The application of molecular modeling techniques to the determination of oligosaccharide solution conformations

Reviews in Computational Chemistry

Volumn 9, Issue , 1996, Pages 129-165

  Woods, Robert J ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGOSACCHARIDES;

MACROMOLECULAR FORCE FIELD; MOLECULAR MODELING TECHNIQUES; SOLUTION CONFORMATIONS;

MOLECULAR MODELING;

EID: 0030520310     PISSN: 10693599     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (160)

1. T. W. Rademacher, R. B. Parekh, and R. A. Dwek, Annu. Rev. Biochem., 57, 785 (1988). Glycobiology.
2. A. Varki, Glycobtology, 3, 97 (1993). Biological Roles of Oligosaccharides: All of the Theories Are Correct.
3. J.-R. Brisson, H. Baumann, A. Imberty, S. Pérez, and H. J. Jennings, Biochemistry, 31, 4996 (1992). Helical Epitope of the Group B Meningococcal α(2-8)-Linked Sialic Acid Polysaccharide.
4. J. Hayrinen, D. Bitter-Suermann, and J. Finne, Mol. Immun., 26, 523 (1989). Interaction of Meningococcal Group B Monoclonal Antibody and Its Fab Fragment with α2-8-Linked Sialic Acid Polymers: Requirement of a Long Oligosaccharide Segment for Binding.
5. M. R. Wessels, V. Pozsgay, D. L. Kasper, and H. J. Jennings, J. Biol. Chem., 262, 8262 (1987). Structure and Immunochemistry of an Oligosaccharide Repeating Unit of the Capsular Polysaccharide of Type III Group B Streptococcus.
6. D. A. Gumming and J. P. Carver, Biochemistry, 26, 6664 (1987). Virtual and Solution Conformations of Oligosaccharides.
7. L. Poppe and H. van Halbeek, J. Am. Chem. Soc., 113, 363 (1991). Nuclear Magnetic Resonance of Hydroxyl and Amido Protons of Oligosaccharides in Aqueous Solution: Evidence for a Strong Intramolecular Hydrogen Bond in Sialic Acid Residues.
8. L. Poppe and H. van Halbeek, Nature, Struct. Biol., 1, 215 (1994). NMR Spectroscopy of Hydroxyl Protons in Supercooled Carbohydrates.
9. A. Imberty, K. D. Hardman, J. P. Carver, and S. Pérez, Glycobiology, 1, 631 (1991). Molecular Modeling of Protein-Carbohydrate Interactions. Docking of Monosaccharides in the Binding Site on Concanavalin A.
10. W. I. Weis, K. Drickamer, and W. A. Hendrickson, Nature, 360, 127 (1992). Structure of a C-Type Mannose-Binding Protein Complexed with an Oligosaccharide.
11. Y. Bourne, P. Rougé, and C. Cambillau, J. Biol. Chem., 267, 197 (1992). X-Ray Structure of a Biantennary Octasaccharide-Lectin Complex Refined at 2.3-Å Resolution.
12. S. Pérez, A. Imberty, and J. P. Carver, Adv. Comput. Biol., 1, 147 (1994). Molecular Modeling: An Essential Component in the Structure Determination of Oligosaccharides and Polysaccharides.
13. D. A. Pearlman and P. A. Kollman, in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, W. F. van Gunsteren and P. K. Weiner, Eds., ESCOM, Leiden, 1989, pp. 101ff. Free Energy Perturbation Calculations: Problems and Pitfalls Along the Gilded Road.
14. 3 in the Gas Phase.
15. W. F. van Gunsteren, in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, W. F. van Gunsteren and P. K. Weiner, Eds., ESCOM, Leiden, 1989, pp. 27ff. Methods for Calculation of Free Energies and Binding Constants: Successes and Problems.
16. T. P. Straatsma, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 9, pp. 81-127. Free Energy by Molecular Simulation.
17. 2YH Molecules.
18. W. A. Szarek and D. Horton, Eds., Anomeric Effect: Origin and Consequences, ACS Symposium Series 87, American Chemical Society: Washington, DC, 1979.
19. I. Tvaroska and T. Bleha, Adv. Carbohydr. Chem. Biochem., 47, 45 (1989). Anomeric and Exo-Anomeric Effects in Carbohydrate Chemistry.
20. For a discussion of basis sets, see, for example, D. Feller and E. R. Davidson, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 1-43. Basis Sets for Ab Initio Molecular Orbital Calculations and Intermolecular Interactions.
21. C. W. Andrews, B. Fraser-Reid, and J. P. Bowen, J. Am. Chem. Soc., 113, 8293 (1991). An Ab Initio Study (6-31G*) of Transition States in Glycoside Hydrolysis Based on Axial and Equatorial 2-Methoxytetrahydropyrans.
22. N. L. Allinger, M. Rahman, and J.-H. Lii, J. Am. Chem. Soc., 112, 8293 (1990). A Molecular Mechanics Force Field (MM3) for Alcohols and Ethers.
23. W. Caminati and C. Giorgio, J. Mol. Spectrosc., 90, 572 (1981). Conformation of Ethylene Glycol from the Rotational Spectra of the Nontunneling O-Monodeuterated Species.
24. R. G. Snyder and G. Zerbi, Spectrochim. Acta, 23A, 391 (1967). Vibrational Analysis of Ten Simple Aliphatic Ethers: Spectra, Assignments, Valence Force Field and Molecular Conformations.
25. T. M. Connor and K. A. McLaughlin, J. Phys. Chem., 69, 1888 (1965). High Resolution Nuclear Magnetic Resonance Studies of the Chain Conformation of Polyethylene Oxide.
26. 1H-NMR Studies of (6R)- and (6S)-Deuterated D-Hexoses: Assignment of the Preferred Rotamers About C5-C6 Bond of D-Glucose and D-Galactose Derivatives in Solutions.
27. 2H,)-2-Acetamido-2-deoxy-D-glucopyranose and Conformational Analysis of 2-Acetamido-2-deoxy-D-glucopyranose.
28. 1H-NMR Studies of (6R)- and (6S;-Deuterated (1-6)-Linked Disaccharides: Assignment of the Preferred Rotamers about C5-C6 Bond of (1-6)-Disaccharides in Solution.
29. C. J. Cramer and D. G. Truhlar, J. Am. Chem. Soc., 115, 5745 (1993). Quantum Chemical Conformational Analysis of Glucose in Aqueous Solution.
30. See also, C. J. Cramer and D. G. Truhlar, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1995, Vol. 6, pp. 1-72. Continuum Solvation Models: Classical and Quantum Mechanical Implementations.
31. J. W. Brady, J. Am. Chem. Soc., 108, 8153 (1986). Molecular Dynamics Simulations of α-D-Glucose.
32. L. M. J. Kroon-Batenburg and J. Kroon, Biopolymers, 29, 1243 (1990). Solvent Effect on the Conformation of the Hydroxymethyl Group Established by Molecular Dynamics Simulations of Methyl-β-D-Glucoside in Water.
33. N. L. Allinger, Y. H. Yuh, and J.-H. Lii, J. Am. Chem. Soc., 111, 8551 (1989). Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 1.
34. G. A. Jeffrey and H. Maluszynska, Int. J. Quantum Chem., Quantum Biol. Symp., 8, 231 (1981). Hydrogen-Bonding Geometry and Patterns in Carbohydrates and Amino Acids.
35. G. A. Jeffrey, in Molecular Structure and Biological Activity, J. F. Griffin and W. L. Duax, Eds., Elsevier Science Publishing, New York, 1982, pp. 135-150. Hydrogen Bonding in Amino Acids and Carbohydrates.
36. G. A. Jeffrey and J. Mitra, Acta Crystallogr., 39, 469 (1983). The Hydrogen-Bonding Patterns in the Pyranose and Pyranoside Crystal Structures.
37. A. D. French and J. W. Brady, in Computer Modeling of Carbohydrate Molecules, A. D. French and J. W. Brady, Eds., ACS Symposium Series 430, American Chemical Society, Washington, DC, 1990, pp. 1-19. Computer Modeling of Carbohydrate Molecules: An Introduction.
38. M. Khalil, R. J. Woods, D. F. Weaver, and V. H. Smith Jr., J. Comput. Chem., 12, 584 (1990). An Examination of Intermolecular and Intramolecular Hydrogen Bonding in Biomolecules by AM1 and MNDO/M Semiempirical Methodologies.
39. P. L. Polavarapu and C. S. Ewig, J. Comput. Chem., 13, 1255 (1992). Ab Initio Computed Molecular Structures and Energies of the Conformers of Glucose.
40. Y. Bourne, H. van Tilbeurgh, and C. Cambillau, Curr. Opinion Struct. Biol., 3, 681 (1993). Protein-Carbohydrate Interactions.
41. ∝ Oligosaccharide.
42. D. R. Bundle and N. M. Young, Curr. Opin. Struct. Biol., 2, 666 (1992). Carbohydrate-Protein Interactions in Antibodies and Lectins.
43. B. Shaanan, H. Lis, and N. Sharon, Science, 254, 862 (1991). Structure of a Legume Lectin with an Ordered N-Linked Carbohydrate in Complex with Lactose.
44. N. K. Vyas, M. N. Vyas, and F. A. Quiocho, J. Biol. Chem., 266, 5226 (1991). Comparison of the Periplasmic Receptors for L-Arabinose, D-Glucose/D-Galactose, and D-Ribose.
45. R. J. Woods, C. J. Edge, M. R. Wormald, and R. A. Dwek, in Complex Carbohydrates in Drug Research, K. Bock, H. Clausen, P. Krogsgaard-Larsen, and H. Kofod, Eds., Munksgaard, Copenhagen, 1994, pp. 15-29. GLYCAM_93: A Generalized Parameter Set for Molecular Dynamics Simulations of Glycoproteins and Oligosaccharides. Application to the Structure and Dynamics of a Disaccharide Related to Oligomannose.
46. R. J. Woods, C. J. Edge, and R. A. Dwek, in Modeling the Hydrogen Bond, D. A. Smith, Ed., ACS Symposium Series 569, American Chemical Society, Washington, DC, 1994, pp. 252-268. The Role of Nonbonded Interactions in Determining the Solution Conformations of Oligosaccharides.
47. K. Bock, Pure Appl. Chem., 55, 605 (1983). The Preferred Conformation of Oligosaccharides in Solution Inferred from High Resolution NMR Data and Hard Sphere ExoAnomeric Calculations.
48. H. Thøgersen, R. U. Lemieux, K. Bock, and B. Meyer, Can. J. Chem., 60, 44 (1982). Further Justification for the Exo-anomeric Effect. Conformational Analysis Based on Nuclear Magnetic Resonance Spectroscopy of Oligosaccharides.
49. I. Pettersson and T. Liljefors, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 9., pp. 167-189. Molecular Mechanics Calculated Conformational Energies of Organic Molecules: A Comparison of Force Fields.
50. S. W. Homans, Biochemistry, 29, 9110 (1990). A Molecular Mechanical Force Field for the Conformational Analysis of Oligosaccharidees: Comparison of Theoretical and Crystal Structures of Manα(1-3)Manβ(1-4)GlcNAc.
51. R. J. Woods, R. A. Dwek, C. J. Edge, and B. Fraser-Reid, J. Phys. Chem., 99, 3832 (1995). Molecular Dynamics Simulations of Glycoproteins and Oligosaccharides. 1. GLYCAM_93 Parameter Development.
52. K. Rasmussen, Acta Chem. Scand., A36, 323 (1982). Conformation and Anomer Ratio of D-Glucopyranose in Different Potential Energy Functions.
53. S. N. Ha, A. Giammona, M. Field, and J. W. Brady, Carbohydr. Res., 180, 207 (1988). A Revised Potential-Energy Surface for Molecular Mechanics Studies of Carbohydrates.
54. M. Prabhakaran and S. C. Harvey, Biopolymers, 26, 1087 (1987). Asymmetric Oscillations in Cyclodextrin - A Molecular Dynamics Study.
55. M. Clark, R. D. Cramer III, and N. Van Opdenbosch, J. Comput. Chem., 10, 982 (1989). Validation of the General Purpose Tripos 5.2 Force Field.
56. A. T. Hagler, S. Lifson, and P. Dauber, J. Am. Chem. Soc., 101, 5122 (1979). Consistent Force Field Studies of Intermolecular Forces in Hydrogen-Bonded Crystals. 2. A Benchmark for the Objective Comparison of Alternative Force Fields.
