The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation

Biophysical Journal

Volumn 91, Issue 8, 2006, Pages 2976-2990

  Kastenholz, Mika A ^a   Schwartz, Thomas U ^b   Hünenberger, Philippe H ^a  

^a ETH ZURICH   (Switzerland)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA; DNA B; DNA Z; GUANOSINE;

ARTICLE; DNA CONFORMATION; DNA STRUCTURE; HYDROGEN BOND; IONIC STRENGTH; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; SIMULATION; SOLVATION; THERMODYNAMICS;

EID: 33749514776     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.083667     Document Type: Article

References (139)

1. Wang, A. H., G. J. Quigley, F. J. Kolpak, J. L. Crawford, J. H. van Boom, G. van der Marel, and A. Rich. 1979. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 282:680-686.
2. Rich, A., and Z. Shuguang. 2003. Z-DNA: the long road to biological function. Nature Rev. Gen. 4:566-573.
3. Saenger, W. 1984. Principles of Nucleic Acid Structure. Springer Verlag, New York.
4. Wells, R., and S. Harvey, editors. 1989. Unusual DNA Structures. Springer, New York.
5. Ghosh, A., and M. Bansal. 2003. A glossary of DNA structures from A to Z. Acta Crystallogr. D. 59:620-626.
6. Watson, J. D., and F. H. C. Crick. 1953. Molecular structure of nucleic acids - a structure for deoxyribose nucleic acid. Nature. 171:737-738.
7. Pohl, F. M., and T. M. Jovin. 1972. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly(dG-dC). J. Mol. Biol. 67:375-396.
8. Ho, P. S., and B. H. M. Mooers. 1997. Z-DNA crystallography. Biopolymers. 44:65-90.
9. Sponer, J., H. A. Gabb, J. Leszczynski, and P. Hobza. 1997. Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study. Biophys. J. 73:76-87.
10. Pohl, F. M. 1983. Salt-induced transition between two double-helical forms of oligo(DC-DG). Cold Spring Harb. Symp. Quant. Biol. 47:113-117.
11. Kollman, P. A., P. K. Weiner, and A. Dearing. 1981. Theoretical studies of the structure and energies of basepaired nucleotides and the dissociation kinetics of a proflavine-dinucleotide complex. Ann. N. Y. Acad. Sci. 367:250-268.
12. Gueron, M., and J. P. Demaret. 1992. A simple explanation of the B-to-Z transition of DNA. Proc. Natl. Acad. Sci. USA. 89:5740-5743.
13. Misra, V. K., and B. Honig. 1996. The electrostatic contribution to the B-to-Z transition of DNA. Biochemistry. 35:1115-1124.
14. Gueron, M., J. P. Demaret, and M. Filoche. 2000. A unified theory of the B-Z transition of DNA in high and low concentrations of multivalent ions. Biophys. J. 78:1070-1083.
15. Demaret, J. P., and M. Gueron. 2000. The sensitivity of the B-Z transition of DNA to multivalent cations in high and low concentrations: a unified electrostatic interpretation. J. Biomol. Struct. Dyn. S2:377-382.
16. Rich, A., A. Nordheim, and A. H. Wang. 1984. The chemistry and biology of left-handed Z-DNA. Annu. Rev. Biochem. 53:791-846.
17. Haniford, D. B., and D. E. Pulleyblank. 1983. The in vivo occurrence of Z DNA. J. Biomol. Struct. Dyn. 1:593-609.
18. Sugiyama, H., K. Kawai, A. Matsunaga, K. Fujimoto, I. Saito, H. Robinson, and A. H. Wang. 1996. Synthesis, structure and thermodynamic properties of 8-methylguanine-containing oligonucleotides: Z-DNA under physiological salt conditions. Nucleic Acids Res. 24:1272-1278.
19. Tashiro, R., and H. Sugiyama. 2003. A nanothermometer based on the different π-stackings of B- and Z-DNA. Ang. Chem. Intl. Ed. 42:6018-6020.
20. Mao, C., W. Sun, Z. Shen, and N. C. Seeman. 1999. A nanomechanical device based on the B-Z transition of DNA. Nature. 397:144-146.
21. Seeman, N. C., and A. M. Belcher. 2002. Emulating biology: building nanostructures from the bottom up. Proc. Natl. Acad. Sci. USA. 99:6451-6455.
22. Tashiro, R., and H. Sugiyama. 2005. Biomolecule-based switching devices that respond inversely to thermal stimuli. J. Am. Chem. Soc. 127:2094-2097.
23. Rich, A. 1996. The biology of left-handed Z-DNA. J. Biol. Chem. 271:11595-11598.
24. Stollar, B. D. 1997. Why the difference between B-DNA and Z-DNA? Lupus. 6:327-328.
25. Belmont, P., J. F. Constant, and M. Demeunynck. 2001. Nucleic acid conformation diversity: from structure to function and regulation. Chem. Soc. Rev. 30:70-81.
26. Gagna, C. E., and W. C. Lambert. 2003. The halting arrival of left-handed Z-DNA. Med. Hypotheses. 60:418-423.
27. Kim, Y. G., K. Lowenhaupt, D. Y. Oh, K. K. Kim, and A. Rich. 2004. Evidence that Vaccinia virulence factor ER binds to Z-DNA in vivo: implications for development of a therapy for poxvirus infection. Proc. Natl. Acad. Sci. USA. 101:1514-1518.
28. Liu, L. F., and J. C. Wang. 1987. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA. 84:7024-7027.
29. Wittig, B., T. Dorbic, and A. Rich. 1991. Transcription is associated with Z-DNA formation in metabolically active permeabilized mammalian cell nuclei. Proc. Natl. Acad. Sci. USA. 88:2259-2263.
30. Wittig, B., S. Wolfl, T. Dorbic, W. Vahrson, and A. Rich. 1992. Transcription of human c-Myc in permeabilized nuclei is associated with formation of Z-DNA in three discrete regions of the gene. EMBO J. 11:4653-4663.
31. Cerna, A., A. Cuadrado, N. Jouve, S. M. D. de la Espina, and C. de la Torre. 2004. Z-DNA, a new in situ marker for transcription. Eur. J. Histochem. 48:49-55.
32. Kmiec, E. B., K. J. Angelides, and W. K. Holloman. 1985. Left-handed DNA and the synaptic pairing reaction promoted by Ustilago rec1 protein. Cell. 40:139-145.
33. Blaho, J. A., and R. D. Wells. 1987. Left-handed Z-DNA binding by the recA protein of Escherichia coli. J. Biol. Chem. 262:6082-6088.
34. Jaworski, A., W. T. Hsieh, J. A. Blaho, J. E. Larson, and R. D. Wells. 1987. Left-handed DNA in vivo. Science. 238:773-777.
35. Schwartz, T., M. A. Rould, K. Lowenhaupt, A. Herbert, and A. Rich. 1999. Crystal structure of the Z-α domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science. 284:1841-1845.
36. Oh, D. Y., Y. G. Kim, and A. Rich. 2002. Z-DNA-binding proteins can act as potent effectors of gene expression in vivo. Proc. Natl. Acad. Sci. USA. 99:16666-16671.
37. Champ, P. C., S. Maurice, J. M. Vargason, T. Camp, and P. S. Ho. 2004. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Res. 32:6501-6510.
38. Gagna, C. E., H. R. Kuo, and W. C. Lambert. 1999. Terminal differentiation and left-handed Z-DNA: a review. Cell Biol. Int. 23:1-5.
39. Suram, A., L. K. S. Rao, K. S. Latha, and M. A. Viswamitra. 2002. First evidence to show the topological change of DNA from B-DNA to Z-DNA conformation in the hippocampus of Alzheimer's brain. Neuromol. Med. 2:289-297.
40. Hegde, M. L., S. Anitha, K. S. Latha, M. S. Mustak, R. Stein, R. Ravid, and K. S. J. Rao. 2004. First evidence for helical transitions in supercoiled DNA by amyloid β-peptide (1-42) and aluminum - a new insight in understanding Alzheimer's disease. J. Mol. Neurosci. 22:19-31.
41. Jovin, T. M., D. M. Soumpasis, and L. P. McIntosh. 1987. The transition between B-DNA and Z-DNA. Annu. Rev. Phys. Chem. 38:521-560.
42. Voet, D., and J. G. Voet. 1995. Biochemistry, 2nd Ed. Wiley, New York.
43. Haschemeyer, A. E., and A. Rich. 1967. Nucleoside conformations - an analysis of steric barriers to rotation about the glycosidic bond. J. Mol. Biol. 27:369-384.
44. Harvey, S. C. 1983. DNA structural dynamics: longitudinal breathing as a possible mechanics for the B ↔ Z transition. Nucleic Acids Res. 11:4867-4878.
