Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model
10.1016/s0006-3495(99)77471-0
Crossref journal-article
Elsevier BV
Biophysical Journal (78)
Bibliography

Williams, D. J., & Hall, K. B. (1999). Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model. Biophysical Journal, 76(6), 3192–3205.

Authors 2
  1. D. Jeremy Williams (first)
  2. Kathleen B. Hall (additional)
References 61 Referenced 49
  1. 10.1006/jmbi.1995.0381 / J. Mol. Biol. / Structure of the P1 helix from group I self-splicing introns by Allain (1995)
  2. 10.1021/ja00130a011 / J. Am. Chem. Soc. / Multiple molecular dynamics simulations of the anticodon loop of tRNA(Asp) in aqueous solutions with counterions by Auffinger (1995)
  3. 10.1006/jmbi.1997.1370 / J. Mol. Biol. / Rules governing the orientation of the 2′-hydroxyl group in RNA by Auffinger (1997)
  4. 10.1016/S0959-440X(94)90316-6 / Curr. Opin. Struct. Biol. / Molecular dynamics studies of DNA by Beveridge (1994)
  5. 10.1021/ja00007a023 / J. Am. Chem. Soc. / Evidence for the stochastic nature of base pair opening in DNA: a Brownian dynamics simulation by Briki (1991)
  6. {'key': '10.1016/S0006-3495(99)77471-0_bib6', 'series-title': 'X-PLOR 3.1: A System for X-ray Crystallography and NMR', 'author': 'Brunger', 'year': '1992'} / X-PLOR 3.1: A System for X-ray Crystallography and NMR by Brunger (1992)
  7. 10.1002/pro.5560070314 / Protein Sci. / Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin by Caves (1998)
  8. 10.1006/jmbi.1996.0330 / J. Mol. Biol. / Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution by Cheatham (1996)
  9. 10.1021/ja963641w / J. Am. Chem. Soc. / Molecular dynamics simulations highlight the structural differences among DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes by Cheatham (1997)
  10. 10.1021/ja00119a045 / J. Am. Chem. Soc. / Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins by Cheatham (1995)
  11. 10.1038/346680a0 / Nature / Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC by Cheong (1990)
  12. 10.1093/nar/24.19.3693 / Nucleic Acids Res. / Hydration of the RNA duplex r(CGCAAAUUUGCG)2 determined by NMR by Conte (1996)
  13. 10.1021/ja00124a002 / J. Am. Chem. Soc. / A second generation force field for the simulation of proteins, nucleic acids, and organic molecules by Cornell (1995)
  14. 10.1002/bip.360310304 / Biopolymers / Molecular dynamics simulations of small peptides: dependence on dielectric model and pH by Daggett (1991)
  15. 10.1063/1.464397 / J. Phys. Chem. / Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems by Darden (1993)
  16. 10.1002/jcc.540160702 / J. Comp. Chem. / Accurate modeling of the intramolecular electrostatic energy of proteins by Dudek (1995)
  17. 10.1002/bip.360220408 / Biopolymers / Solvent effects on the dynamics of (dG-dC)3 by Freier (1983)
  18. 10.1002/bip.360331005 / Biopolymers / Molecular dynamics simulations of poly(dA)·poly(dT): comparisons between implicit and explicit solvent representations by Fritsch (1993)
  19. 10.1002/jcc.540151111 / J. Comp. Chem. / A rapidly convergent simulation method: mixed Monte Carlo/stochastic dynamics by Guarnieri (1994)
  20. 10.1021/ja952745o / J. Am. Chem. Soc. / Conformational memories and the exploration of biologically relevant peptide conformations: an illustration for the gonadotropin-releasing hormone by Guarnieri (1996)
  21. 10.1021/bi00199a035 / Biochemistry / Interactions of RNA hairpins with the human U1A N-terminal RNA binding domain by Hall (1994)
  22. 10.1002/prot.340050109 / Proteins / Treatment of electrostatic effects in macromolecular modeling by Harvey (1989)
  23. 10.1126/science.1712983 / Science / Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops by Heus (1991)
  24. 10.1002/bip.360240302 / Biopolymers / Dielectric effects in biopolymers: the theory of ionic saturation revisited by Hingerty (1985)
  25. 10.1021/ja981307p / J. Am. Chem. Soc. / Free energy analysis of the conformational preferences of A and B forms of DNA in solution by Jayaram (1998)
  26. 10.1021/ja00004a079 / J. Am. Chem. Soc. / Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations by Jean-Charles (1991)
  27. 10.1021/bi972995c / Biochemistry / What affects the effect of 2′-alkoxy modifications? 1. Stabilization of 2′-methoxy substitutions in uniformly modified DNA oligonucleotides by Lesnik (1998)
  28. 10.1002/(SICI)1097-458X(199612)34:13<S11::AID-OMR17>3.0.CO;2-X / Magn. Reson. Chem. / NMR assignment of a 2′-hydroxyl proton from the UUCG tetraloop through long-range correlations with 13C by Lynch (1996)
  29. 10.1021/jp952835f / J. Phys. Chem. / Comparison of continuum and explicit models of solvation: potentials of mean force for alanine dipeptide by Marrone (1996)
  30. 10.1002/bip.360311316 / Biopolymers / Distance-dependent dielectric constants and their application to double-helical DNA by Mazur (1991)
  31. {'key': '10.1016/S0006-3495(99)77471-0_bib31', 'series-title': 'Dynamics of Proteins and Nucleic Acids', 'author': 'McCammon', 'year': '1987'} / Dynamics of Proteins and Nucleic Acids by McCammon (1987)
  32. 10.1021/ja00057a045 / J. Am. Chem. Soc. / Molecular dynamics simulations of the hydrated d(CGCGAATTCGCG)2 dodecamer by Miaskiewicz (1993)
