PITOMBA: Parameter interface for oligosaccharide molecules based on atoms

Journal of Chemical Theory and Computation

Volumn 10, Issue 11, 2014, Pages 5068-5080

  Rusu, Victor H ^a,b   Baron, Riccardo ^a   Lins, Roberto D ^b  

^a UNIVERSITY OF UTAH   (United States)

^b FEDERAL UNIVERSITY OF PERNAMBUCO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84909619785     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500455u     Document Type: Article

References (81)

1. Marradi, M.; Martín-Lomas, M.; Penadés, S. Glyconanoparticles: Polyvalent Tools to Study Carbohydrate-Based Interactions. In Advances in Carbohydrate Chemistry and Biochemistry; Horton, D., Ed.; Academic Press: New York, 2010; Vol. 64, pp 211-290.
2. Hollingsworth, R. I.; Wang, G. Toward a Carbohydrate-Based Chemistry: Progress in the Development of General-Purpose Chiral Synthons From Carbohydrates Chem. Rev. 2000, 100, 4267-4282
3. Dwek, R. A.; Butters, T. D. Introduction: Glycobiology Understanding the Language and Meaning of Carbohydrates Chem. Rev. 2002, 102, 283-284
4. McReynolds, K. D.; Gervay-Hague, J. Chemotherapeutic Interventions Targeting HIV Interactions with Host-Associated Carbohydrates Chem. Rev. 2007, 107, 1533-1552
5. Murrey, H. E.; Hsieh-Wilson, L. C. The Chemical Neurobiology of Carbohydrates Chem. Rev. 2008, 108, 1708-1731
6. López, C. A.; de Vries, A. H.; Marrink, S. J. Amylose Folding Under the Influence of Lipids Carbohydr. Res. 2012, 364, 1-7
7. Straathof, A. J. J. Transformation of Biomass Into Commodity Chemicals Using Enzymes or Cells Chem. Rev. 2013, 114, 1871-1908
8. Sapsford, K. E.; Algar, W. R.; Berti, L.; Gemmill, K. B.; Casey, B. J.; Oh, E.; Stewart, M. H.; Medintz, I. L. Functionalizing Nanoparticles with Biological Molecules: Developing Chemistries That Facilitate Nanotechnology Chem. Rev. 2013, 113, 1904-2074
9. Rauch, J.; Kolch, W.; Laurent, S.; Mahmoudi, M. Big Signals From Small Particles: Regulation of Cell Signaling Pathways by Nanoparticles Chem. Rev. 2013, 113, 3391-3406
10. Reith, D.; Pütz, M.; Müller-Plathe, F. Deriving Effective Mesoscale Potentials From Atomistic Simulations J. Comput. Chem. 2013, 24, 1624-1636
11. Lyubartsev, A. P.; Laaksonen, A. Calculation of Effective Interaction Potentials From Radial Distribution Functions: A Reverse Monte Carlo Approach Phys. Rev. E 1995, 52, 3730-3737
12. Moritsugu, K.; Smith, J. C. Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian Biophys. J. 2007, 93, 3460-3469
13. Hynninen, A.-P.; Matthews, J. F.; Beckham, G. T.; Crowley, M. F.; Nimlos, M. R. Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water J. Chem. Theory Comput. 2011, 7, 2137-2150
14. Molinero, V.; Goddard, W. A. M3B: A Coarse Grain Force Field for Molecular Simulations of Malto-Oligosaccharides and Their Water Mixtures J. Phys. Chem. B 2004, 108, 1414-1427
15. Liu, P.; Izvekov, S.; Voth, G. A. Multiscale Coarse-Graining of Monosaccharides J. Phys. Chem. B 2007, 111, 11566-11575
16. Bu, L.; Beckham, G. T.; Crowley, M. F.; Chang, C. H.; Matthews, J. F.; Bomble, Y. J.; Adney, W. S.; Himmel, M. E.; Nimlos, M. R. The Energy Landscape for the Interaction of the Family 1 Carbohydrate-Binding Module and the Cellulose Surface Is Altered by Hydrolyzed Glycosidic Bonds J. Phys. Chem. B 2009, 113, 10994-11002
17. López, C. A.; Rzepiela, A. J.; de Vries, A. H.; Dijkhuizen, L.; Hünenberger, P. H.; Marrink, S. J. Martini Coarse-Grained Force Field: Extension to Carbohydrates J. Chem. Theory Comput. 2009, 5, 3195-3210
18. Wohlert, J.; Berglund, L. A. A Coarse-Grained Model for Molecular Dynamics Simulations of Native Cellulose J. Chem. Theory Comput. 2011, 7, 753-760
19. Srinivas, G.; Cheng, X.; Smith, J. C. A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils J. Chem. Theory Comput. 2011, 7, 2539-2548
20. Markutsya, S.; Kholod, Y. A.; Devarajan, A.; Windus, T. L.; Gordon, M. S.; Lamm, M. H. A Coarse-Grained Model for β- d -Glucose Based on Force Matching Theor. Chem. Acc. 2012, 131, 1162-1176
21. Bellesia, G.; Chundawat, S. P. S.; Langan, P.; Redondo, A.; Dale, B. E.; Gnanakaran, S. Coarse-Grained Model for the Interconversion Between Native and Liquid Ammonia-Treated Crystalline Cellulose J. Phys. Chem. B 2012, 116, 8031-8037
22. Glass, D. C.; Moritsugu, K.; Cheng, X.; Smith, J. C. REACH Coarse-Grained Simulation of a Cellulose Fiber Biomacromolecules 2012, 13, 2634-2644
23. Markutsya, S.; Devarajan, A.; Baluyut, J. Y.; Windus, T. L.; Gordon, M. S.; Lamm, M. H. Evaluation of Coarse-Grained Mapping Schemes for Polysaccharide Chains in Cellulose J. Chem. Phys. 2013, 138, 214108
24. Mayo, S. L.; Olafson, B. D.; Goddard, W. A. DREIDING: A Generic Force Field for Molecular Simulations J. Phys. Chem. 1990, 94, 8897-8909
25. Ercolessi, F.; Adams, J. B. Interatomic Potentials From First-Principles Calculations: The Force-Matching Method EPL (Europhysics Letters) 1994, 26, 583-588
26. Izvekov, S.; Parrinello, M.; Burnham, C. J.; Voth, G. A. Effective Force Fields for Condensed Phase Systems From Ab Initio Molecular Dynamics Simulation: A New Method for Force-Matching J. Chem. Phys. 2004, 120, 10896-10912
27. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
28. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The Missing Term in Effective Pair Potentials J. Phys. Chem. 1987, 91, 6269-6271
29. Im, W.; Lee, M. S.; Brooks, C. L. Generalized Born Model with a Simple Smoothing Function J. Comput. Chem. 2003, 24, 1691-1702
30. López, C. A.; Sovova, Z.; van Eerden, F. J.; de Vries, A. H.; Marrink, S. J. Martini Force Field Parameters for Glycolipids J. Chem. Theory Comput. 2013, 9, 1694-1708
31. Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1676
32. Lins, R. D.; Hünenberger, P. H. A New GROMOS Force Field for Hexopyranose-Based Carbohydrates J. Comput. Chem. 2005, 26, 1400-1412
33. MacKerell, A. D.; Bashford, D.; Bellott; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
34. Moritsugu, K.; Smith, J. C. REACH Coarse-Grained Biomolecular Simulation: Transferability Between Different Protein Structural Classes Biophys. J. 2008, 95, 1639-1648
35. Moritsugu, K.; Kurkal-Siebert, V.; Smith, J. C. REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics Biophys. J. 2009, 97, 1158-1167
36. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
37. Autieri, E.; Sega, M.; Pederiva, F.; Guella, G. Puckering Free Energy of Pyranoses: A NMR and Metadynamics-Umbrella Sampling Investigation J. Chem. Phys. 2010, 133, 095104
38. Spiwok, V.; Králová, B.; Tvaroška, I. Modelling of B- d -Glucopyranose Ring Distortion in Different Force Fields: A Metadynamics Study Carbohydr. Res. 2010, 345, 530-537
39. Barnett, C. B.; Naidoo, K. J. Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations J. Phys. Chem. B 2010, 114, 17142-17154
40. Kirschner, K. N.; Yongye, A. B.; Tschampel, S. M.; González-Outeiriño, J.; Daniels, C. R.; Foley, B. L.; Woods, R. J. GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates J. Comput. Chem. 2008, 29, 622-655
41. Allinger, N. L.; Yuh, Y. H.; Lii, J. H. Molecular Mechanics. The MM3 Force Field for Hydrocarbons. 1 J. Am. Chem. Soc. 1989, 111, 8551-8566
42. 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
43. Pol-Fachin, L.; Rusu, V. H.; Verli, H.; Lins, R. D. GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates J. Chem. Theory Comput. 2012, 8, 4681-4690
44. Riniker, S.; van Gunsteren, W. F. A Simple, Efficient Polarizable Coarse-Grained Water Model for Molecular Dynamics Simulations J. Chem. Phys. 2011, 134, 084110
45. Roothaan, C. C. J. New Developments in Molecular Orbital Theory Rev. Mod. Phys. 1951, 23, 69-89
46. Hehre, W. J. Self-Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules J. Chem. Phys. 1972, 56, 2257-2261
47. Berendsen, H.; Postma, J.; van Gunsteren, W. F.; Hermans, J. Intermolecular Forces; Pullman, B., Ed.; Reidel Publishing Company: Dordrecht, 1981; pp 331-342.
48. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-1472
49. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. A Generalized Reaction Field Method for Molecular Dynamics Simulations J. Chem. Phys. 1995, 102, 5451-5459
50. Bussi, G.; Donadio, D.; Parrinello, M. Canonical Sampling Through Velocity Rescaling J. Chem. Phys. 2007, 126, 014101
51. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath J. Chem. Phys. 1984, 81, 3684-3690
52. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
53. Bennett, C. H. Efficient Estimation of Free Energy Differences From Monte Carlo Data J. Comput. Phys. 1976, 22, 245-268
54. Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Avoiding Singularities and Numerical Instabilities in Free Energy Calculations Based on Molecular Simulations Chem. Phys. Lett. 1994, 222, 529-539
55. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. J. A.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, Ö.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, Revision D.01; Gaussian, Inc.: Wallingford, CT, 2009.
56. Schuler, L. D.; Daura, X.; van Gunsteren, W. F. An Improved GROMOS96 Force Field for Aliphatic Hydrocarbons in the Condensed Phase J. Comput. Chem. 2001, 22, 1205-1218
57. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Universal Quantum Mechanical Model for Solvation Free Energies Based on Gas-Phase Geometries J. Phys. Chem. B 1998, 102, 3257-3271
58. Gonçalvez, P. F. B.; Stassen, H. Calculation of the Free Energy of Solvation From Molecular Dynamics Simulations Pure Appl. Chem. 2004, 76, 231-240
59. Jämbeck, J. P. M.; Mocci, F.; Lyubartsev, A. P.; Laaksonen, A. Partial Atomic Charges and Their Impact on the Free Energy of Solvation J. Comput. Chem. 2013, 34, 187-197
60. Mark, H. X-ray Investigation of Carbohydrates Chem. Rev. 2013, 26, 169-186
61. Le Bail, P.; Bizot, H.; Pontoire, B.; Buléon, A. Polymorphic Transitions of Amylose-Ethanol Crystalline Complexes Induced by Moisture Exchanges Starch/Stärke 1995, 47, 229-232
62. Müller, J. J.; Gernat, C.; Schulz, W.; Müller, E.-C.; Vorwerg, W.; Damaschun, G. Computer Simulations of X-ray Scattering Curves: Gelation and Crystallization Process in Amylose Solutions Biopolymers 1995, 35, 271-288
