Theoretical studies of nucleic acids and nucleic acid-protein complexes using charmm

Computational Studies of RNA and DNA

Volumn , Issue , 2006, Pages 73-94

  MacKerell Jr , Alexander D ^a   Nilsson, Lennart ^b  

^a UNIVERSITY OF MARYLAND SCHOOL OF PHARMACY   (United States)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

CHARMM; DNA; empirical force field; proteins; RNA

Indexed keywords

EID: 38549117905     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-4851-3_3     Document Type: Chapter

References (136)

1. Becker, O. M., MacKerell, A. D., Jr., Roux, B. & Watanabe, M., Eds. (2001). Computational Biochemistry and Biophysics. New York: Marcel-Dekker, Inc.
2. MacKerell, A. D., Jr. (2004). Empirical Force Fields for Biological Macromolecules: Overview and Issues. J. Comput. Chem. 25, 1584-1604.
3. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., Debolt, S., Ferguson, D., Seibel, G. & Kollman, P. (1995). AMBER. Comp. Phys. Commun. 91, 1-41.
4. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983). CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 4, 187-217.
5. Ponder, J. (2002). Tinker: Software Tools for Molecular Design. Washington University School of Medicine, St. Louis.
6. Van Gunsteren, W. F. (1987). GROMOS. Groningen Molecular Simulation Program Package. University of Groningen, Groningen.
7. Lindahl, E., Hess, B. & Van der Spoel, D. (2001). GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 7, 306-317.
8. Ewig, C. S., Berry, R., Dinur, U., Hill, J.-R., Hwang, M.-J., Li, H., Liang, C., Maple, J., Peng, Z., Stockfisch, T. P., Thacher, T. S., Yan, L., Ni, X. & Hagler, A. T. (2001). Derivation of Class II Force Fields. VIII Derivation of a General Quantum Mechanical Force Field for Organic Compounds. J. Comput. Chem. 22, 1782-1800.
9. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Zakrzewski, V. G., Montgomery, J. A., Jr., Stratmann, R. E., Burant, J. C., Dapprich, S., Millam, J. M., Daniels, A. D., Kudin, K. N., Strain, M. C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G. A., Ayala, P. Y., Cui, Q., Morokuma, K., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Cioslowski, J., Ortiz, J. V., Baboul, A. G., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Andres, J. L., Gonzalez, C., Head-Gordon, M., Replogle, E. S. & Pople, J. A. (1998). Gaussian 98. Gaussian, Inc., Pittsburgh, PA.
10. Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordan, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K. A., Su, S., Windus, T. L., Dupuis, M. & Montgomery, J. A. (1993). General Atomic and Molecular Electronic Structure System. J. Comput. Chem. 14, 1347-1363.
11. Harrison, R. J., Nichols, J. A., Straatsma, T. P., Dupuis, M., Bylaska, E. J., Fann, G. I., Windus, T. L., Apra, E., Anchell, J., Bernholdt, D., Borowski, P., Clark, T., Clerc, D., Dachsel, H., Jong, B. D., Deegan, M., Dyall, K., Elwood, D., Fruchtl, H., Glendenning, E., Gutowski, M., Hess, A., Jaffe, J., Johnson, B., Ju, J., Kendall, R., Kobayashi, R., R. Kutteh, Z. L., Littlefield, R., X. Long, B. M., Nieplocha, J., Niu, S., Rosing, M., Sandrone, G., Stave, M., Taylor, H., Thomas, G., Lenthe, J. V., Wolinski, K., Wong, A. & Zhang, Z. (2000). NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.0 4.0 edit. Pacific Northwest National Laboratory, Richland, WA, 99352-0999, USA.
12. Kong, J., White, C. A., Krylov, A. I., Sherrill, C. D., Adamson, R. D., Furlani, T. R., Lee, M. S., Lee, A. M., Gwaltney, S. R., Adams, T. R., Ochsenfeld, C., Gilbert, A. T. B., Kedziora, G. S., Rassolov, V. A., Maurice, D. R., Nair, N., Shao, Y., Besley, N. A., Maslen, P. E., Dombroski, J. P., Daschel, H., Zhang, W., Korambath, P. P., Baker, J., Byrd, E. F. C., Voorhis, T. V., Oumi, M., Hirata, S., Hsu, C.-P., Ishikawa, N., Florian, J., Warshel, A., Johnson, B. G., Gill, P. M. W., Head-Gordon, M., & Pople, J. A. (2000). Q-Chem 2.0: A high-performance ab initio electronic structure program. J. Comput. Chem. 21, 1532-1548
13. Jaguar. (1991-2000). 4.1 edit. Schrödinger, Inc., Portland, OR.
14. MacKerell, A. D., Jr., Wiórkiewicz-Kuczera, J. & Karplus, M. (1995). An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117, 11946-11975.
15. Foloppe, N. & MacKerell, A. D., Jr. (2000). All-atom empirical force field for nucleic acids: 1) Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21, 86-104.
16. MacKerell, A. D., Jr. & Banavali, N. K. (2000). All-atom empirical force field for nucleic acids: 2) Application to solution MD simulations of DNA. J. Comput. Chem. 21, 105-120.
17. Nilsson, L. & Karplus, M. (1986). Empirical Energy Functions for Energy Minimization and Dynamics of Nucleic Acids. J. Comput. Chem. 7, 591-616.
18. Cheatham, T. E., III, Cieplak, P. & Kollman, P. A. (1999). A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16, 845-861.
19. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. & Kollman, P. A. (1995). A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 117, 5179-5197.
20. Langley, D. R. (1998). Molecular dynamics simulations of environment and sequence dependent DNA conformation: The development of the BMS nucleic acid force field and comparison with experimental results. J. Biomol. Struct. Dyn. 16, 487-509.
21. Soares, T. A., Hunenberger, P. H., Kastenholz, M. A., Kraeutler, V., Lenz, T., Lins, R., Oostenbrink, C. & Van Gunsteren, W. (2005). An improved nucleic acid parameter set for the GROMOS force field. J. Comput. Chem. 26, 725-737.
22. Foloppe, N., Hartmann, B., Nilsson, L. & MacKerell, A. D., Jr. (2002). Intrinsic Conformational Energetics Associated with the Glycosyl Torsion in DNA: A Quantum Mechanical Study. Biophys. J. 82, 1554-1569.
23. Garcia-Viloca, M., Gao, J., Karplus, M. & Truhlar, D. G. (2004). How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations. Science 303, 186-195.
24. MacKerell, A. D., Jr., Brooks, B., Brooks, C. L., III, Nilsson, L., Roux, B., Won, Y. & Karplus, M. (1998). CHARMM: The Energy Function and Its Paramerization with an Overview of the Program. In Encyclopedia of Computational Chemistry (Schreiner, P. R., ed.), Vol. 1, pp. 271-277. John Wiley & Sons, Chichester.
25. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A. R. & Schneider, B. (1992). The Nucleic Acid Database: A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63, 751-759.
26. Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D. & Zardecki, C. (2002). The protein data bank. Acta Crystallogr D Biol Crystallogr 58, 899-907.
27. Macke, T. J. & Case, D. A. (1998). Modeling Unusual Nucleic Acid Structures. In Molecular Modeling of Nucleic Acids (J. SantaLucia, J., ed.), Vol. 682, pp. 379-392. American Chemical Society, Washington, DC.
28. Lu, X. J. & Olson, W. K. (2003). 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31, 5108-5121.
29. Beveridge, D. L. & DiCapua, F. M. (1989). Free Energy via Molecular Simulations: Applications to Chemical and Biomolecular Systems. Annu.Rev.Biophys.Biophys.Chem. 18, 431-492.
30. Tuckerman, M. E. & Martyna, G. J. (2000). Understanding Modern Molecular Dynamics: Techniques and Applications. J. Phys. Chem. B 104, 159-178.
31. Ma, J. (2005). Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure (Camb) 13, 373-380.
32. Feig, M. & Brooks, C. L., III (2004). Recent advances in the development and application of implicit solvent models in biomolecular simulations. Curr. Opin. Struct. Biol. 14, 217-224.
33. Srinivasan, J., Cheatham, I., T.E., Ceiplak, P., Kollman, P. A. & Case, D. A. (1998). Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helicies. J. Amer. Chem. Soc. 120, 9401-9409.
34. Kollman, P. A., Massova, I., Reyes, C, Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A. & Cheatham, T. E., III (2000). Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models. Acc. Chem. Res. 33, 889-897.
35. Habtemariam, B., Anisimov, V. M. & MacKerell, A. D., Jr. (2005). Cooperative Binding of DNA and CBF|3 to the Runt Domain of the CBFa Studied via MD simulations. Nucleic Acid Res. 33, 4212-4222.
36. Dickerson, R. E. (1998). DNA bending: The prevalence of kinkiness and the virtures of normality. Nucleic Acids Res. 26, 1906-1926.
37. Humphrey, W., Dalke, A. & Schulten, K. (1996). VMD: Visual molecular dynamics. J. Mol. Graph. 14, 33-38.
38. Feig, M., MacKerell, A. D., Jr. & Brooks, C. L., III (2002). Force field influence on the observation of 7t-helical protein structures in molecular dynamics simulations. J. Phys. Chem. B 107, 2831-2836.
39. MacKerell, A. D., Jr., Feig, M. & Brooks, C. L., III (2004). Accurate treatment of protein backbone conformational energetics in empirical force fields. J Am Chem Soc 126, 698-699.
40. MacKerell, A. D., Jr., Feig, M. & Brooks, C. L., III (2004). Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comp. Chem. 25, 1400-1415.
41. Tidor, B., Irikura, K K, Brooks, B. R. & Karplus, M. (1983). Dynamics of DNA Oligomers. J. Biomol. Struct. Dyn. 1, 231-252.
42. Nordlund, T. M., Andersson, S., Nilsson, L., Rigler, R., Graeslund, A. & McLaughlin, L. W. (1989). Structure and Dynamics of a Fluorescent DNA Oligomer Containing the Ecori Recognition Sequence: Fluorescence, Molecular Dynamics, and NMR Studies. Biochemistry. 28, 9095-103.
43. Nilsson, L., Åhgren-Stålhandske, A., Sjögren, A. S., Hahne, S. & Sjöberg, B.-M. (1990). Three-Dimensional Model and Molecular Dynamics Simulation of the Active Site of the Self-Splicing Intervening Sequence of the Bacteriophage T4 nrdb Messenger RNA. Biochemistry. 29, 10317-22.
44. Singh, U. C, Weiner, S. J. & Kollman, P. (1985). Molecular Dynamics Simulations of d(C-G-C-G-A){middle dot} d(T-C-G-C-G) with and without "Hydrated" Counterions. Proc. Natl. Acad. Sci. USA 82, 755-759.
45. 2. J. Mol. Biol. 188, 455-475.
46. Härd, T. & Nilsson, L. (1992). Free-Energy Calculations Predict Sequence Specificity in DNA-Drug Complexes. Nucleosides & Nucleotides 11, 167-173.
47. MacKerell, A. D., Jr. (1997). Influence of Magnesium Ions on Duplex DNA Structural, Dynamic, and Solvation Properties. J Phys Chem B 101, 646-650.
48. Pastor, N, MacKerell, A. D., Jr. & Weinstein, H. (1999). TIT for TAT: The Properties of Inosine and Adenosine in TATA Box DNA. J. Biomol. Struct. & Design 16, 787-810.
49. MacKerell, A. D., Jr. & Lee, G. U. (1999). Structure, Force and Energy of Double-Stranded DNA Oligonucleotides Under Tensile Loads. Eur. J. Biophys. 28, 415-426.
50. Barsky, D., Foloppe, N., Ahmadia, S., Wilson, D. M., III & MacKerell, A. D., Jr. (2000). New Insights into the Structure of Abasic DNA from Molecular Dynamics Simulations. Nucleic Acids Res. 28, 2613-2626.
51. 2. J. Chem. Phys. 104, 6052-6057.
52. Yang, L. & Pettitt, B. M. (1996). B to A Transition of DNA on the Nanosecond Time Scale. J. Phys. Chem. 100, 2550-2566.
53. Feig, M. & Pettitt, B. M. (1998). Structural Equilibrium of DNA represented with Different Force Fields. Biophys. J. 75, 134-149.
54. MacKerell, J., A. D. (1998). Observations on the A versus B Equilibrium in Molecular Dynamics Simulations of Duplex DNA and RNA. In Molecular Modeling of Nucleic Acids (SantaLucia, J., J., ed.), Vol. 682, pp. 304-311. American Chemical Society, Washington, DC.
55. MacKerell, A. D., Jr., Banavali, N. B. & Foloppe, N. (2001). Development and Current Status of the CHARMM Force Field for Nucleic Acids. Biopolymers 56, 257-265.
56. Cheatham, T. E., III & Young, M. A. (2001). Molecular Dynamics Simulation of Nucleic Acids: Successes, Limitations, and Promise. Biopolymers 56, 232-256.
57. Dick, B. G., Jr. & Overhauser, A. W. (1958). Theory of the Dielectric Constants of Alkali Halide Crystals. Phys. Rev. 112, 90-103.
58. Cochran, W. (1959). Lattice Dynamics of Alkali Halides. Phil. Mag. 4, 1082-1086.
59. Rick, S. W. & Stuart, S. J. (2002). Potentials and Algorithms for Incorporating Polarizability in Computer Simulations. Rev. Comp. Chem. 18, 89-146.
60. Lamoureux, G. & Roux, B. (2003). Modelling Induced Polarizability with Drude Oscillators: Theory and Molecular Dynamics Simulation Algorithm. J. Chem. Phys. 119, 5185-5197.
61. Lamoureux, G., MacKerell, A. D., Jr. & Roux, B. (2003). A simple polarizable model of water based on classical Drude oscillators. J. Chem. Phys. 119, 5185-5197.
62. Lamoureux, G., Harder, E., Vorobyov, I. V., Roux, B. & MacKerell, A. D., Jr. (2005). A polarizable model of water for molecular dynamics simulations of biomolecules. Chem. Phys. Lett. In press.
63. Vorobyov, I. V., Anisimov, V. M. & MacKerell, A. D., Jr. (2005). Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model. J. Phys. Chem. B 109, 18988-18999
64. Anisimov, V. M., Lamoureux, G., Vorobyov, I. V., Huang, N., Roux, B. & MacKerell, A. D., Jr. (2005). Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. J. Chem. Theory. Comp. 1, 153-168.
65. Lahiri, A. & Nilsson, L. (1997). Properties of dianionic oxyphosphorane intermediates from hybrid QM/MM simulation: Implications for ribozyme reactions. J. Mol. Struct.-Theochem 419, 51-55.
66. Norberg, J. & Nilsson, L. (1995). Potential of Mean Force Calculations of the Stacking Unstacking Process in Single-Stranded Deoxyribodinucleoside Monophosphates. Biophys. J. 69, 2277-2285.
67. Norberg, J. & Nilsson, L. (1995). Stacking Free Energy Profiles For All 16 Natural Ribodinucleoside Monophosphates in Aqueous Solution. J. Am. Chem. Soc. 117, 10832-10840.
68. Norberg, J. & Nilsson, L. (1995). Temperature Dependence of the Stacking Propensity of Adenylyl-3' 5'-Adenosine. J. Phys. Chem. 99, 13056-13058.
69. Norberg, J. & Nilsson, L. (1998). Solvent Influence on Base Stacking. Biophys J. 74, 394-402.
70. Foloppe, N. & Nilsson, L. (2005). Towards a full characterization of nucleic acid components in aqueous solution: Simulations of nucleosides. J. Phys. Chem. B. 109, 9119-9131.
71. Lahiri, A., Sarzynska, J., Nilsson, L. & Kulinski, T. (2005). Molecular Dynamics Simulation of the Preferred Conformations of 2-Thiouridine in Aqueous Solution. Theor. Chem. Acc., submitted.
72. Hart, K., Nyström, B., Öhman, M. & Nilsson, L. (2005). Molecular dynamics simulations and free energy calculations of base flipping in dsRNA. RNA 11, 609-618.
73. Banavali, N. K. & MacKerell, A. D., Jr. (2002). Free Energy and Structural Pathways of Base Flipping in a DNA GCGC containing sequence. J. Mol. Biol. 319, 141-160.
74. Feig, M. & Pettitt, B. M. (1997). Experiment vs Force Fields: DNA Conformation from Molecular Dynamics Simulations. J. Phys. Chem. B 101, 7361-7363.