  33. 10.1016/S0006-3495(97)78298-5 / Biophys. J. / Observation of an A-DNA to B-DNA transition in a non-helical nucleic acid hairpin molecule using molecular dynamics by Miller (1997)
  34. 10.1006/jmbi.1997.1113 / J. Mol. Biol. / Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics by Miller (1997)
  35. 10.1002/jcc.540110405 / J. Comp. Chem. / MacroModel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics by Mohamadi (1990)
  36. 10.1021/ja9625945 / J. Am. Chem. Soc. / Time evolution of NMR proton chemical shifts of an RNA hairpin during a molecular dynamics simulation by Nowakowski (1996)
  37. 10.1021/ja00049a043 / J. Am. Chem. Soc. / Molecular dynamics analysis of NMR relaxation in a zinc-finger peptide by Palmer (1992)
  38. 10.1038/5891 / Nature Struct. Biol. / A potential smoothing algorithm accurately predicts transmembrane helix packing by Pappu (1999)
  39. 10.1021/j100345a090 / J. Phys. Chem. / The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method by Piela (1989)
  40. {'key': '10.1016/S0006-3495(99)77471-0_bib40', 'series-title': 'Numerical Recipes: The Art of Scientific Computing', 'author': 'Press', 'year': '1992'} / Numerical Recipes: The Art of Scientific Computing by Press (1992)
  41. 10.1021/jp961992r / J. Phys. Chem. / The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii by Qiu (1997)
  42. 10.1073/pnas.85.19.7231 / Proc. Natl. Acad. Sci. USA / Energetic coupling between DNA bending and base pair opening by Ramstein (1988)
  43. 10.1016/0021-9991(77)90098-5 / J. Comp. Phys. / Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes by Ryckaert (1977)
  44. 10.1093/nar/18.13.3831 / Nucleic Acids Res. / Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides by Sakata (1990)
  45. 10.1006/jmbi.1998.2172 / J. Mol. Biol. / Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model by Schaefer (1998)
  46. 10.1021/bi00140a022 / Biochemistry / Cutoff size does influence molecular dynamics results on solvated polypeptides by Schreiber (1992)
  47. 10.1021/ja9727023 / J. Am. Chem. Soc. / Combined locally enhanced sampling and particle mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid by Simmerling (1998)
  48. 10.1016/S0006-3495(96)79758-8 / Biophys. J. / Understanding the thermodynamic stability of an RNA hairpin and its mutant by Singh (1996)
  49. 10.1002/(SICI)1096-987X(19971115)18:14<1750::AID-JCC4>3.0.CO;2-J / J. Comput. Chem. / Conformational sampling with Poisson-Boltzmann forces and a stochastic dynamics/Monte Carlo method: application to alanine dipeptide by Smart (1997)
  50. 10.1016/S0040-4039(00)79789-9 / Tetrahedron Lett. / Molecular modeling of intramolecular hydrogen bonding in simple oligoamides 2. GB/SA CH2Cl2 by Smith (1991)
  51. 10.1002/bip.360331007 / Biopolymers / Molecular dynamics analysis of a ribonuclease C-peptide analogue by Soman (1993)
  52. 10.1021/ja981844+ / J. Am. Chem. Soc. / Continuum solvent studies of the stability of DNA, RNA, and phosphoramidite-DNA helices by Srinivasan (1998)
  53. 10.1021/ja00172a038 / J. Am. Chem. Soc. / Semianalytical treatment of solvation for molecular mechanics and dynamics by Still (1990)
  54. 10.1021/jp953053p / J. Phys. Chem. / Nucleic acid structures, energetics, and dynamics by Tinoco (1996)
  55. 10.1073/pnas.85.5.1364 / Proc. Natl. Acad. Sci. USA / CUUCGG hairpins: extraordinarily stable RNA secondary structure associated with various biochemical processes by Tuerk (1988)
  56. 10.1080/08927028808080941 / Mol. Simul. / A leap-frog algorithm for stochastic dynamics by van Gunsteren (1988)
  57. 10.1021/bi00227a016 / Biochemistry / Structure of an unusually stable RNA hairpin by Varani (1991)
  58. 10.1021/jp952581y / J. Phys. Chem. / Conformations of 1,2-dimethoxyethane in gas and solution phase from molecular mechanics and Monte Carlo/stochastic dynamics simulations by Williams (1996)
  59. 10.1073/pnas.87.21.8467 / Proc. Natl. Acad. Sci. USA / Architecture of ribosomal RNA: constraints on the sequence of “tetra-loops.” by Woese (1990)
  60. 10.1016/S0006-3495(97)78263-8 / Biophys. J. / A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation by Young (1997)
  61. 10.1021/ja00116a001 / J. Am. Chem. Soc. / Molecular dynamics of RNA with the OPLS force field. Aqueous simulations of a hairpin containing a tetranucleotide loop by Zichi (1995)
Dates
Type When
Created 16 years, 7 months ago (Jan. 6, 2009, 2:21 a.m.)
Deposited 6 years, 8 months ago (Dec. 22, 2018, 4:21 p.m.)
Indexed 2 months, 1 week ago (June 26, 2025, 9:29 a.m.)
Issued 26 years, 3 months ago (June 1, 1999)
Published 26 years, 3 months ago (June 1, 1999)
Published Print 26 years, 3 months ago (June 1, 1999)
Funders 0

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@article{Williams_1999, title={Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model}, volume={76}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/s0006-3495(99)77471-0}, DOI={10.1016/s0006-3495(99)77471-0}, number={6}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Williams, D. Jeremy and Hall, Kathleen B.}, year={1999}, month=jun, pages={3192–3205} }