57. M. Dauchez, J. Mazurier, J. Montreuil, and G. Vergoten, Biochemie, 74, 63 (1992). Molecular Dynamics Simulations of a Monofucosylated Biantennary Glycan of the N-Acetyllactosamine Type: The Human Lactotransferrin Glycan.
58. P. V. Balaji, P. K. Qasba, and V. S. R. Rao, Biochemistry, 32, 12599 (1993). Molecular Dynamics Simulations of Asialoglycoprotein Receptor Ligands.
59. J. L. Asensio, R. López, A. Fernández-Mayoralas, and J. Jiménez-Barbero, Tetrahedron, 50, 6417 (1994). Conformational Studies on β-Galactopyranosyl-(1-3) and (1-4)-Xylopyranosides by NMR, Molecular Mechanics, Molecular Dynamics, and Semiempirical Calculations.
60. F. A. Momany, R. F. McGuire, A. W. Burgess, and H. A. Scheraga, J. Phys. Chem., 79, 2361 (1975). Energy Parameters in Polypeptides. VII. Geometric Parameters, Partial Atomic Charges, Nonbonded Interactions, Hydrogen Bond Interactions, Intrinsic Torsion Potentials for the Naturally Occurring Amino Acids.
61. A. I. Kitaygorodsky, Tetrahedron, 14, 230 (1961). The Interaction Curve of Non-Bonded Carbon and Hydrogen Atoms and Its Application.
62. G. A. Jeffrey, J. A. Pople, J. S. Binkley, and S. Vishveshwara, J. Am. Chem. Soc., 100, 373 (1978). Application of Ab Initio Molecular Orbital Calculations to the Structural Moieties of Carbohydrates.
63. R. U. Lemieux and S. Koto, Tetrahedron, 30, 1933 (1974). The Conformational Properties of Glycosidic Linkages.
64. 1H-NMR and HSEA Calculation.
65. R. U. Lemieux, K. Bock, L. T. J. Delbaere, S. Koto, and V. S. Rao, Can. J. Chem., 58, 631 (1980). The Conformations of Oligosaccharides Related to the ABH and Lewis Human Blood Group Determinants.
66. D. Neuhaus and M. P. Williamson, The Nuclear Oberhauser Effect in Structural and Conformational Analysis, VCH Publishers, New York, 1989.
67. L. Poppe and H. van Halbeek, J. Am. Chem. Soc., 114, 1092 (1992). The Rigidity of Sucrose: Just an Illusion?
68. I. Tvaroška and S. Pérez, Carbohydr. Res., 149, 389 (1986). Conformational-Energy Calculations for Oligosaccharides: A Comparison of Methods and a Strategy of Calculation.
69. 1.
70. R. J. Woods, W. A. Szarek, and V. H. Smith Jr., J. Chem. Soc. Chem. Commun., 334 (1991). A Comparison of Semiempirical and Ab Initio Methods for the Study of Structural Features of Relevance in Carbohydrate Chemistry.
71. H. Paulsen, T. Peters, V. Sinnwell, R. Lebhun, and B. Meyer, Liebigs Ann. Chem., 951 (1984). Bestimmung der Konformationen von Tri- und Tetrasaccharid-Sequenzen der Core-Strukrur von N-Glycoproteinen. Problem der (1-6)-glycosidischen Bindung.
72. L. Poppe, R. Stuike-Prill, B. Meyer, and H. van Halbeek, J. Biomol. NMR, 2, 109 (1992). The Solution Conformation of Sialyl-α-(2-6)-Lactose Studied by Modern NMR Techniques and Monte Carlo Simulations.
73. K. B. Wiberg and M. A. Murcko, J. Am. Chem. Soc., 111, 4821 (1989). Rotational Barriers. 4. Dimethoxymethane. The Anomeric Effect Revisited.
74. W. Mackie, B. Sheldrick, D. Akrigg, and S. Pérez, Int. J. Biol. Macromol. 8, 43 (1986). Crystal and Molecular Structure of Mannotriose and Its Relationship to the Conformations and Packing of Mannan and Glucomannan Chains and Mannobiose.
75. S. Diner, J. P. Malrieu, and P. Claverie, Theor. Chim. Acta, 13, 1 (1969). Localized Bond Orbitals and the Correlation Problem.
76. P. S. Epstein, Phys. Rev., 28, 695 (1926). The Stark Effect from the Point of View of Schroedinger's Quantum Theory.
77. R. K. Nesbet, Proc. Roy. Soc. London A, 230, 312 (1955). Configuration Interaction in Orbital Theories.
78. R. Potenzone Jr. and A. J. Hopfinger, Carbohydr. Res., 40, 323 (1975). Conformational Analysis of Glycosaminoglycans. I. Charge Distributions, Torsional Potentials, and Steric Maps.
79. D. A. Cumming and J. P. Carver, Biochemistry, 26, 6676 (1987). Reevaluation of Rotamer Populations for 1,6-Linkages: Reconciliation with Potential Energy Calculations.
80. 2OH.
81. T. Peters, B. Meyer, R. Stuike-Prill, R. Somorjai, and J.-R. Brisson, Carbohydr. Res., 238, 49 (1993). A Monte Carlo Method for Conformational Analysis of Saccharides.
82. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys., 21, 1087 (1953). Equation of State Calculations by Fast Computing Machines.
83. T. Weimar, B. Meyer, and T. Peters, J. Biomol. NMR, 3, 399 (1993). Conformational Analysis of α-D-Fuc-(1-4)-β-D-GlcNAc-OMe. One-Dimensional Transient NOE Experiments and Metropolis Monte Carlo Simulations.
84. 1H-NMR Spectroscopy in Combination with Energy Calculations by Hard-Sphere Exo-Anomeric and Molecular Mechanics Force-Field with Hydrogen-Bonding Potential.
85. 2 Torsional Terms.
86. G. A. Jeffrey and R. Taylor, J. Comput. Chem., 1, 99 (1980). The Application of Molecular Mechanics to the Structures of Carbohydrates.
87. L. Norskov-Lauritsen and N. L. Allinger, J. Comput. Chem., 5, 326 (1984). A Molecular Mechanics Treatment of the Anomeric Effect.
88. J. P. Bowen, A. Pathiaseril, S. Profeta Jr., and N. L. Allinger, J. Am. Chem. Soc., 52, 5162 (1987). New Molecular Mechanics (MM2) Parameters for Ketones and Aldehydes.
89. J. P. Bowen, V. V. Reddy, D. G. Patterson Jr., and N. L. Allinger, J. Org. Chem., 53, 5471 (1988). Molecular Mechanics (MM2) Parameters for Divinyl Ethers and Aromatic Halide Derivatives.
90. R. J. Woods, C. W. Andrews, and J. P. Bowen, J. Am. Chem. Soc., 114, 850 (1992). Molecular Mechanical Investigation of the Properties of Oxocarbenium Ions. 1. Parameter Development.
91. R. J. Woods, C. W. Andrews, and J. P. Bowen, J. Am. Chem. Soc., 114, 859 (1992). Molecular Mechanical Investigation of the Properties of Oxocarbenium Ions. 2. Application to Glycoside Hydrolysis.
92. L. R. Schmitz and N. L. Allinger, J. Am. Chem. Soc., 112, 8307 (1990). Molecular Mechanics Calculations on Aliphatic Amines.
93. J.-H. Lii and N. L. Allinger, J. Comput. Chem., 12, 186 (1990). The MM3 Force Field for Amides, Polypeptides and Proteins.
94. J. P. Bowen and N. L. Allinger, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1991, Vol. 2, pp. 81-97. Molecular Mechanics: The Art and Science of Parameterization.
95. A. D. French, R. S. Rowland, and N. L. Allinger, in Computer Modeling of Carbohydrate Molecules, A. D. French and J. W. Brady, Eds., ACS Symposium Series 430, American Chemical Society, Washington, DC, 1990, pp. 120-140. Modeling of Glucopyranose. The Flexible Monomer of Amylose.
96. ∝ and Derivatives.
97. P.-G. Nyholm and I. Pascher, Int. J. Biol. Macromol., 15, 43 (1993). Steric Presentation and Recognition of the Saccharide Chains of Glycolipids at the Cell Surface: Favoured Conformations of the Saccharide-Lipid Linkage Calculated Using Molecular Mechanics (MM3).
98. J.-M. Lehn and G. Ourisson, Bull. Soc. Chim. Fr., 1113 (1963). Étude de Cétones cycliques (XIV). Conformation des Bromo-2 et Dibromo-2,3 céto-3 triterpènes.
