. 2005, 127, 12-13.
70. Houston, D. R.; Recklies, A. D.; Krupa, J. C.; van Aalten, D. M. F. Structure and ligand-induced conformational change of the 39-kDa glycoprotein from human articular chondrocytes. J. Biol. Chem. 2003, 278(32); 30206-30212.
71. Davies, G.; Ducros, V.-A.; Varrot, A.; Zechel, D. Mapping the conformational itinerary of b-glycosidases by X-ray crystallography. Biochem. Soc. Trans. 2003, 31, 523-527.
72. Cremer, D.; Pople, J. A. A general definition of ring puckering coordinates. J. Am. Chem. Soc. 1975, 97(6), 1354-1358.
73. Hill, A. D.; Reilly, P. J. Puckering coordinates of monocyclic rings by triangular decomposition. J. Chem. Inf. Model. 2007, 47, 1031-1035.
74. Barnett, C. B.; Naidoo, K. J. Free energies from adaptive reaction coordinate forces (FEARCF): an application to ring puckering. Mol. Phys. 2009, 107, 8-12.
75. Rees, D. A. Conformational analysis of polysaccharides. Part V. The characterisation of linkage conformations (chain conformations) by optical rotation at a single wavelength. J. Chem. Soc. B 1970, 877-887.
76. Gandhi, N. S.; Mancera, R. L. Can current force fields reproduce ring puckering in 2-O-sulfo-a-L-iduronic acid? A molecular dynamics simulation study. Carbohydr. Res. 2010, 345, 689-695.
77. Babin, V.; Sagui, C. Conformational free eneries of methyl-a-L-iduronic and methyl-B-D-glucuronic acids in water. J. Chem. Phys. 2010, 132, 104108.
78. Brant, D. A. Shapes and motions of polysaccharide chains. Pure Appl. Chem. 1997, 69(9), 1885-1892.
79. Engelsen, S. B.; Cros, S.; Mackie, W.; Pérez, S. A molecular builder for carbohydrates: Application to polysaccharides and complex carbohydrates. Biopolymers 1996, 39(3), 417-433.
80. Xia, J.; Daly, R. P.; Chuang, F.-C.; Parker, L.; Jensen, J. H.; Margulis, C. J. Sugar Folding: A novel structural prediction tool for oligosaccharides and polysaccharides 1. J. Chem. Theory Comput. 2007, 3(4), 1620-1628.
81. Xia, J.; Daly, R. P.; Chuang, F.-C.; Parker, L.; Jensen, J. H.; Margulis, C. J. Sugar folding: A novel structural prediction tool for oligosaccharides and polysaccharides 2. J. Chem. Theory Comput. 2007, 3(4), 1629-1643.
82. Fernandes, C. L.; Sachett, L. G.; Pol-Fachin, L.; Verli, H. GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins. Carbohydr. Res. 2010, 345, 663-671.
83. Brant, D. A.; Dimpfl, W. L. A theoretical interpretation of the aqueous solution properties of amylose and its derivatives. Macromolecules 1970, 3(5), 655-665.
84. Stortz, C. A. Potential energy surfaces of carrageenan models: carrabiose, b (1→4)-linked D-galactobiose, and their sulfated derivatives. Carbohydr. Res. 2002, 337, 2311-2323.
85. Perico, A.; Mormino, M.; Urbani, R.; Cesàro, A.; Tylianakis, E.; Dais, P.; Brant, D. A. Local dynamics of carbohydrates. 1. Dynamics of simple glycans with different chain linkages. J. Phys. Chem. B 1999, 103, 8162-8171.
86. Gouvion, C.; Mazeau, K.; Tvaroška, I. The role of chemical structure on the stereochemistry of the a-(1-4) diaxial glycosidic linkage. J. Mol. Struct. (Theochem) 1995, 344, 157-170.
87. Stortz, C. A.; French, A. D. Disaccharide conformational maps: adiabaticity in analogues with variable ring shapes. Mol. Simul. 2008, 34(4), 373-389.
88. Immel, S.; Lichtenthaler, F. W. The conformation of sucrose in water: a molecular dynamics approach. Liebigs Ann. 1995, 1925-1937.
89. Ha, S. N.; Giammona, A.; Field, M.; Brady, J. W. A revised potential-energy surface for molecular studies of carbohydrates. Carbohydr. Res. 1988, 180, 207-221.
90. Schmidt, R. K.; Teo, B.; Brady, J. W. Use of umbrella sampling in the calculation of the potential of mean force for maltose in vacuum from molecular dynamics simulations. J. Phys. Chem 1995, 99, 11339-11343.
91. Naidoo, K. J.; Brady, J. W. Calculation of the Ramachandran potential of mean force for a disaccharide in aqueous solution. J. Am. Chem. Soc. 1999, 121(10), 2244-2252.
92. Ueda, K.; Brady, J. W. The conformational free-energy map for solvated neocarrabiose. Carbohydr. Res. 2004, 339, 1953-1960.
93. Kuttel, M. M. Carbohydrate conformational dynamics and thermodynamics. Ph.D. thesis, University of Cape Town, 2003.
94. Kuttel, M. M. Conformational free energy maps for globobiose (a-D-Gal-(1→4)-b-D-Gal) in implicit and explict aqueous solution. Carbohydr. Res. 2008, 343(6); 1091-1098.
95. Campen, R. K.; Verde, A. V.; Kubicki, J. D. Influence of glycosidic linkage neighbors on disaccharide conformation in vacuum. J. Phys. Chem. B 2007, 111, 13775-13785.