Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1986 Nov;83(21):8147–8151. doi: 10.1073/pnas.83.21.8147

Ultrasonic absorption evidence for enhanced volume fluctuations in the tobacco mosaic virus protein helical aggregate

R Cerf 1, Y Dormoy 1
PMCID: PMC386884  PMID: 16593775

Abstract

The increased ultrasonic absorption brought about by self-assembly of biomolecules is analyzed for the assembly process from the 20S aggregate to the helical rod of tobacco mosaic virus protein in solution, designated here as the 20S → P-helix transition. The analysis is based on theoretical developments in ultrasonic relaxation spectrometry presented previously and illustrates the possibility that this technique can be used for characterizing fluctuations. The analysis makes use of NMR data for the system in solution and of x-ray diffraction data for the closely related transition from the two-ring disk to the virion. These x-ray data comprise the high-resolution structures and the Debye-Waller temperature factors of the main chain atoms of both the two-ring disk in crystals and the virion in oriented gel form. First, reduced ultrasonic spectra are obtained for the 4S, 20S, and helical rod aggregates. The fluctuation-enhancement factor for the helical rod is determined independently of any deconvolution into normal modes of relaxation and is shown not to depend on the particular procedure of reduction employed. The increase of ultrasonic absorption in the 20S → P-helix transition primarily reveals enhancement of the relaxing system's normal-mode volume fluctuations. The observed relaxations probably involve one conformational process per subunit. The normal-mode volume fluctuations are then estimated from a bimodal least-squares best fit to the data, and a lower bound for the reaction volume associated with the fast steps is obtained. Two mechanisms are considered as follows: (i) a destabilization process in which the free-energy difference between two states is reduced and (ii) an increase in reaction volumes of local conformation changes in the helical aggregate, resulting from the formation of a “carboxyl cage-like” structure and from the change in environment produced inside the cage. Increased reaction volumes would not be detected with x-ray diffraction. The possible occurrence of fluctuations at the RNA binding site raises the question of whether a quaternary structure that exhibits significant conformational fluctuations must be present for the binding of the nucleic acid.

Keywords: relaxation spectrometry, conformational fluctuations, segmental mobility, protein assemblies, tobacco mosaic virus loop

Full text

PDF
8147

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Beece D., Eisenstein L., Frauenfelder H., Good D., Marden M. C., Reinisch L., Reynolds A. H., Sorensen L. B., Yue K. T. Solvent viscosity and protein dynamics. Biochemistry. 1980 Nov 11;19(23):5147–5157. doi: 10.1021/bi00564a001. [DOI] [PubMed] [Google Scholar]
  2. Caspar D. L., Holmes K. C. Structure of dahlemense strain of tobacco mosaic virus: a periodically deformed helix. J Mol Biol. 1969 Nov 28;46(1):99–133. doi: 10.1016/0022-2836(69)90060-6. [DOI] [PubMed] [Google Scholar]
  3. Cerf R. Absolute measurement of enhanced fluctuations in assemblies of biomolecules by ultrasonic techniques. Biophys J. 1985 Jun;47(6):751–756. doi: 10.1016/S0006-3495(85)83977-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cerf R., Michels B., Schulz J. A., Witz J., Pfeiffer P., Hirth L. Ultrasonic absorption evidence of structural fluctuations in viral capsids. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1780–1782. doi: 10.1073/pnas.76.4.1780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Davis J. S., Gutfreund H. The scope of moderate pressure changes for kinetic and equilibrium studies of biochemical systems. FEBS Lett. 1976 Dec 31;72(2):199–207. doi: 10.1016/0014-5793(76)80971-4. [DOI] [PubMed] [Google Scholar]
  6. Durham A. C., Finch J. T., Klug A. States of aggregation of tobacco mosaic virus protein. Nat New Biol. 1971 Jan 13;229(2):37–42. doi: 10.1038/newbio229037a0. [DOI] [PubMed] [Google Scholar]
  7. Jardetzky O., Akasaka K., Vogel D., Morris S., Holmes K. C. Unusual segmental flexibility in a region of tobacco mosaic virus coat protein. Nature. 1978 Jun 15;273(5663):564–566. doi: 10.1038/273564a0. [DOI] [PubMed] [Google Scholar]
  8. Jones W. C., Rothgeb T. M., Gurd F. R. Nuclear magnetic resonance studies of sperm whale myoglobin specifically enriched with 13C in the methionine methyl groups. J Biol Chem. 1976 Dec 10;251(23):7452–7460. [PubMed] [Google Scholar]
  9. Lakowicz J. R., Weber G. Quenching of protein fluorescence by oxygen. Detection of structural fluctuations in proteins on the nanosecond time scale. Biochemistry. 1973 Oct 9;12(21):4171–4179. doi: 10.1021/bi00745a021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Mandelkow E., Stubbs G., Warren S. Structures of the helical aggregates of tobacco mosaic virus protein. J Mol Biol. 1981 Oct 25;152(2):375–386. doi: 10.1016/0022-2836(81)90248-5. [DOI] [PubMed] [Google Scholar]
  11. Michels B., Dormoy Y., Cerf R., Schulz J. A., Witz J. Ultrasonic absorption in tobacco mosaic virus and its protein aggregates. J Mol Biol. 1985 Jan 5;181(1):103–110. doi: 10.1016/0022-2836(85)90328-6. [DOI] [PubMed] [Google Scholar]
  12. Munro I., Pecht I., Stryer L. Subnanosecond motions of tryptophan residues in proteins. Proc Natl Acad Sci U S A. 1979 Jan;76(1):56–60. doi: 10.1073/pnas.76.1.56. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Namba K., Stubbs G. Structure of tobacco mosaic virus at 3.6 A resolution: implications for assembly. Science. 1986 Mar 21;231(4744):1401–1406. doi: 10.1126/science.3952490. [DOI] [PubMed] [Google Scholar]
  14. Raghavendra K., Adams M. L., Schuster T. M. Tobacco mosaic virus protein aggregates in solution: structural comparison of 20S aggregates with those near conditions for disk crystallization. Biochemistry. 1985 Jun 18;24(13):3298–3304. doi: 10.1021/bi00334a034. [DOI] [PubMed] [Google Scholar]
  15. Robach Y., Michels B., Cerf R., Braunwald J., Tripier-Darcy F. Ultrasonic absorption evidence for structural fluctuations in frog virus 3 and its subparticles. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3981–3985. doi: 10.1073/pnas.80.13.3981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Stubbs G., Warren S., Holmes K. Structure of RNA and RNA binding site in tobacco mosaic virus from 4-A map calculated from X-ray fibre diagrams. Nature. 1977 May 19;267(5608):216–221. doi: 10.1038/267216a0. [DOI] [PubMed] [Google Scholar]
  17. Wagner G., Wüthrich K. Dynamic model of globular protein conformations based on NMR studies in solution. Nature. 1978 Sep 21;275(5677):247–248. doi: 10.1038/275247a0. [DOI] [PubMed] [Google Scholar]
  18. Westhof E., Altschuh D., Moras D., Bloomer A. C., Mondragon A., Klug A., Van Regenmortel M. H. Correlation between segmental mobility and the location of antigenic determinants in proteins. Nature. 1984 Sep 13;311(5982):123–126. doi: 10.1038/311123a0. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES