Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 1999 Jun;76(6):2879–2886. doi: 10.1016/S0006-3495(99)77443-6

Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

D I Svergun 1
PMCID: PMC1300260  PMID: 10354416

Abstract

A method is proposed to restore ab initio low resolution shape and internal structure of chaotically oriented particles (e.g., biological macromolecules in solution) from isotropic scattering. A multiphase model of a particle built from densely packed dummy atoms is characterized by a configuration vector assigning the atom to a specific phase or to the solvent. Simulated annealing is employed to find a configuration that fits the data while minimizing the interfacial area. Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data.

Full Text

The Full Text of this article is available as a PDF (1.1 MB).

Selected References

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

  1. Ashton A. W., Boehm M. K., Gallimore J. R., Pepys M. B., Perkins S. J. Pentameric and decameric structures in solution of serum amyloid P component by X-ray and neutron scattering and molecular modelling analyses. J Mol Biol. 1997 Sep 26;272(3):408–422. doi: 10.1006/jmbi.1997.1271. [DOI] [PubMed] [Google Scholar]
  2. Ban N., Freeborn B., Nissen P., Penczek P., Grassucci R. A., Sweet R., Frank J., Moore P. B., Steitz T. A. A 9 A resolution X-ray crystallographic map of the large ribosomal subunit. Cell. 1998 Jun 26;93(7):1105–1115. doi: 10.1016/s0092-8674(00)81455-5. [DOI] [PubMed] [Google Scholar]
  3. Berglund H., Rak A., Serganov A., Garber M., Härd T. Solution structure of the ribosomal RNA binding protein S15 from Thermus thermophilus. Nat Struct Biol. 1997 Jan;4(1):20–23. doi: 10.1038/nsb0197-20. [DOI] [PubMed] [Google Scholar]
  4. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  5. Bilgin N., Ehrenberg M., Ebel C., Zaccai G., Sayers Z., Koch M. H., Svergun D. I., Barberato C., Volkov V., Nissen P. Solution structure of the ternary complex between aminoacyl-tRNA, elongation factor Tu, and guanosine triphosphate. Biochemistry. 1998 Jun 2;37(22):8163–8172. doi: 10.1021/bi9802869. [DOI] [PubMed] [Google Scholar]
  6. Capel M. S., Engelman D. M., Freeborn B. R., Kjeldgaard M., Langer J. A., Ramakrishnan V., Schindler D. G., Schneider D. K., Schoenborn B. P., Sillers I. Y. A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. Science. 1987 Dec 4;238(4832):1403–1406. doi: 10.1126/science.3317832. [DOI] [PubMed] [Google Scholar]
  7. Chacón P., Morán F., Díaz J. F., Pantos E., Andreu J. M. Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys J. 1998 Jun;74(6):2760–2775. doi: 10.1016/S0006-3495(98)77984-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Davies C., Ramakrishnan V., White S. W. Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution. Structure. 1996 Sep 15;4(9):1093–1104. doi: 10.1016/s0969-2126(96)00115-3. [DOI] [PubMed] [Google Scholar]
  9. Frank J., Zhu J., Penczek P., Li Y., Srivastava S., Verschoor A., Radermacher M., Grassucci R., Lata R. K., Agrawal R. K. A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature. 1995 Aug 3;376(6539):441–444. doi: 10.1038/376441a0. [DOI] [PubMed] [Google Scholar]
  10. Kirkpatrick S., Gelatt C. D., Jr, Vecchi M. P. Optimization by simulated annealing. Science. 1983 May 13;220(4598):671–680. doi: 10.1126/science.220.4598.671. [DOI] [PubMed] [Google Scholar]
  11. Kjeldgaard M., Nissen P., Thirup S., Nyborg J. The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Structure. 1993 Sep 15;1(1):35–50. doi: 10.1016/0969-2126(93)90007-4. [DOI] [PubMed] [Google Scholar]
  12. Koch M. H., Stuhrmann H. B. Neutron-scattering studies of ribosomes. Methods Enzymol. 1979;59:670–706. doi: 10.1016/0076-6879(79)59121-6. [DOI] [PubMed] [Google Scholar]
  13. Krueger J. K., Olah G. A., Rokop S. E., Zhi G., Stull J. T., Trewhella J. Structures of calmodulin and a functional myosin light chain kinase in the activated complex: a neutron scattering study. Biochemistry. 1997 May 20;36(20):6017–6023. doi: 10.1021/bi9702703. [DOI] [PubMed] [Google Scholar]
  14. May R. P., Nowotny V., Nowotny P., Voss H., Nierhaus K. H. Inter-protein distances within the large subunit from Escherichia coli ribosomes. EMBO J. 1992 Jan;11(1):373–378. doi: 10.1002/j.1460-2075.1992.tb05060.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ramakrishnan V., White S. W. The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA. Nature. 1992 Aug 27;358(6389):768–771. doi: 10.1038/358768a0. [DOI] [PubMed] [Google Scholar]
  16. Schönbrunn E., Svergun D. I., Amrhein N., Koch M. H. Studies on the conformational changes in the bacterial cell wall biosynthetic enzyme UDP-N-acetylglucosamine enolpyruvyltransferase (MurA). Eur J Biochem. 1998 Apr 15;253(2):406–412. doi: 10.1046/j.1432-1327.1998.2530406.x. [DOI] [PubMed] [Google Scholar]
  17. Skarzynski T., Mistry A., Wonacott A., Hutchinson S. E., Kelly V. A., Duncan K. Structure of UDP-N-acetylglucosamine enolpyruvyl transferase, an enzyme essential for the synthesis of bacterial peptidoglycan, complexed with substrate UDP-N-acetylglucosamine and the drug fosfomycin. Structure. 1996 Dec 15;4(12):1465–1474. doi: 10.1016/s0969-2126(96)00153-0. [DOI] [PubMed] [Google Scholar]
  18. Svergun D. I., Aldag I., Sieck T., Altendorf K., Koch M. H., Kane D. J., Kozin M. B., Grüber G. A model of the quaternary structure of the Escherichia coli F1 ATPase from X-ray solution scattering and evidence for structural changes in the delta subunit during ATP hydrolysis. Biophys J. 1998 Nov;75(5):2212–2219. doi: 10.1016/S0006-3495(98)77665-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Svergun D. I., Burkhardt N., Pedersen J. S., Koch M. H., Volkov V. V., Kozin M. B., Meerwink W., Stuhrmann H. B., Diedrich G., Nierhaus K. H. Solution scattering structural analysis of the 70 S Escherichia coli ribosome by contrast variation. II. A model of the ribosome and its RNA at 3.5 nm resolution. J Mol Biol. 1997 Aug 29;271(4):602–618. doi: 10.1006/jmbi.1997.1191. [DOI] [PubMed] [Google Scholar]
  20. Svergun D. I., Richard S., Koch M. H., Sayers Z., Kuprin S., Zaccai G. Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):2267–2272. doi: 10.1073/pnas.95.5.2267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Waksman G., Krishna T. S., Williams C. H., Jr, Kuriyan J. Crystal structure of Escherichia coli thioredoxin reductase refined at 2 A resolution. Implications for a large conformational change during catalysis. J Mol Biol. 1994 Feb 25;236(3):800–816. [PubMed] [Google Scholar]
  22. Wang J., Smerdon S. J., Jäger J., Kohlstaedt L. A., Rice P. A., Friedman J. M., Steitz T. A. Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer. Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):7242–7246. doi: 10.1073/pnas.91.15.7242. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES