Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model

Biophysical Journal

Volumn 76, Issue 6, 1999, Pages 3192-3205

  Williams, D Jeremy ^a   Hall, Kathleen B ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; DYNAMICS; NUCLEAR MAGNETIC RESONANCE; NUCLEIC ACID STRUCTURE; RNA STRUCTURE; SIMULATION; SOLVATION; STOCHASTIC MODEL; THERMODYNAMICS; VACUUM;

ACRONICTA LEPORINA;

EID: 0033064123     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77471-0     Document Type: Article

References (61)

1. Allain, F. H. T., and G. Varani. 1995. Structure of the Pl helix from group I self-splicing introns. J. Mol. Biol. 250:333-353.
2. Auffinger, P., S. Louise-May, and E. Westhof. 1995. Multiple molecular dynamics simulations of the anticodon loop of tRNA(Asp) in aqueous solutions with counterions. J. Am. Chem. Soc. 117:6720-6726.
3. Auffinger, P., and E. Westhof. 1997. Rules governing the orientation of the 2′-hydroxyl group in RNA. J. Mol. Biol. 274:54-63.
4. Beveridge, D. L., and G. Ravishanker. 1994. Molecular dynamics studies of DNA. Curr. Opin. Struct. Biol. 4:246-255.
5. Briki, F., J. Ramstein, R. Lavery, and D. Genest. 1991. Evidence for the stochastic nature of base pair opening in DNA: a Brownian dynamics simulation. J. Am. Chem. Soc. 113:2490-2493.
6. Brunger, A. T. 1992. X-PLOR 3.1: A System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT.
7. Caves, L. S. D., J. D. Evanseck, and M. Karplus. 1998. Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. Protein Sci. 7:649-666.
8. Cheatham, T. E., III, and P. A. Kollman. 1996. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J. Mol. Biol. 259:434-444.
9. Cheatham, T. E., III, and P. A. Kollman. 1997. Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes. J. Am. Chem. Soc. 119: 4805-4825.
10. Cheatham, T. E., III, J. L. Miller, T. Fox, T. A. Darden, and P. A. Kollman. 1995. Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J. Am. Chem. Soc. 117:4193-4194.
11. Cheong, C., G. Varani, and I. Tinoco, Jr. 1990. Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC. Nature. 346: 680-682.
12. 2 determined by NMR. Nucleic Acids Res. 24:3693-3699.
13. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117: 5179-5197.
14. Daggett, V., P. A. Kollman, and I. D. Kuntz. 1991. Molecular dynamics simulations of small peptides: dependence on dielectric model and pH. Biopolymers. 31:285-304.
15. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J. Phys. Chem. 98:10089-10092.
16. Dudek, M. J., and J. W. Ponder. 1995. Accurate modeling of the intramolecular electrostatic energy of proteins. J. Comp. Chem. 16:791-816.
17. 3. Biopolymers. 22:1107-1131.
18. Fritsch, V., G. Ravishanker, D. L. Beveridge, and E. Westhof. 1993. Molecular dynamics simulations of poly(dA)·poly(dT): comparisons between implicit and explicit solvent representations. Biopolymers. 33: 1537-1552.
19. Guarnieri, F., and W. C. Still. 1994. A rapidly convergent simulation method: mixed Monte Carlo/stochastic dynamics. J. Comp. Chem. 15: 1302-1310.
20. Guarnieri, F., and H. Weinstein. 1996. Conformational memories and the exploration of biologically relevant peptide conformations: an illustration for the gonadotropin-releasing hormone. J. Am. Chem. Soc. 118: 5580-5589.
21. Hall, K. B. 1994. Interactions of RNA hairpins with the human U1A N-terminal RNA binding domain. Biochemistry. 33:10076-10088.
22. Harvey, S. C. 1989. Treatment of electrostatic effects in macromolecular modeling. Proteins. 5:78-92.
23. Heus, H. A., and A. Pardi. 1991. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science. 253:191-194.
24. Hingerty, B. E., R. H. Ritchie, T. L. Ferrell, and J. E. Turner. 1985. Dielectric effects in biopolymers: the theory of ionic saturation revisited. Blopolymers. 24:427-439.
25. Jayaram, B., D. Sprous, M. A. Young, and D. L. Beveridge. 1998. Free energy analysis of the conformational preferences of A and B forms of DNA in solution. J. Am. Chem. Soc. 120:10629-10633.
26. Jean-Charles, A., A. Nicholls, K. Sharp, B. Honig, A. Tempczyk, T. F. Hendrickson, and W. C. Still. 1991. Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations. J. Am. Chem. Soc. 113:1454-1455.
27. Lesnik, E. A., and S. M. Freier. 1998. What affects the effect of 2′-alkoxy modifications? 1. Stabilization of 2′-methoxy substitutions in uniformly modified DNA oligonucleotides. Biochemistry. 37:6991-6997.
28. 13C. Magn. Reson. Chem. 34:S11-S17.
29. Marrone, T. J., M. K. Gilson, and J. A. McCammon. 1996. Comparison of continuum and explicit models of solvation: potentials of mean force for alanine dipeptide. J. Phys. Chem. 100:1439-1441.
30. Mazur, J., and R. L. Jernigan. 1991. Distance-dependent dielectric constants and their application to double-helical DNA. Biopolymers. 31: 1615-1629.
31. McCammon, J. A., and S. Harvey. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
