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Biophys J. Jun 2001; 80(6): 2946–2953.
PMCID: PMC1301478

Determination of domain structure of proteins from X-ray solution scattering.

Abstract

An ab initio method for building structural models of proteins from x-ray solution scattering data is presented. Simulated annealing is employed to find a chain-compatible spatial distribution of dummy residues which fits the experimental scattering pattern up to a resolution of 0.5 nm. The efficiency of the method is illustrated by the ab initio reconstruction of models of several proteins, with known and unknown crystal structure, from experimental scattering data. The new method substantially improves the resolution and reliability of models derived from scattering data and makes solution scattering a useful technique in large-scale structural characterization of proteins.

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Selected References

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  • Arjunan P, Umland T, Dyda F, Swaminathan S, Furey W, Sax M, Farrenkopf B, Gao Y, Zhang D, Jordan F. Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution. J Mol Biol. 1996 Mar 1;256(3):590–600. [PubMed]
  • Bada M, Walther D, Arcangioli B, Doniach S, Delarue M. Solution structural studies and low-resolution model of the Schizosaccharomyces pombe sap1 protein. J Mol Biol. 2000 Jul 14;300(3):563–574. [PubMed]
  • Bennett WS, Jr, Steitz TA. Structure of a complex between yeast hexokinase A and glucose. II. Detailed comparisons of conformation and active site configuration with the native hexokinase B monomer and dimer. J Mol Biol. 1980 Jun 25;140(2):211–230. [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]
  • Chacón P, Díaz JF, Morán F, Andreu JM. Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. J Mol Biol. 2000 Jun 23;299(5):1289–1302. [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]
  • Curry S, Mandelkow H, Brick P, Franks N. Crystal structure of human serum albumin complexed with fatty acid reveals an asymmetric distribution of binding sites. Nat Struct Biol. 1998 Sep;5(9):827–835. [PubMed]
  • Diamond R. Real-space refinement of the structure of hen egg-white lysozyme. J Mol Biol. 1974 Jan 25;82(3):371–391. [PubMed]
  • Edwards AM, Arrowsmith CH, Christendat D, Dharamsi A, Friesen JD, Greenblatt JF, Vedadi M. Protein production: feeding the crystallographers and NMR spectroscopists. Nat Struct Biol. 2000 Nov;7 (Suppl):970–972. [PubMed]
  • Guo DY, Smith GD, Griffin JF, Langs DA. Use of globic scattering factors for protein structures at low resolution. Acta Crystallogr A. 1995 Nov 1;51(Pt 6):945–947. [PubMed]
  • Huang ES, Subbiah S, Levitt M. Recognizing native folds by the arrangement of hydrophobic and polar residues. J Mol Biol. 1995 Oct 6;252(5):709–720. [PubMed]
  • Kirkpatrick S, Gelatt CD, Jr, Vecchi MP. Optimization by simulated annealing. Science. 1983 May 13;220(4598):671–680. [PubMed]
  • Kleywegt GJ. Validation of protein models from Calpha coordinates alone. J Mol Biol. 1997 Oct 24;273(2):371–376. [PubMed]
  • König S, Svergun D, Koch MH, Hübner G, Schellenberger A. The influence of the effectors of yeast pyruvate decarboxylase (PDC) on the conformation of the dimers and tetramers and their pH-dependent equilibrium. Eur Biophys J. 1993;22(3):185–194. [PubMed]
  • Miyazawa S, Jernigan RL. Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues. Proteins. 1999 Jan 1;34(1):49–68. [PubMed]
  • Steitz TA, Fletterick RJ, Anderson WF, Anderson CM. High resolution x-ray structure of yeast hexokinase, an allosteric protein exhibiting a non-symmetric arrangement of subunits. J Mol Biol. 1976 Jun 14;104(1):197–122. [PubMed]
  • Subbiah S. Low-resolution real-space envelopes: an approach to the ab initio macromolecular phase problem. Science. 1991 Apr 5;252(5002):128–133. [PubMed]
  • Sugio S, Kashima A, Mochizuki S, Noda M, Kobayashi K. Crystal structure of human serum albumin at 2.5 A resolution. Protein Eng. 1999 Jun;12(6):439–446. [PubMed]
  • Svergun DI. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 1999 Jun;76(6):2879–2886. [PMC free article] [PubMed]
  • Svergun DI, Bećirević A, Schrempf H, Koch MH, Grüber G. Solution structure and conformational changes of the Streptomyces chitin-binding protein (CHB1). Biochemistry. 2000 Sep 5;39(35):10677–10683. [PubMed]
  • Svergun DI, Malfois M, Koch MH, Wigneshweraraj SR, Buck M. Low resolution structure of the sigma54 transcription factor revealed by X-ray solution scattering. J Biol Chem. 2000 Feb 11;275(6):4210–4214. [PubMed]
  • Svergun DI, Petoukhov MV, Koch MH, König S. Crystal versus solution structures of thiamine diphosphate-dependent enzymes. J Biol Chem. 2000 Jan 7;275(1):297–302. [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]
  • Thomas PD, Dill KA. An iterative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11628–11633. [PMC free article] [PubMed]

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