45. Goto, S. 1984. Characterization of intermediate conformational states in the B reversible Z transitions of poly(DG-DC)·POLY(DG-DC). Biopolymers. 23:2211-2222.
46. Manzini, G., L. E. Xodo, F. Quadrifoglio, J. H. van Boom, and G. A. van der Marel. 1987. dC-dG alternating oligonucleotides: thermodynamic and kinetic aspects of the B-Z transformation. J. Biomol. Struct. Dyn. 4:651-662.
47. Olson, W. K. 1981. Understanding the Motions of DNA. In Biomolecular Stereodynamics. R. H. Sarma and M. H. Sarma, editors. Adenine, New York. 327-343.
48. Sundaralingam, M., and E. Westhof. 1981. Structural motifs of the nucleotidyl unit and the handedness of polynucleotide helices. Int. J. Quantum Chem. (Suppl. 8):287-306.
49. Chaires, J. B., and J. M. Sturtevant. 1988. Thermodynamics of the B to Z transition in poly(DGDC). Biopolymers. 27:1375-1387.
50. Saenger, W., and U. Heinemann. 1989. Raison d'être and structural model for the B-Z transition of poly d(G-C)·poly d(G-C). FEBS Lett. 257:223-227.
51. Ivanov, V., K. Grzeskowiak, and G. Zocchi. 2003. Evidence for an intermediate state in the B-to-Z transition of DNA. J. Phys. Chem. B. 107:12847-12850.
52. Ha, S. C., K. Lowenhaupt, Y.-G. Kim, K. K. Kim, and A. Rich. 2005. Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature. 437:1183-1186.
53. Klimasauskas, S., S. Kumar, R. J. Roberts, and X. Cheng. 1994. Hhal methyltransferase flips its target base out of the DNA helix. Cell. 76:357-369.
54. Chen, Y. Z., and E. W. Prohofsky. 1994. Nonlinear effects and thermal expansion as expressed in self-consistent phonon calculations on the temperature dependence of a phase change: application to the B to Z conformation change in DNA. Phys. Rev. E. 49:3444-3451.
55. Ho, P. S. 1994. The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proc. Natl. Acad. Sci. USA. 91:9549-9553.
56. Cheatham, T. E., and M. A. Young. 2000. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers. 56:232-256.
57. Brown, B. A., K. Lowenhaupt, C. M. Wilbert, E. B. Hanlon, and A. Rich. 2000. The Z-α domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. Proc. Natl. Acad. Sci. USA. 97:13532-13536.
58. van Lier, J. J. C., M. T. Smits, and H. M. Buck. 1983. B-Z Transition in methylated DNA - a quantum-chemical study. Eur. J. Biochem. 132:55-62.
59. van Gunsteren, W. F., T. C. Beutler, F. Fraternali, P. M. King, A. E. Mark, and P. E. Smith. 1993. Computation of free energy in practice: choice of approximations and accuracy limiting factors. In Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, Vol. 2. W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, editors. ESCOM Science Publishers, Leiden, The Netherlands. 267-314.
60. Beutler, T. C., and W. F. van Gunsteren. 1994. The computation of a potential of mean force: choice of the biasing potential in the umbrella sampling technique. J. Chem. Phys. 100:1492-1497.
61. Mezei, M., and D. L. Beveridge. 1986. Free energy simulations. Ann. Acad. Sci. NY. 482:1-23.
62. Kollman, P. 1993. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93:2395-2417.
63. Radmer, R. J., and P. A. Kollman. 1997. Free energy calculation methods: a theoretical and empirical comparison of numerical errors and a new method for qualitative estimates of free energy changes. J. Comput. Chem. 18:902-919.
64. Mark, A. E. 1998. Free energy perturbation calculations. In Encyclopedia of Computational Chemistry, Vol. 2. P. von Rague Schleyer, editor. John Wiley and Sons, New York. 1070-1083.
65. Dang, L. X., D. A. Pearlman, and P. A. Kollman. 1990. Why do A·T basepairs inhibit Z-DNA formation? Proc. Natl. Acad. Sci. USA. 87:4630-4634.
66. Pearlman, D. A., and P. A. Kollman. 1990. The calculated free energy effects of 5-Methyl Cytosine on the B to Z transition in DNA. Biopolymers. 29:1193-1209.
67. Soumpasis, D. M. 1984. Statistical mechanics of the B → Z transition of DNA: contribution of diffuse ionic interactions. Proc. Natl. Acad. Sci. USA. 81:5116-5120.
68. Fenley, M. O., G. S. Manning, and W. K. Olson. 1990. A numerical counterion condensation analysis of the B-Z transition of DNA. Biopolymers. 30:1205-1213.
69. Montoro, J. C. G., and J. L. F. Abascal. 1996. A method for the computer simulation of the free-energy difference in conformational changes of polyelectrolytes. Application to the B- to Z-DNA transition. Europhys. Lett. 34:471-476.
70. Montoro, J. C. G., and J. L. F. Abascal. 1997. The free energy difference between simple models of B- and Z-DNA: computer simulation and theoretical predictions. J. Chem. Phys. 106:8239-8253.
71. Zhou, H., Y. Zhang, and Z.-C. Ou-Yang. 2000. Elastic property of single double-stranded DNA molecules: theoretical study and comparison with experiments. Phys. Rev. E. 62:1045-1058.
72. Abascal, J. L. F., and J. C. G. Montoro. 2000. Computer simulation results for the free-energy difference between B-DNA and Z-DNA. J. Phys. Cond. Mat. 12:A327-A332.
73. Abascal, J. L. F., and J. C. G. Montoro. 2004. Computer simulation of the thermodynamics of the B-Z-DNA transition: effect of the ionic size and charge. Mol. Phys. 102:2141-2148.
74. Dong, R. X., and X. L. Yan. 2004. The theoretical study of the effects of salt on structure transition of B-DNA to Z-DNA. Acta Sinica Physica. 53:4414-4419.
75. Elber, R., A. Ghosh, and A. Cardenas. 2002. Long time dynamics of complex systems. Acc. Chem. Res. 35:396-403.
76. Lim, W., and Y. P. Feng. 2005. The stretched intermediate model of B-Z DNA transition. Biophys. J. 88:1593-1607.
77. Lim, W., and Y. P. Feng. 2005. Applying the stochastic difference equation to DNA conformational transitions: a study of B-Z and B-A DNA transitions. Biopolymers. 78:107-120.
78. Jares-Erijman, E. A., and T. M. Jovin. 1996. Determination of DNA helical handedness by fluorescence resonance energy transfer. J. Mol. Biol. 257:597-617.
79. Ghosh, A., C. S. Rapp, and R. A. Friesner. 1998. A generalized Born model based on a surface integral formulation. J. Phys. Chem. B. 102:10983-10990.
80. Gnanakaran, S., H. Nymeyer, J. Portman, K. Y. Sanbonmatsu, and A. E. Garcia. 2003. Peptide folding simulations. Curr. Opin. Struct. Biol. 13:168-174.
81. Zhou, R. H., and B. J. Berne. 2002. Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water? Proc. Natl. Acad. Sci. USA. 99:12777-12782.
82. Zhou, R. H., G. Krilov, and B. J. Berne. 2004. Comment on "Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?" The Poisson-Boltzmann equation. J. Phys. Chem. B. 108:7528-7530.
83. Song, M. Y., S. Kim, and M. S. Jhon. 1988. A theoretical study on the hydration of B-and Z-DNA double helices. J. Mol. Struct. 179:427-437.
84. Chalikian, T. V., A. P. Sarvazyan, G. E. Plum, and K. J. Breslauer. 1994. Influence of base composition, base sequence, and duplex structure on DNA hydration: apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25°C. Biochemistry. 33:2394-2401.
85. Schneider, B., and H. M. Berman. 1995. Hydration of the DNA bases is local. Biophys. J. 69:2661-2669.
86. Feig, M., and B. M. Pettitt. 1998. A molecular simulation picture of DNA hydration around A- and B-DNA. Biopolymers. 48:199-209.
87. Schneider, B., K. Patel, and H. M. Berman. 1998. Hydration of the phosphate group in double-helical DNA. Biophys. J. 75:2422-2434.
88. Barciszewski, J., J. Jurczak, S. Porowski, T. Specht, and V. A. Erdmann. 1999. The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions. Eur. J. Biochem. 260:293-307.
89. Kang, N. S., K. T. No, and M. S. Jhon. 2003. A study of the hydrogen-bonded network around the left-handed and right-handed DNA in an ionic solution. Mol. Sim. 29:83-89.
90. Pal, S. K., and A. H. Zewail. 2004. Dynamics of water in biological recognition. Chem. Rev. 104:2099-2123.
91. Schlitter, J., M. Engels, P. Krüger, E. Jacoby, and A. Wollmer. 1993. Targeted molecular dynamics simulation of conformational change - application to the T ↔ R transition in insulin. Mol. Sim. 10:291-309.
92. Schlitter, J., M. Engels, and P. Krüger. 1994. Targeted molecular dynamics - a new approach for searching pathways of conformational transitions. J. Mol. Graph. 12:84-89.
93. Díaz, J. F., B. Wroblowski, J. Schlitter, and Y. Engelborghs. 1997. Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum. Proteins Struct. Funct. Genet. 28:434-451.
94. Schlitter, J., W. Swegat, and T. Mülders. 2001. Distance-type reaction coordinates for modeling activated processes. J. Mol. Model. (Online). 7:171-177.
95. Zwanzig, R. W. 1954. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J. Chem. Phys. 22:1420-1426.
96. Rosemeyer, H., and F. Seela. 2002. Modified purine nucleosides as dangling ends of DNA duplexes: the effect of the nucleobase polarizability on stacking interactions. J. Chem. Soc., Perkin Trans. 2. 4:746-750.
97. Wang, A. H. J., G. J. Quigley, F. J. Kolpak, G. van der Marel, J. H. van Boom, and A. Rich. 1981. Left-handed double helical DNA - variations in the backbone conformation. Science. 211:171-176.
98. Gessner, R. V., G. J. Quigley, A. H. J. Wang, G. A. van der Marel, and A. Rich. 1985. Structural basis for stabilization of Z-DNA by cobalt hexamine and magnesium cations. Biochemistry. 24:237-240.
99. 3+(6) salt of d(CGCGCG) at 1.2 Å resolution. J. Biomol. Struct. Dyn. 4:521-534.
100. Gessner, R. V., C. A. Rederick, G. J. Quigley, A. Rich, and A. H. J. Wang. 1989. The molecular structure of the left-handed Z-DNA double helix at 1.0-Å atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG). J. Biol. Chem. 264:7921-7935.
101. Norberg, J., and L. Nilsson. 1996. Glass transition in DNA from molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 93:10173-10176.
102. Malinina, L., V. Tereshko, E. Ivanova, J. A. Subirana, V. Zarytova, and Y. Nekrasov. 1998. Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG). Biophys. J. 74:2482-2490.
103. Ho, P. S., M. J. Ellison, G. J. Quigley, and A. Rich. 1986. A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J. 5:2737-2744.
104. van Gunsteren, W. F., S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi. 1996. Biomolecular Simulation: The GROMOS96 Manual and User Guide. Vdf Hochschulverlag AG an der ETH Zürich, Zürich, Switzerland.
105. Scott, W. R. P., P. H. Hünenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krüger, and W. F. van Gunsteren. 1999. The GROMOS biomolecular simulation program package. J. Phys. Chem. A. 103:3596-3607.
106. Soares, T. A., P. H. Hünenberger, M. A. Kastenholz, V. Kräutler, T. Lenz, R. D. Lins, C. Oostenbrink, and W. F. van Gunsteren. 2005. An improved nucleic-acid parameter set for the GROMOS force field. J. Comput. Chem. 26:725-737.
107. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces. B. Pullman, editor. Reidel, Dordrecht, The Netherlands. 331-342.
108. Barker, J. A., and R. O. Watts. 1973. Monte Carlo studies of the dielectric properties of water-like models. Mol. Phys. 26:789-792.
109. Tironi, I. G., R. Sperb, P. E. Smith, and W. F. van Gunsteren. 1995. A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102:5451-5459.
110. Glättli, A., X. Daura, and W. F. van Gunsteren. 2002. Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/L. J. Chem. Phys. 116:9811-9828.
111. Madura, J. D., and B. M. Pettitt. 1988. Effect of truncating long-range interactions in aqueous ionic solution simulations. Chem. Phys. Lett. 150:105-108.
112. Schreiber, H., and O. Steinhauser. 1992. Molecular dynamics studies of solvated polypeptides: why the cut-off scheme does not work. Chem. Phys. 168:75-89.
113. Schreiber, H., and O. Steinhauser. 1992. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry. 31:5856-5860.
114. Smith, P. E., and W. F. van Gunsteren. 1993. Methods for the evaluation of long range electrostatic forces in computer simulations of molecular systems. In Computer Simulation of Biomolecular Systems, Vol. 2. Theoretical and Experimental Applications. P. K. van Gunsteren, W. F. and Weiner, and A. J. Wilkinson, editors. ESCOM Science Publishers, Leiden, The Netherlands. 182-212.