75. Sarzynska, J., Kulinski, T. & Nilsson, L. (2000). Conformational Dynamics of a 5S rRNA Hairpin Domain Containing Loop D and a Single Nucleotide Bulge. Biophys. J. 79, 1213-1227.
76. Nina, M. & Simonson, T. (2002). Molecular Dynamics of the tRNAAla Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments. J. Phys. Chem. B 106, 3696-3705.
77. Tang, Y. & Nilsson, L. (1999). Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution. Biophys. J. 77, 1284-305.
78. Phe: Codon-anticodon Interaction. Biophys. J. 79, 2276-2289.
79. Pan, Y. & MacKerell, A. D., Jr. (2003). Altered Structural Fluctuations in Duplex RNA versus DNA: A conformational switch involving base pair opening. Nucleic Acid Res. 31, 7131-7140.
80. Pan, Y., Priyakumar, D. & MacKerell, A. D., Jr. (2005). Conformational Determinants of Tandem GU Mismatches in RNA: Insights from molecular dynamics simulations and quantum mechanical calculations. Biochemistry 44, 1433-1443.
81. Sarzynska, J. & Kulinski, T. (2005). Dynamics and Stability of GCAA Tetraloops with 2-Aminopurine and Purine Substitutions. J. Biomol. Struct. Dyn. 22, 425-439.
82. Sarzynska, J., Nilsson, L. & Kulinski, T. (2003). Effects of Base Substitutions in an RNA Hairpin from Molecular Dynamics and Free Energy Simulations. Biophys. J. 85, 3445-3459.
83. McFail-Isom, L., Sines, C. C. & Williams, L. D. (1999). DNA structure: Cations in charge? Curr. Opin. Struct. Biol. 9, 298-304.
84. Hamelberg, D., Williams, L. D. & Wilson, W. D. (2001). Influence of the dynamic positions of cations on the structure of the DNA minor groove: Sequence-dependent effects. J. Am. Chem. Soc. 123, 7745-7755.
85. Banavali, N. K. & Roux, B. (2005). Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. J. Am. Chem. Soc. 127, 6866-6876.
86. Pastor, N. (2005). The B-to A-DNA Transition and the Reorganization of Solvent at the DNA Surface. Biophys. J. 88, 3262-3275.
87. Wong, K.-Y. & Pettitt, B. M. (2004). Orientation of DNA on a surface from simulation. Biopolymers 73, 570-578.
88. Darden, T. A., York, D. & Pedersen, L. G. (1993). Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089-10092.
89. Norberg, J. & Nilsson, L. (2000). On the Truncation of Long-Range Electrostatic Interactions in DNA. Biophys. J. 79, 1537-1553.
90. Steinbach, P. J. & Brooks, B. R. (1994). New Spherical-Cutoff Methods of Long-Range Forces in Macromolecular Simulations. J. Comput. Chem. 15, 667-683.
91. Brooks, C. L., III & Karplus, M. (1983). Deformable Stochastic Boundaries in Molecular Dynamics. J. Chem. Phys. 79, 6312-6325.
92. Beglov, D. & Roux, B. (1994). Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations. J. Chem. Phys. 100, 9050-9063.
93. 2 in aqeous solution from molecular dynamics simulations. J. Biomol. NMR 7, 305-314.
94. Norberg, J. & Nilsson, L. (1995). NMR Relaxation Times, Dynamics, and Hydration of a Nucleic Acid Fragment from Molecular Dynamics Simulations. J. Phys. Chem. 99, 14876-14884.
95. Feig, M. & Pettitt, B. M. (1999). Sodium and chlorine ions as part of the DNA solvation shell. Biophys. J. 77, 1769-1781.
96. Mohan, V., Smith, P. E. & Pettitt, B. M. (1993). Evidence for a New Spine of Hydration: Solvation of DNA Triple Helices. J. Am. Chem. Soc. 115, 9297-9298.
97. Mohan, V., Smith, P. E. & Pettitt, B. M. (1993). Molecular dynamics simulation of ions and water around triplex DNA. J. Phys. Chem. 97, 12984-12990.
98. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. (1983). Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 79, 926-935.
99. Priyakumar, U. D. & MacKerell, A. D., Jr. (2005). Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER and BMS. J. Chem. Theory Comput. In Press.
100. Feig, M., Zacharias, M. & Pettitt, B. M. (2001). Conformations of an Adenine Bulge in a DNA Octamer and Its Influence on DNA Structure from Molecular Dynamics Simulations. Biophys. J. 81, 353-370.
101. Range, K., Mayaan, E. & Maher, L. J., III (2005). The contribution of phosphate-phosphate repulsions to the free energy of DNA bending. Nucleic Acid Res. 33, 1257-1268.
102. Weerasinghe, S., Smith, P. E., Mohan, V., Cheng, Y.-K. & Pettitt, B. M. (1995). Nanosecond dynamics and structure of a model DNA triple helix in salt water solution. J. Amer. Chem. Soc. 117, 2147-2158.
103. MacKerell, A. D., Jr. (2001). Atomistic Models and Force Fields. In Computational Biochemistry and Biophysics (Watanabe, M., ed.), pp. 7-38. Marcel Dekker, Inc., New York.
104. MacKerell, A. D., Jr. (2005). http://www.pharmacy.umaryland.edu/faculty/ amackere/param/force-field-dev.htm.
105. Marquez, V. E., Wang, P., Nicklaus, M. C., Maier, M., Manoharan, M., Christman, J. K., Banavali, N. K. & MacKerell, A. D., Jr. (2001). Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites. Nucleos. Nucleot. & Nucl. Acids 20, 451-459.
106. Wang, P., Nicklaus, M. C., Marquez, V. E., Brank, A. S., Christman, J., Banavali, N. K. & MacKerell, A. D., Jr. (2000). Use of Oligodeoxyribonucleotides with Conformationally Constrained Abasic Sugar Targets to Probe the Mechanism of Base Flipping by HhaI DNA (Cytosine C5)-Methyltransferase. J. Amer. Chem. Soc. 122, 12422-12434.
107. Horton, J. R., Ratner, G., Banavali, N. K., Huang, N., Choi, Y., Maier, M. A., Marquez, V. E., MacKerell, A. D., Jr. & Cheng, X. (2004). Caught in the act: Visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res. 32, 3877-3886.
108. Sen, S. & Nilsson, L. (1998). Molecular Dynamics of Duplex Systems Involving PNA: Structural and Dynamical Consequences of the Nucleic Acid Backbone. J. Amer. Chem. Soc. 120, 619-631.
109. Sen, S. & Nilsson, L. (2001). MD Simulations of Homomorphous PNA, DNA and RNA Single Strands: Characterization and Comparison of Conformations and Dynamics. J. Am. Chem. Soc. 123, 7414-7422.
110. Banavali, N. K. & MacKerell, A. D., Jr. (2001). Reevaluation of Stereoelectric Contributions to the Conformational Properties of the Phosphodiester and N3'-Phosphoramidate Moieties of Nucleic Acids. J. Am. Chem. Soc. 128, 6747-6755.
111. Banavali, N. K. & MacKerell, A. D., Jr. (2001). Reexamination of the Intrinsic, Dynamic, and Hydration Properties of Phosphoramidate DNA. Nucl. Acids. Res. 29, 3219-3230.
112. Wong, K.-Y. & Pettitt, B. M. (2001). A study of DNA tethered to a surface by an all-atom molecular dynamics simulation. Theor. Chem. Acc. 106, 233-235.
113. MacKerell, A. D., Nilsson, L., Rigler, R. & Saenger, W. (1988). Molecular Dynamics Simulations of Ribonuclease T1: Analysis of the Effect of Solvent on the Structure, Fluctuations, and Active Site of the Free Enzyme. Biochemistry 27, 4547-4556.
114. MacKerell, A. D., Jr., Rigler, R., Nilsson, L., Heinemann, U. & Saenger, W. (1988). Molecular dynamics simulations of ribonuclease T1: Effect of solvent on the interaction with 2'GMP. European Biophysics Journal 16, 287-297.
115. MacKerell, A. D., Jr., Rigler, R., Hahn, U. & Saenger, W. (1991). Thermodynamic analysis of the equilibrium, association and dissociation of 2'GMP and 3'GMP with ribonuclease T1 at pH 5.3. Biochim. Biophy. Acta 1073, 357-365.