99. U. Burkert and N. L. Allinger, Molecular Mechanics, ACS Monograph 177, American Chemical Society, Washington, DC, 1982.
100. D. B. Boyd (unpublished work) points out the error in the way Figure 2.4 (p. 29) of this reference is drawn. A corrected representation is given in Figure 6 of the present chapter.
101. D. E. Williams, J. Comput. Chem., 9, 745 (1988). Representation of the Electrostatic Potential by Atomic Multipole and Bond Dipole Models.
102. R. Taylor, J. Mol. Struct., 71, 211 (1981). An Empirical Potential for the O-H ⋯ O Hydrogen Bond.
103. H. Umeyama and K. Morokuma, J. Am. Chem. Soc., 99, 1316 (1977). The Origin of Hydrogen Bonding. An Energy Decomposition Study.
104. A. Gavezzotti and G. Filippini, J. Phys. Chem., 98, 4831 (1994). Geometry of the Intermolecular X-H ⋯ Y (X, Y = N, O) Hydrogen Bond and the Calibration of Empirical Hydrogen-Bond Potentials.
105. A. D. French, D. P. Miller, and A. Aabloo, Int. J. Biol. Macromol., 15, 30 (1993). Miniature Crystal Models of Cellulose Polymorphs and Other Carbohydrates.
106. K. B. Lipkowitz, K. Green, and J.-A. Yang, Chirality, 4, 205 (1992). Structural Characteristics of Cyclodextrins in the Solid State.
107. A. D. French and M. K. Dowd, J. Mol. Struct. (THEOCHEM), 286, 183 (1993). Exploration of Disaccharide Conformations by Molecular Mechanics.
108. A. D. French, N. Mouhous-Riou, and S. Pérez, Carbohydr. Res., 247, 51 (1993). Computer Modeling of the Tetrasaccharide Nystose.
109. A Aabloo, A. D. French, R.-H. Mikelsaar, and A. J. Pertsin, Cellulose, 1, 161 (1994). Studies of Crystalline Native Celluloses Using Potential Energy Calculations.
110. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta Jr., and P. Weiner, J. Am. Chem. Soc., 106, 765 (1984). A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins.
111. S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comput. Chem., 7, 230 (1986). An All Atom Force Field for Simulations of Proteins and Nucleic Acids.
112. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187 (1983). CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations.
113. W. F. van Gunsteren, H. J. C. Berendsen, J. Hermans, W. G. J. Hol, and J. P. M. Postma, Proc. Natl. Acad. Sci. U.S.A., 80, 4315 (1983). Computer Simulation of the Dynamics of Hydrated Protein Crystals and Its Comparison with X-Ray Data.
114. J. Åqvist, W. F. van Gunsteren, M. Leijonmark, and O. Tapia, J. Mol. Biol., 183, 461 (1985). A Molecular Dynamics Study of the C-Terminal Fragment of the L7/L12 Ribosomal Protein. Secondary Structure Motion in a 150 Picosecond Trajectory.
115. W. L. Jorgensen, J. Am. Chem. Soc., 103, 335 (1981). Transferable Intermolecular Potential for Water, Alcohols, and Ethers. Application to Liquid Water.
116. J. W. Brady and R. K. Schmidt, J. Phys. Chem., 97, 958 (1993). The Role of Hydrogen Bonding in Carbohydrates: Molecular Dynamics Simulations of Maltose in Aqueous Solution.
117. C. Mukhopadhyay and C. A. Bush, Biopolymers, 34, 11 (1994). Molecular Dynamics Simulation of Oligosaccharides Containing N-Acetyl Neuraminic Acid.
118. B. J. Hardy and A. Sarko, J. Comput. Chem., 14, 831 (1993). Conformational Analysis and Molecular Dynamics Simulation of Cellobiose and Larger Cellooligomers.
119. G. Widmalm and R. M. Venable, Biopolymers, 34, 1079 (1994). Molecular Dynamics Simulation and NMR Study of a Blood Group H Trisaccharide.
120. J. N. Scarsdale, P. Ram, J. H. Prestegard, and R. K. Yu, in Computer Modeling of Carbohydrate Molecules, A. D. French and J. W. Brady, Eds., ACS Symposium Series 430, American Chemical Society, Washington, DC, 1990, pp. 240-265. Molecular Mechanics NMR Pseudoenergy Protocol to Determine Solution Conformation of Complex Oligosaccharides.
