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Biomolecular dynamics: A report from a workshop in Gysinge, Sweden, October 4–7, 1982

Published online by Cambridge University Press:  17 March 2009

Olle Edholm ,
Lennart Nilsson ,
Otto Berg ,
Måns Ehrenberg ,
Flora Claesens ,
Astrid Gräslund ,
Bo Jönsson  and
Olle Teleman
Olle Edholm
Affiliation:
Department of Theoretical Physics, Royal Institute of Technology, S-100 44 Stockholm, Sweden
Lennart Nilsson
Affiliation:
Department of Medical Biophysics, Karolinska Institutet, Box 60400, S-104 01 Stockholm, Sweden
Otto Berg
Affiliation:
Department of Theoretical Physics, Royal Institute of Technology, S-100 44 Stockholm, Sweden
Måns Ehrenberg
Affiliation:
Department of Molecular Biology, Biomedicai Center, Box 590, S-751 24 Uppsala, Sweden
Flora Claesens
Affiliation:
Department of Medical Biophysics, Karolinska Institutet, Box 60400, S-104 01 Stockholm, Sweden
Astrid Gräslund
Affiliation:
Department of Biophysics, Arrhenius Laboratory, University of Stockholm, S-106 91 Stockholm, Sweden
Bo Jönsson
Affiliation:
Department of Physical Chemistry 2, Chemical Center, Box 740, S-220 07 Lund, Sweden
Olle Teleman
Affiliation:
Department of Physical Chemistry 2, Chemical Center, Box 740, S-220 07 Lund, Sweden
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Extract

From the results of X-ray crystallography a wealth of information is now available concerning the detailed molecular structure of proteins, nucleic acids, and membrane components. This has made it possible to apply successfully various spectroscopie techniques for time resolved studies as well as theoretical simulations of internal molecular dynamics in the biological macromolecules and molecular aggregates. We were particularly pleased to see professor Ivar Waller among the participants of the workshop since new use of the wellknown Debye–Waller factor has greatly contributed to this development. A molecular picture is presently emerging including the dimension of time which ultimately will give us a detailed understanding of the functional interactions between biomolecules in general, and in particular enzyme catalysis, nucleic acid functions, and transport of matter and information through membranes.

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 17 , Issue 2 , May 1984 , pp. 125 - 151
Copyright
Copyright © Cambridge University Press 1984

