Molecular Dynamics Simulation of the Anticodon Arm of Phenylalanine Transfer RNA

  • Lennart Nilsson
  • Martin Karplus
Part of the NATO ASI Series book series (NSSA, volume 110)


Nucleic acid structures (Saenger, 1984), range from the classical double helices of A- and B-DNA, the detailed 3 D structures of crystalline tRNA (Kim et al., 1974; Ladner et al., 1975) to various DNA oligonucleotides in both left handed and right handed helical forms, for which there now is a wealth of experimental data (Saenger, 1984). This structural diversity has prompted numerous theoretical studies of the equilibrium properties of nucleic acids (see Olson, 1982, and references therein). By contrast only a very limited number of dynamical simulations of DNA (Levitt, 1983; Tidor et al., 1983) and tRNA (Harvey et al., 1984) have been reported.


Hydrogen Bond Length tRNA Molecule Anticodon Loop Nucleic Acid Structure Anisotropy Decay 
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  1. Brooks, B. R., Bruccoleri, R. E., Olafson, B.D., States, D. J., Swaminathan, S., and Karplus, M., 1983, CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comp. Chem., 4:187.CrossRefGoogle Scholar
  2. Brunger, A. T., Brooks, C. B., Karplus, M., 1985, Proc. Natl. Acad. Sci. USA, in pressGoogle Scholar
  3. Claesens, F., and Rigler, R., 1985, Conformational Dynamics of the Anticodon Loop in Yeast tRNAPhe as Sensed by the Fluorescence of Wybutine, Eur. Biophys. J., in pressGoogle Scholar
  4. Edholm, O., Nilsson, L., Berg, O., Ehrenberg, M., Claesens, F., Gräslund, A., Jönsson, B., and Teleman, O., 1984, Biomolecular dynamics. A report from a workshop in Gysinge, Sweden, October 4–7, 1982., Quart Rev. Biophys., 17:125.CrossRefGoogle Scholar
  5. Harvey, S. C., and McCammon, J. A., 1982, Macromolecular Conformational Energy Minimization: An Algorithm Varying Pseudodihedral Angles, Computers & Chemistry, 6:173.CrossRefGoogle Scholar
  6. Harvey, S. C., Prabhakaran, M., and McCammon, J. A., 1985, Molecular-Dynamics Simulation of Phenylalanine Transfer RNA. I. Methods and General Results, Biopolymers, 24:1169.CrossRefGoogle Scholar
  7. Harvey, S. C., Prabhakaran, M., Mao, B., and McCammon, J. A., 1984, Phenylalanine Transfer RNA: Molecular Dynamics Simulation, Science, 223:1189.CrossRefGoogle Scholar
  8. Ichiye, T., and Karplus, M., 1983, Fluorescence Depolarization of Tryptophan Residues in Proteins: A Molecular Dynamics Study, Biochemistry, 222:2284.Google Scholar
  9. Karplus, M., and McCammon, J. A., 1983, Dynamics of Proteins: Elements and Function, Ann. Rev. Biochem., 53:263.CrossRefGoogle Scholar
  10. Kim, S. H., Suddath, F. L., Quigley, G. J., McPherson, A., Sussman, J. L., Wang, A. H. J., Seeman, N. C., and Rich, A., 1974, Three-Dimensional Tertiary Structure of Yeast Phenylalanine Transfer RNA, Science, 185:435.CrossRefGoogle Scholar
  11. Ladner, J. E., Jack, A., Robertus, J. D., Brown, R. S., Rhodes, D., Clark, B. F. C., and Klug, A., 1975, Structure of Yeast Phenylalanine Transfer RNA at 2.5 Å Resolution, Proc. Natl. Acad. Sci. USA, 72:4414.CrossRefGoogle Scholar
  12. Levitt, M., 1983, Computer Simulation of DNA Double-helix Dynamics, Cold Spring Harbor Symp. Quant. Biol., 47:251.CrossRefGoogle Scholar
  13. Nilsson, L., and Karplus, M., 1985, Empirical Energy Functions for Energy Minimizations and Dynamics of Nucleic Acids, Submitted for publication.Google Scholar
  14. Nilsson, L., Rigler, R., and Laggner, P., 1982, Structural Variability of tRNA: Small-Angle X-ray Scattering of the Yeast tRNAPhe-Escherichia coli tRNA2 Glu Complex, Proc. Natl. Acad. Sci. USA; 79:5891.CrossRefGoogle Scholar
  15. Olson, W. K., Theoretical Studies of Nucleic Acid Conformation: Potential Energies, Chain Statistics, and Model Building, 1982, in: “Topics in Nucleic Acid Structure, Part 2”, S. Neidle, ed., MacMillan Press, London.Google Scholar
  16. Quigley, G.J., Teeter, M. M., and Rich, A., 1978, Structural Analysis of Spermine and Magnesium Ion Bidning to Yeast Phenylalanine Transfer RNA, Proc. Natl. Acad. Sci. USA; 75:64.CrossRefGoogle Scholar
  17. Rigler, R., and Wintermeyer, W., 1983, Dynamics of tRNA, Ann. Rev. Biophys. Bioeng., 12:475.CrossRefGoogle Scholar
  18. Ryckaert, J. P., Cicotti, G., and Berendsen, H. J. C., 1977, J. Comp. Phys., 23:327.CrossRefGoogle Scholar
  19. Saenger, W., 1984, “Principles of Nucleic Acid Structure”, Springer-Verlag, New York.CrossRefGoogle Scholar
  20. Tidor, B., Irikura, K. K., Brooks, B. R., and Karplus, M., 1983, Dynamics of DNA Oligomers, J. Biomol. Struct. Dyn., 1:231.Google Scholar
  21. Verlet, L., 1967, Phys. Rev., 159:98.CrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1986

Authors and Affiliations

  • Lennart Nilsson
    • 1
  • Martin Karplus
    • 2
  1. 1.Department of Medical BiophysicsKarolinska InstitutetStockholmSweden
  2. 2.Department of ChemistryHarvard UniversityCambridgeUSA

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