121. R. J. Woods, C. J. Edge, and R. A. Dwek, Nature, Struct. Biol., 1, 499 (1994). Protein Surface Oligosaccharides and Protein Function.
122. S. Melberg and K. Rasmussen, Carbohydr. Res., 76, 23 (1979). The Non-Bonded Interactions in D-Glucose and β-Maltose: An Ab Initio Study of Conformations Produced by Empirical Force-Field Calculations.
123. S. Melberg and K. Rasmussen, Carbohydr. Res., 78, 215 (1980). Conformations of Disaccharides by Empirical, Force-Field Calculations. III. β-Gentiobiose.
124. C. Mukhopadhyay and C. A. Bush, Biopolymers, 31, 1737 (1991). Molecular Dynamics Simulation of Lewis Blood Groups and Related Oligosaccharides.
125. C. Mukhopadhyay, K. E. Miller, and C. A. Bush, Biopolymers, 34, 21 (1994). Conformation of the Oligosaccharide Receptor for E-Selectin.
126. Z.-Y. Yan and C. A. Bush, Biopolymers, 29, 799 (1990). Molecular Dynamics Simulations and the Conformational Mobility of Blood Group Oligosaccharides.
127. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Phys. Chem., 79, 926 (1983). Comparison of Simple Potential Functions for Simulating Liquid Water.
128. C. J. Edge, U. C. Singh, R. Bazzo, G. L. Taylor, R. A. Dwek, and T. W. Rademacher, Biochemistry, 29, 1971 (1990). 500-Picosecond Molecular Dynamics in Water of the Manα(1-2)Manoc Glycosidic Linkage Present in Asn-Linked Oligomannose-Type Structures on Glycoproteins.
129. E. W. Wooten, C. J. Edge, R. Bazzo, R. A. Dwek, and T. W. Rademacher, Carbohydr. Res., 203, 13 (1990). Uncertainties in Structural Determinations of Oligosaccharide Conformation, Using Measurements of Nuclear Overhauser Effects.
130. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc., 107, 3902 (1985). AM1: A New General Purpose Quantum Mechanical Molecular Model.
131. I. Tvaroska and J. P. Carver, J. Chem. Res., 0123 (1991). Theoretical Studies on the Conformation of Saccharides. XV. AM1 Calculation of Relative Stabilities and Geometries of Conformers.
132. S. W. Homans and M. Forster, Glycobiology, 2, 143 (1992). Application of Restrained Minimization, Simulated Annealing and Molecular Dynamics Simulations for the Conformational Analysis of Oligosaccharides.
133. T. J. Rutherford, J. Partridge, C. T. Weller, and S. W. Homans, Biochemistry, 32, 12715 (1993). Characterization of the Extent of Internal Motions in Oligosaccharides.
134. T. J. Rutherford, D. G. Spackman, P. J. Simpson, and S. W. Homans, Glycobiology, 4, 59 (1994). 5 Nanosecond Molecular Dynamics and NMR Study of Conformational Transitions in the Sialyl-Lewis X Antigen.
135. ∝ Group.
136. G. Widmalm, A. R. Byrd, and W. Egan, Carbohydr. Res., 229, 195 (1992). A Conformational Study of α-L-Rhap-(1-2)-α-L-Rhap-(1-OMe) by NMR Nuclear Overhauser Effect Spectroscopy (NOESY) and Molecular Dynamics Calculations.
137. P. D. Thomas, V. J. Basus, and T. L. James, Proc. Natl. Acad. Sci. U.S.A., 88, 1237 (1991). Protein Solution Structure Determination Using Distances from Two-Dimensional Nuclear Overhauser Effect Experiments: Effect of Approximations on the Accuracy of Derived Structures.
138. S. Ha, J. Gao, B. Tidor, J. W. Brady, and M. Karplus, J. Am. Chem. Soc., 113, 1553 (1991). Solvent Effect on the Anomeric Equilibrium in D-Glucose: A Free Energy Simulation Analysis.
139. P. D. J. Grootenhuis and C. A. G. Haasnoot, Mol. Simulation, 10, 75 (1993). A CHARMm Based Force Field for Carbohydrates Using the CHEAT Approach: Carbohydrates Hydroxyl Groups Represented by Extended Atoms.