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References

REFERENCES

Alder, B. J. & Wainwright, T. E. (1959). Studies in molecular dynamics. I. General method. J. chem. Phys. 31, 459–466.CrossRefGoogle Scholar
Alvarado-Urbina, G., Sathe, G. M., Liu, W. C., Gillen, M. F., Duck, P. D., Bender, R. & Ogilvie, K. K. (1981). Automated synthesis of gene fragments. Science, N. Y. 214, 270–274.CrossRefGoogle ScholarPubMed
Artymiuk, P. J., Blake, C. C. F., Grace, D. E. P., Oatley, S. J., Phillips, D. C. & Sternberg, M. J. E. (1979). Crystallographic studies of the dynamic properties of lysozyme. Nature, Land. 280, 563–568.CrossRefGoogle ScholarPubMed
Austin, R. H., Beeson, K. W., Eisenstein, L., Frauenfelder, H. & Gunsalus, I. C. (1975). Dynamics of ligand binding to myoglobin. Biochemistry, Philad. 14, 5355–5373.CrossRefGoogle ScholarPubMed
Beece, D., Eisenstein, L., Frauenfelder, H., Good, D., Marden, M. C., Reinisch, L., Reynolds, A. H., Sorensen, L. B. & Yue, K. T. (1980). Solvent viscosity and protein dynamics. Biochemistry, Philad. 19, 5147–5157.CrossRefGoogle ScholarPubMed
Biebricher, C. K., Eigen, M. & Luce, R. J. (1981). Product analysis of RNA generated de novo by Qβ replicase. J. molec. Biol. 148, 369–390.CrossRefGoogle Scholar
Claesens, F. & Rigler, R. (1982). Conformational dynamics of the anticodon loop in yeast tRNAphe. Proc. Int. Symposium on Synthetic Oligonucleotides in Molecular Biology, Uppsala, Sweden, Aug. 1982.Google Scholar
Cooke, R., Crowder, M. S. & Thomas, D. D. (1982). Orientation of spin labels attached to cross-bridges in contracting muscle fibres. Nature, Lond. 300, 776–778.CrossRefGoogle ScholarPubMed
Frauenfelder, H., Petsko, G. A. & Tsernoglou, D. (1979). Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature, Lond. 280, 558–563.CrossRefGoogle ScholarPubMed
Haasnoot, C. A. G., De Bruin, S. H., Berendsen, R. G., Janssen, H. G. J. M., Binnendijk, T. J. J. & Hilbers, C. W. (1983). Structure, kinetics and thermodynamics of DNA hairpin fragments in solution. J. Biomolecular Structure and Dynamics 1, 115–129.CrossRefGoogle ScholarPubMed
Hartmann, H., Parak, F., Steigemann, W., Petsko, G. A., Ringe Ponzi, D. & Frauenfelder, H. (1982 a). Conformational substates in a protein: Structure and dynamics of metmyoglobin at 80 K. Proc. natn. Acad. Sci. U.S.A. 79, 4967–4971.CrossRefGoogle Scholar
Hartmann, B., Pilet, J., Ptak, M., Ramstein, J., Malfoy, B. & Leng, M. (1982 b). The B═Z transition of poly(dI-br5dC)poly(dI-br5dC). A quantitative description of the Z-form dynamic structure. Nucl. Acids Res. 10, 3261–3277.CrossRefGoogle Scholar
Harvey, S. C. & McCammon, J. A. (1981). Intramolecular flexibility in phenylalanine transfer RNA. Nature, Lond. 294, 286–287.CrossRefGoogle ScholarPubMed
Heerschap, A., Haasnoot, C. A. G. & Hilbers, C. W. (1982). Nuclear magnetic resonance studies on yeast tRNAphe. I. Assignment of the iminoproton resonances of the acceptor and D-stem by means of Nuclear Overhauser Effect experiments at 500 MHz. Nucl. Acids Res. 10, 6981–7000.CrossRefGoogle Scholar
Heerschap, A., Haasnoot, C. A. G. & Hilbers, C. W. (1983). Nuclear magnetic resonance studies on yeast tRNAphe. II. Assignment of the iminoproton resonance of the anticodon and T-stem by means of Nuclear Overhauser Effect experiments at 500 MHz. Nucl. Acids Res. 11, 4483–4499.CrossRefGoogle Scholar
Huxley, H. E., Simmons, R. M., Faruqi, A. R., Kress, M., Bordas, J. & Koch, M. H. J. (1981). Millisecond time-resolved changes in X-ray reflections from contracting muscle during rapid mechanical transients, recorded using synchroton radiation. Proc. natn. Acad. Sci. U.S.A. 78, 2297–2301.CrossRefGoogle Scholar
Jönsson, B., Wennerström, H. & Halle, B. (1980). Ion distributions in lamellar liquid crystal. A comparison between results from Monte Carlo simulations and solutions of the Poisson–Boltzmann equation. J. phys. Chem. 84, 2179–2185.CrossRefGoogle Scholar
Karplus, M. & McCammon, J. A. (1981). The internal dynamics of globular proteins. CRC Crit. Rev. Biochem. 9, 293–349.CrossRefGoogle ScholarPubMed
Knapp, E. W., Fischer, S. F. & Parak, F. (1982). Protein dynamics from Mössbauer spectra. The temperature dependence. J. phys. Chem. 86, 5042–5047.CrossRefGoogle Scholar
Knapp, E. W., Fischer, S. F. & Parak, F. (1983). The influence of protein dynamics on Mössbauer spectra. J. chem. Phys. 78, 4701–4711.CrossRefGoogle Scholar
Kolb, H.-A., Läuger, P. & Bamberg, E. (1975). Correlation analysis of electrical noise in lipid bilayer membranes. Kinetics of gramicidin-A channels. J. Membrane Biol. 20, 133–154.CrossRefGoogle ScholarPubMed