116. MacKerell, J., A. D., Sommer, M. S. & Karplus, M. (1995). pH Dependence of Binding Reactions from Free Energy Simulations and Macroscopic Continuum Electrostatic Calculations: Application to 2'GMP/3'GMP Binding to Ribonuclease T1. J. Mol. Biol. 247, 774-807.
117. Sen, S. & Nilsson, L. (1999). Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation. Biophys. J. 77, 1782-1800.
118. Sen, S. & Nilsson, L. (1999). Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex. Biophys. J. 77, 1801-10.
119. Eriksson, M. A. & Nilsson, L. (1999). Structural and dynamic differences of the estrogen receptor DNA-binding domain, binding as a dimer and as a monomer to DNA: Molecular dynamics simulation studies [published erratum appears in Eur Biophys J 1999;28(4):356]. Eur Biophys. J. 28, 102-11.
120. Eriksson, M. A. L. & Nilsson, L. (1995). Structure, Thermodynamics and Cooperativity of the Glucocorticoid Receptor DNA-Binding Domain in Complex With Different Response Elements-Molecular Dynamics Simulation and Free Energy Perturbation Studies. J. Mol. Biol. 253, 453-472.
121. Eriksson, M. A. L., Hard, T. & Nilsson, L. (1995). Molecular Dynamics Simulations of the Glucocorticoid Receptor DNA-Binding Domain in Complex With DNA and Free in Solution. Biophys. J. 68, 402-426.
122. Eriksson, M. A. & Nilsson, L. (1998). Structural and dynamic effects of point mutations in the recognition helix of the glucocorticoid receptor DNA-binding domain. Protein Eng. 11, 589-600.
123. Tang, Y. & Nilsson, L. (1999). Effect of G40R Mutation on the Binding of Human SRY Protein to DNA: A Molecular Dynamics View. Proteins 35, 101-113.
124. Tang, Y. & Nilsson, L. (1998). Interaction of hu man SRY protein with DNA: A molecular dynamics study. Proteins 31, 417-433.
125. Duan, J. & Nilsson, L. (2002). The role of residue 50 and hydration water molecules in homeodomain DNA recognition. Eur. Biophys. J. 31, 306-316.
126. Duan, J. & Nilsson, L. (2005). The Effect of Zn Ion on p53 DNA Recognition and Stability of the DNA Binding Domain. submitted.
127. MacKerell, J., A. D., Rigler, R., Nilsson, L., Hahn, U. & Saenger, W. (1987). Protein Dynamics: A time-resolved fluorescence, energetic and molecular dynamics study of ribonuclease T1. Biophysical Chemistry 26, 247-261.
128. Lynch, T. W., Kosztin, D., McLean, M. A., Schulten, K. & Sligar, S. G. (2002). Dissecting the Molecular Origins of Specific Protein-Nucleic Acid Recognition: Hydrostatic Pressure and Molecular Dynamics. Biophys. J. 82, 93-98.
129. Villa, E., Balaeff, A. & Schulten, K. (2005). Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc. Natl. Acad. Sci. USA 102, 6783-6788.
130. Priyakumar, U. D. & MacKerell, A. D., Jr. (2006). Computational Approaches for Investigating Base Flipping in Oligonucleotides. Chem. Rev. 106, 489-505.
131. Huang, N. & MacKerell, A. D., Jr. (2004). Atomistic view of base flipping in DNA. Phil Trans Royal Soc, London, A 362, 1439-1460.
132. Huang, N., Banavali, N. K. & MacKerell, A. D., Jr. (2003). Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc. Natl. Acad. Sci. USA 100, 68-73.
133. Huang, N. & MacKerell, A. D., Jr. (2005). Specificity in protein-DNA interactions: Energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. J. Mol. Biol. 345, 265-274.
134. Banavali, N. K. & Roux, B. (2002). Atomic Radii for Continuum Electrostatic Calculations on Nucleic Acids. J. Phys. Chem. B 106, 11026-11035.
135. Bandyopadhyay, S., Tarek, M. & Klein, M. L. (1999). Molecular Dynamics Study of a Lipid-DNA Complex. J. Phys. Chem. B 103, 10075-10080.
136. MacKerell, A. D., Jr. & Nilsson, L. (2001). Nucleic Acid Simulations. In Computational Biochemistry and Biophysics (Watanabe, M., ed.), pp. 441-464. Marcel Dekker, Inc., New York.