140. S. J. Angyal, Angew. Chem. Int. Ed. Engl., 8, 157 (1969). The Composition and Conformation of Sugars in Solution.
141. S. Lifson, A. T. Hagler, and P. Dauber, J. Am. Chem. Soc., 101, 5111 (1979). Consistent Force Field Studies of Intermolecular Forces in Hydrogen-Bonded Crystals. 1. Carboxylic Acids, Amides, and the C=O ⋯ H - Hydrogen Bonds.
142. U. C. Singh and P. A. Kollman, J. Comput. Chem., 5, 129 (1984). An Approach to Computing Electrostatic Charges for Molecules.
143. T. R. Stouch and D. E. Williams, J. Comput. Chem., 13, 622 (1992). Conformational Dependence of Electrostatic Potential Derived Charges of a Lipid Headgroup: Glycerylphosphorylcholine.
144. D. E. Williams, Biopolymers, 29, 1367 (1990). Alanyl Dipeptide Potential-Derived Net Atomic Charges and Bond Dipoles, and Their Variation with Molecular Conformation.
145. R. J. Woods, M. Khalil, W. Pell, S. H. Moffat, and V. H. Smith Jr., J. Comput. Chem., 11, 297 (1990). Derivation of Net Atomic Charges from Molecular Electrostatic Potentials.
146. C. I. Bayly, P. Cieplak, W. D. Cornell, and P. A. Kollman, J. Phys. Chem., 97, 10269 (1993). A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model.
147. J. Kong and J.-M. Yan, Int. J. Quantum Chem., 46, 239 (1993). The Effects of Atomic Multipole Moments Obtained by the Potential-Derived Method on Hydrogen Bonding.
148. D. S. Hartsough and K. M. Merz Jr., J. Am. Chem. Soc., 115, 6529 (1993). Protein Dynamics and Solvation in Aqueous and Nonaqueous Environments.
149. 13C-N.M.R.-Spectral Study of Synthetic Methyl D-Manno-Oligosaccharides.
150. R. J. Woods, Curr. Opinion Struct. Biol., 5, 591 (1995). Three-dimensional Structures of Oligosaccharides.
151. H. Masoud, M. B. Perry, J.-R. Brisson, D. Uhrin, and J. C. Richards, Can. J. Chem., 72, 1466 (1994). Structural Elucidation of the Backbone Oligosaccharide from the Lipopolysaccharide of Moraxella catarrhalis Serotype A.
152. D. R. Bundle, H. Baumann, J.-R. Brisson, S. M. Gagné, A. Zdanov, and M. Cygler, Biochemistry, 33, 5183 (1993). Solution Structure of a Trisaccharide-Antibody Complex: Comparison of NMR Measurements with a Crystal Structure.
153. H. van Halbeek, Curr. Opinion Struct. Biol., 4, 697 (1994). NMR Developments in Structural Studies of Carbohydrates and Their Complexes.
154. J. Dabrowski and L. Poppe, J. Am. Chem. Soc., 111, 1510 (1989). Hydroxyl and Amido Groups as Long-Range Sensors in Conformational Analysis by Nuclear Overhauser Enhancement: A Source of Experimental Evidence for Conformational Flexibility of Oligosaccharides.
155. S. W. Homans, Glycobiology, 3, 551 (1993). Conformation and Dynamics of Oligosaccharides in Solution.
156. A. Imberty, S. Pérez, M. Hricovini, R. N. Shah, and J. P. Carver, Int. J. Biol. Macromol., 15, 17 (1993). Flexibility in a Tetrasaccharide Fragment from the High Mannose Type of N-Linked Oligosaccharides.
157. A. E. Torda and W. F. van Gunsteren, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1992, Vol. 3, pp. 143-172. Molecular Modeling Using Nuclear Magnetic Resonance Data.
158. 158
159. T. M. Glennon, Y. -J. Zheng, S. M. LeGrand, B. A. Shutzberg and K. M. Merz Jr., J. Comput. Chem., 15, 1019 (1994). A Force Field for Monosaccharides and (1-4) Linked Polysaccharides.
160. S. Reiling, M. Schlenkrich, and J. Brickmann, J. Comput. Chem., 17, 450 (1996). Force Field Parameters for Carbohydrates.