• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of biophysjLink to Publisher's site
Biophys J. Jun 1999; 76(6): 2879–2886.
PMCID: PMC1300260

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

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 (1.0M).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Ashton AW, Boehm MK, Gallimore JR, Pepys MB, Perkins SJ. 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. [PubMed]
  • Ban N, Freeborn B, Nissen P, Penczek P, Grassucci RA, Sweet R, Frank J, Moore PB, Steitz TA. A 9 A resolution X-ray crystallographic map of the large ribosomal subunit. Cell. 1998 Jun 26;93(7):1105–1115. [PubMed]
  • 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. [PubMed]
  • Bilgin N, Ehrenberg M, Ebel C, Zaccai G, Sayers Z, Koch MH, Svergun DI, Barberato C, Volkov V, Nissen P, et al. Solution structure of the ternary complex between aminoacyl-tRNA, elongation factor Tu, and guanosine triphosphate. Biochemistry. 1998 Jun 2;37(22):8163–8172. [PubMed]
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, 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. [PubMed]
  • Capel MS, Engelman DM, Freeborn BR, Kjeldgaard M, Langer JA, Ramakrishnan V, Schindler DG, Schneider DK, Schoenborn BP, Sillers IY, et al. A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. Science. 1987 Dec 4;238(4832):1403–1406. [PubMed]
  • Chacón P, Morán F, Díaz JF, Pantos E, Andreu JM. Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys J. 1998 Jun;74(6):2760–2775. [PMC free article] [PubMed]
  • Davies C, Ramakrishnan V, White SW. 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. [PubMed]
  • Frank J, Zhu J, Penczek P, Li Y, Srivastava S, Verschoor A, Radermacher M, Grassucci R, Lata RK, Agrawal RK. A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature. 1995 Aug 3;376(6539):441–444. [PubMed]
  • Kirkpatrick S, Gelatt CD, Jr, Vecchi MP. Optimization by simulated annealing. Science. 1983 May 13;220(4598):671–680. [PubMed]
  • 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. [PubMed]
  • Koch MH, Stuhrmann HB. Neutron-scattering studies of ribosomes. Methods Enzymol. 1979;59:670–706. [PubMed]
  • Krueger JK, Olah GA, Rokop SE, Zhi G, Stull JT, 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. [PubMed]
  • May RP, Nowotny V, Nowotny P, Voss H, Nierhaus KH. Inter-protein distances within the large subunit from Escherichia coli ribosomes. EMBO J. 1992 Jan;11(1):373–378. [PMC free article] [PubMed]
  • Ramakrishnan V, White SW. The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA. Nature. 1992 Aug 27;358(6389):768–771. [PubMed]
  • Schönbrunn E, Svergun DI, Amrhein N, Koch MH. 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. [PubMed]
  • Skarzynski T, Mistry A, Wonacott A, Hutchinson SE, Kelly VA, 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. [PubMed]
  • Svergun DI, Burkhardt N, Pedersen JS, Koch MH, Volkov VV, Kozin MB, Meerwink W, Stuhrmann HB, Diedrich G, Nierhaus KH. 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. [PubMed]
  • Svergun DI, Aldag I, Sieck T, Altendorf K, Koch MH, Kane DJ, Kozin MB, 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. [PMC free article] [PubMed]
  • Svergun DI, Richard S, Koch MH, 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. [PMC free article] [PubMed]
  • Waksman G, Krishna TS, Williams CH, 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]
  • Wang J, Smerdon SJ, Jäger J, Kohlstaedt LA, Rice PA, Friedman JM, Steitz TA. 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. [PMC free article] [PubMed]

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

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...