115. Norberg, J., and L. Nilsson. 2000. On the truncation of long-range electrostatic interactions in DNA. Biophys. J. 79:1537-1553.
116. Patra, M., M. Karttunen, M. T. Hyvonen, E. Falck, P. Lindqvist, and I. Vattulainen. 2003. Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. Biophys. J. 84:3636-3645.
117. Yonetani, Y. 2005. A severe artifact in simulation of liquid water using a long cut-off length: appearance of a strange layer structure. Chem. Phys. Lett. 406:49-53.
118. van der Spoel, D., and P. J. van Maaren. 2006. The origin of layer structure artifacts in simulations of liquid water. J. Chem. Theor. Comput. 2:1-11.
119. Ala acceptor stem: comparison between continuum reaction field and particle-mesh Ewald electrostatic treatments. J. Phys. Chem. B. 106:3696-3705.
120. Luty, B. A., and W. F. van Gunsteren. 1996. Calculating electrostatic interactions using the particle-particle particle-mesh method with nonperiodic long-range interactions. J. Phys. Chem. 100:2581-2587.
121. Hünenberger, P. H., and J. A. McCammon. 1999. Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: a continuum electrostatics study. J. Chem. Phys. 110:1856-1872.
122. Hünenberger, P. H., and J. A. McCammon. 1999. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys. Chem. 78:69-88.
123. Weber, W., P. H. Hünenberger, and J. A. McCammon. 2000. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. J. Phys. Chem. B. 104:3668-3675.
124. Boresch, S., and O. Steinhauser. 2001. The dielectric self-consistent field method. I. Highways, byways, and illustrative results. J. Chem. Phys. 115:10780-10792.
125. Boresch, S., and O. Steinhauser. 2001. The dielectric self-consistent field method. II. Application to the study of finite range effects. J. Chem. Phys. 115:10793-10807.
126. Kastenholz, M. A., and P. H. Hünenberger. 2004. Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods. J. Phys. Chem. B. 108:774-788.
127. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
128. Ryckaert, J.-P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
129. McLachlan, A. D. 1979. Gene duplications in the structural evolution of chymotrypsin. J. Mol. Biol. 128:49-79.
130. Kirkwood, J. G. 1935. Statistical mechanics of fluid mixtures. J. Chem. Phys. 3:300-313.
131. Fixman, M. 1974. Classical statistical mechanics of constraints: a theorem and application to polymers. Proc. Natl. Acad. Sci. USA. 71:3050-3053.
132. van Gunsteren, W. F., and M. Karplus. 1982. Effect of constraints on the dynamics of macromolecules. Macromolecules. 15:1528-1544.
133. Markwick, P. R. L., N. L. Doltsinis, and D. Marx. 2005. Targeted CarCrossed D signParrinello molecular dynamics: elucidating double proton transfer in formic acid dimer. J. Chem. Phys. 122:054112.
134. Williams, A. L. J., C. Cheong, I. J. Tinoco, and L. B. Clark. 1986. Vacuum ultraviolet circular dichroism as an indicator of helical handedness in nucleic acids. Nucleic Acids Res. 14:6649-6659.
135. Bayley, P. M., E. B. Nielsen, and J. A. Schellman. 1969. Rotatory properties of molecules containing two peptide groups - theory. J. Phys. Chem. 73:228-243.
136. Madison, V., and J. Schellman. 1972. Optical activity of polypeptides and proteins. Biopolymers. 11:1041-1076.
137. Lee, H., T. A. Darden, and L. G. Pedersen. 1995. Molecular dynamics simulation studies of a high resolution Z-DNA crystal. J. Chem. Phys. 102:3830-3834.
138. Hünenberger, P. H. 1999. Lattice-sum methods for computing electrostatic interactions in molecular simulations. In Simulation and Theory of Electrostatic Interactions in Solution: Computational Chemistry, Biophysics, and Aqueous Solution. G. Hummer, and L. R. Pratt, editors. American Institute of Physics, New York. 17-83.
139. Glättli, A., X. Daura, D. Seebach, and W. F. van Gunsteren. 2002. Can one derive the conformational preference of a β-peptide from its CD spectrum? J. Am. Chem. Soc. 124:12972-12978.