63. Leloup, V. M.; Colonna, P.; Ring, S. G.; Roberts, K.; Wells, B. Microstructure of Amylose Gels Carbohydr. Polym. 1992, 18, 189-197
64. Shimada, J.; Kaneko, H.; Takada, T.; Kitamura, S.; Kajiwara, K. Conformation of Amylose in Aqueous Solution: Small-Angle X-ray Scattering Measurements and Simulations J. Phys. Chem. B 2000, 104, 2136-2147
65. Imberty, A.; Pérez, S. A Revisit to the Three-Dimensional Structure of B-Type Starch Biopolymers 1988, 27, 1205-1221
66. 2O J. Am. Chem. Soc. 2013, 112, 2789-2796
67. Hsein-Chih, H. W.; Sarko, A. The Double-Helical Molecular Structure of Crystalline B-Amylose Carbohydr. Res. 1978, 61, 7-25
68. Imberty, A.; Chanzy, H.; Pérez, S.; Bulèon, A.; Tran, V. The Double-Helical Nature of the Crystalline Part of α-Starch J. Mol. Biol. 1988, 201, 365-378
69. Hsien-Chih, H. W.; Sarko, A. The Double-Helical Molecular Structure of Crystalline α-Amylose Carbohydr. Res. 1978, 61, 27-40
70. Kurkov, S. V.; Loftsson, T. Cyclodextrins Poorly Soluble Drugs 2013, 453, 167-180
71. Venkatesh, G.; Thulasidhasan, J.; Rajendiran, N. A Spectroscopic and Molecular Modeling Studies of the Inclusion Complexes of Orciprenaline and Terbutaline Drugs with Native and Modified Cyclodextrins J. Inclusion Phenom. Macrocyclic Chem. 2014, 78, 225-237
72. Zhang, J.; Ma, P. X. Cyclodextrin-Based Supramolecular Systems for Drug Delivery: Recent Progress and Future Perspective Adv. Drug Delivery Rev. 2013, 65, 1215-1233
73. Kahle, C.; Holzgrabe, U. Determination of Binding Constants of Cyclodextrin Inclusion Complexes with Amino Acids and Dipeptides by Potentiometric Titration Chirality 2004, 16, 509-515
74. Kolhapurkar, R.; Patil, K. Studies of Volumetric and Activity Behaviors of Binary and Ternary Aqueous Solutions Containing B-Cyclodextrin and Glucose J. Mol. Liq. 2013, 178, 185-191
75. Lindner, K.; Saenger, W. B-Cyclodextrin Dodecahydrate: Crowding of Water Molecules Within a Hydrophobic Cavity Angew. Chem., Int. Ed. Engl. 1978, 17, 694-695
76. Ponce Cevallos, P. A.; Buera, M. P.; Elizalde, B. E. Encapsulation of Cinnamon and Thyme Essential Oils Components (Cinnamaldehyde and Thymol) in B-Cyclodextrin: Effect of Interactions with Water on Complex Stability J. Food Eng. 2010, 99, 70-75
77. Song, L. X.; Bai, L.; Xu, X. M.; He, J.; Pan, S. Z. Inclusion Complexation, Encapsulation Interaction and Inclusion Number in Cyclodextrin Chemistry Coord. Chem. Rev. 2009, 253, 1276-1284
78. Gelb, R. I.; Schwartz, L. M.; Cardelino, B.; Fuhrman, H. S.; Johnson, R. F.; Laufer, D. A. Binding Mechanisms in Cyclohexaamylose Complexes J. Am. Chem. Soc. 2013, 103, 1750-1757
79. Inoue, Y.; Hakushi, T.; Liu, Y.; Tong, L.; Shen, B.; Jin, D. Thermodynamics of Molecular Recognition by Cyclodextrins. 1. Calorimetric Titration of Inclusion Complexation of Naphthalenesulfonates with α-, β-, and γ-Cyclodextrins: Enthalpy-Entropy Compensation J. Am. Chem. Soc. 2013, 115, 475-481
80. Rekharsky, M. V.; Goldberg, R. N.; Schwarz, F. P.; Tewari, Y. B.; Ross, P. D.; Yamashoji, Y.; Inoue, Y. Thermodynamic and Nuclear Magnetic Resonance Study of the Interactions of α- and β-Cyclodextrin with Model Substances: Phenethylamine, Ephedrines, and Related Substances J. Am. Chem. Soc. 2013, 117, 8830-8840
81. Liu, Y.; Cao, R.; Chen, Y.; He, J.-Y. Effect of B-Cyclodextrin Charge Type on the Molecular Recognition Thermodynamics of Reactions with (Ferrocenylmethyl)dimethylaminium Derivatives J. Phys. Chem. B 2013, 112, 1445-1450