32. 2 dodecamer. J. Am. Chem. Soc. 115:1526-1537.
33. Miller, J. L., and P. A. Kollman. 1997a. Observation of an A-DNA to B-DNA transition in a non-helical nucleic acid hairpin molecule using molecular dynamics. Biophys. J. 73:2702-2710.
34. Miller, J. L., and P. A. Kollman. 1997b. Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. J. Mol. Biol. 270:436-450.
35. Mohamadi, F., N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chang, T. Hendrickson, and W. C. Still. 1990. Macro-Model - an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J. Camp. Chem. 11: 440-467.
36. Nowakowski, J., J. L. Miller, P. A. Kollman, and I. Tinoco, Jr. 1996. Time evolution of NMR proton chemical shifts of an RNA hairpin during a molecular dynamics simulation. J. Am. Chem. Soc. 118:12812-12820.
37. Palmer, A. G., III, and D. A. Case. 1992. Molecular dynamics analysis of NMR relaxation in a zinc-finger peptide. J. Am. Chem. Soc. 114: 9059-9067.
38. Pappu, R. V., G. R. Marshall, and J. W. Ponder. 1999. A potential smoothing algorithm accurately predicts transmembrane helix packing. Nature Struct. Biol. 6:50-55.
39. Piela, L., J. Kostrowicki, and H. A. Scheraga. 1989. The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method. J. Phys. Chem. 93:3339-3346.
40. Press, W. H., B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling. 1992. Numerical Recipes: The Art of Scientific Computing, 2nd ed. Cambridge University Press, Cambridge. 689-692.
41. Qiu, D., P. S. Shenkin, F. P. Hollinger, and W. C. Still. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. 101:3005-3014.
42. Ramstein, J., and R. Lavery. 1988. Energetic coupling between DNA bending and base pair opening. Proc. Natl. Acad. Sci. USA. 85: 7231-7235.
43. 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. Comp. Phys. 23: 327-341.
44. Sakata, T., H. Hiroaki, Y. Oda, T. Tanak, M. Ikehara, and S. Uesugi. 1990. Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides. Nucleic Acids Res. 18:3831-3839.
45. Schaefer, M., C. Bartels, and M. Karplus. 1998. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J. Mol. Biol. 284:835-848.
46. Schreiber, H., and O. Steinhauser. 1992. Cutoff size does influence molecular dynamics results on solvated polypeptides. Biochemistry. 31: 5856-5860.
47. Simmerling, C., J. L. Miller, and P. A. Kollman. 1998. Combined locally enhanced sampling and particle mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid. J. Am. Chem. Soc. 120:7149-7155.
48. Singh, S. B., and P. A. Kollman. 1996. Understanding the thermodynamic stability of an RNA hairpin and its mutant. Biophys. J. 70:1940-1948.
49. Smart, J. L., T. J. Marrone, and J. A. McCammon. 1997. Conformational sampling with Poisson-Boltzmann forces and a stochastic dynamics/ Monte Carlo method: application to alanine dipeptide. J. Comput. Chem. 18:1750-1759.
50. Smith, D. A., and S. Vijayakumar. 1991. Molecular modeling of intramolecular hydrogen bonding in simple oligoamides 2. GB/SA CH2C12. Tetrahedron Lett. 32:3617-3620.
51. Soman, K. V., A. Karimi, and D. A. Case. 1993. Molecular dynamics analysis of a ribonuclease C-peptide analogue. Biopolymers. 33: 1567-1580.
52. Srinivasan, J., T. E. Cheatham, III, P. Cieplak, P. A. Kollman, and D. A. Case. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidite-DNA helices. J. Am. Chem. Soc. 120:9401-9409.
53. Still, W. C., A. Tempczyk, R. C. Hawley, and T. Hendrickson. 1990. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112:6127-6129.
54. Tinoco, I., Jr. 1996, Nucleic acid structures, energetics, and dynamics. J. Phys. Chem. 100:13311-13322.
55. Tuerk, C., P. Gauss, C. Thermes, D. R. Groebe, M. Gayle, N. Guild, G. Stormo, Y. D'Aubenton-Carafa, O. C. Uhlenbeck, I. Tinoco, Jr., E. N. Brody, and L. Gold. 1988. CUUCGG hairpins: extraordinarily stable RNA secondary structure associated with various biochemical processes. Proc. Natl. Acad. Sci. USA. 85:1364-1368.
56. van Gunsteren, W. F., and H. J. C. Berendsen. 1988. A leap-frog algorithm for stochastic dynamics. Mol. Simul. 1:173-185.
57. Varani, G., G. Cheong, and I. Tinoco, Jr. 1991. Structure of an unusually stable RNA hairpin. Biochemistry. 30:3280-3289.
58. Williams, D. J., and K. B. Hall. 1996. Conformations of 1,2-dimethoxyethane in gas and solution phase from molecular mechanics and Monte Carlo/stochastic dynamics simulations. J. Phys. Chem. 100: 8224-8229.
59. Woese, C. R., S. Winker, and R. R. Gutell. 1990. Architecture of ribosomal RNA: constraints on the sequence of "terra-loops." Proc. Natl. Acad. Sci. USA. 87:8467-8471.
60. Young, M. A., G. Ravishanker, and D. L. Beveridge. 1997. A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation. Biophys. J. 73:2313-2336.
61. Zichi, D. A. 1995. Molecular dynamics of RNA with the OPLS force field. Aqueous simulations of a hairpin containing a tetranucleotide loop. J. Am. Chem. Soc. 117:2957-2969.