Kossiakoff, A. A. (1982). Protein dynamics investigated by the neutron diffraction-hydrogen exchange technique. Nature, Land. 296, 713–721.CrossRefGoogle ScholarPubMed
Kramers, H. A. (1940). Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7, 284–304.CrossRefGoogle Scholar
Krumhansl, J. A. & Alexander, D. M. (1983). Nonlinear dynamics and conformational excitations in biomolecular materials. In Structure and Dynamics in Nucleic Acids and Proteins (ed. Clementi, E. and Sarma, R. H.), pp. 61–80. New York: Adenine Press.Google Scholar
Krupyanskii, Yu. F., Parak, F., Goldanskii, V. L., Mössbauer, R. L., Gaubman, E. E., Engelmann, H. & Suzdalev, I. P. (1982). Investigation of large intramolecular movements within metmyoglobin by Rayleigh scattering of Mössbauer radiation (RSMR). Z. Naturf. 37C, 57–62.CrossRefGoogle Scholar
Läuger, P., Benz, R., Stark, G., Bamberg, E., Jordan, P. C., Fahr, A. & Brock, W. (1981). Relaxation studies of ion transport systems in lipid bilayer membranes. Q. Rev. Biophys. 14, 513–598.CrossRefGoogle ScholarPubMed
Manning, G. S. (1978). The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11, 179–246.CrossRefGoogle Scholar
McCammon, J. A. (1980). Dynamics of tyrosine ring rotations in a globular protein. Biopolymers 19, 1375–1405.CrossRefGoogle Scholar
Nilsson, L., Rigler, R. & Laggner, P. (1982). Structural variability of tRNA: Small-angle X-ray scattering of the yeast tRNAphe-Escherichia coli tRNAGlu2 complex. Proc. natn. Acad. Sci. U.S.A. 79, 5891–5895.CrossRefGoogle ScholarPubMed
Parak, F., Frolov, E. N., Mössbauer, R. L. & Goldanskii, V. I. (1981). Dynamics of metmyoglobin crystals investigated by nuclear gamma resonance absorption. J. molec. Biol. 145, 825–833.CrossRefGoogle ScholarPubMed
Parak, F., Knapp, E. W. & Kucheida, D. (1982). Protein dynamics. Mössbauer spectroscopy on deoxymyoglobin crystals. J. molec. Biol. 161, 177–194.CrossRefGoogle ScholarPubMed
Patel, D. J., Pardi, A. & Itakura, K. (1982). DNA conformation, dynamics and interactions in solution. Science, N.Y. 216, 581–590.CrossRefGoogle ScholarPubMed
Quigley, G. J., Teeter, M. M. & Rich, A. (1978). Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA. Proc. natn. Acad. Sci. U.S.A. 75, 64–68.CrossRefGoogle ScholarPubMed
Ramstein, J. & Buckingham, R. H. (1981). Tritium exchange on transfer RNA: Slowly exchanging protons sensitive to a change in the dihydrouridine stem. Proc. natn. Acad. Sci. U.S.A. 78, 1567–1571.CrossRefGoogle ScholarPubMed
Ramstein, J. & Leng, M. (1980). Salt-dependent dynamic structure of poly(dG–dC).poly(dG–dC). Nature, Land. 288, 413–415.CrossRefGoogle ScholarPubMed
Redfield, A. G., Kunz, S. D. & Ralph, E. K. (1975). Dynamic range in Fourier transform proton magnetic resonance. J. magn. Reson. 19, 114–117.Google Scholar
Reid, B. R. (1981). NMR studies on RNA structure and dynamics. A. Rev. Biochem. 50, 969–996.CrossRefGoogle ScholarPubMed
Rich, A. & Kim, S. H. (1977). The three-dimensional structure of transfer RNA. Scient. Am. 238, 52–62.CrossRefGoogle Scholar
Rigler, R. & Wintermeyer, W. (1983). Dynamics of tRNA. A. Rev. Biophys. Bioengng. 12, 475–505.CrossRefGoogle ScholarPubMed
Rüterjans, H., Kaun, E., Hull, W. E. & Limbach, H. H. (1983). Evidence for tautomerism in nucleic acid base pairs. 1H NMR study of 15N labelled tRNA. Nucl. Acids Res. 10, 7027–7039.CrossRefGoogle Scholar
Scott, A. C. (1982). The vibrational structure of Davydov solitons. Physica Scripta 25, 651–658.CrossRefGoogle Scholar
Seelig, J. & Seelig, A. (1980). Lipid conformation in model membranes and biological membranes. Q. Rev. Biophys. 13, 19–61.CrossRefGoogle ScholarPubMed
Seelig, J., Tamm, L., Hymel, L. & Fleischer, S. (1981). Deuterium and phosphorus nuclear magnetic resonance and fluorescence depolarization studies of functional reconstituted sarcoplasmic reticulum membrane vesicles. Biochemistry, Philad. 20, 3922–3932.CrossRefGoogle ScholarPubMed
Urry, D. W. (1971). The gramicidin A transmembrane channel: A proposed π(L D) helix. Proc. natn. Acad. Sci. U.S.A. 68, 672–676.CrossRefGoogle Scholar
Van Der Ploeg, P. & Berendsen, H. J. C. (1982). Molecular dynamics simulation of a bilayer membrane. J. chem. Phys. 76, 3271–3276.CrossRefGoogle Scholar
Van Der Ploeg, P. & Berendsen, H. J. C. (1983). Molecular dynamics of a bilayer membrane. Molec. Phys. 49, 233–248.CrossRefGoogle Scholar
Wennerström, H., Jönsson, B. & Linse, P. (1982). The cell model for polyelectrolyte systems. Exact statistical mechanical relations, Monte Carlo simulations, and the Poisson–Boltzmann approximation. J. chem. Phys. 79, 4665–4670.CrossRefGoogle Scholar