Skip to main content
PMC home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1997 Jan;6(1):80–88. doi: 10.1002/pro.5560060109

The crystal structure of the designed trimeric coiled coil coil-VaLd: implications for engineering crystals and supramolecular assemblies.

N L Ogihara 1, M S Weiss 1, W F Degrado 1, D Eisenberg 1
PMCID: PMC2143514  PMID: 9007979

Abstract

The three-dimensional structure of the 29-residue designed coiled coil having the amino acid sequence acetyl-E VEALEKK VAALESK VQALEKK VEALEHG-amide has been determined and refined to a crystallographic R-factor of 21.4% for all data from 10-A to 2.1-A resolution. This molecule is called coil-VaLd because it contains valine in the a heptad positions and leucine in the d heptad positions. In the trigonal crystal, three molecules, related by a crystallographic threefold axis, form a parallel three-helix bundle. The bundles are stacked head-to-tail to form a continuous coiled coil along the c-direction of the crystal. The contacts among the three helices within the coiled coil are mainly hydrophobic: four layers of valine residues alternate with four layers of leucine residues to form the core of the bundle. In contrast, mostly hydrophilic contacts mediate the interaction between trimers: here a total of two direct protein--protein hydrogen bonds are found. Based on the structure, we propose a scheme for designing crystals of peptides containing continuous two-, three-, and four-stranded coiled coils.

Full Text

The Full Text of this article is available as a PDF (2.5 MB).

Selected References

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

  1. Banner D. W., Kokkinidis M., Tsernoglou D. Structure of the ColE1 rop protein at 1.7 A resolution. J Mol Biol. 1987 Aug 5;196(3):657–675. doi: 10.1016/0022-2836(87)90039-8. [DOI] [PubMed] [Google Scholar]
  2. Boice J. A., Dieckmann G. R., DeGrado W. F., Fairman R. Thermodynamic analysis of a designed three-stranded coiled coil. Biochemistry. 1996 Nov 19;35(46):14480–14485. doi: 10.1021/bi961831d. [DOI] [PubMed] [Google Scholar]
  3. Glover J. N., Harrison S. C. Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature. 1995 Jan 19;373(6511):257–261. doi: 10.1038/373257a0. [DOI] [PubMed] [Google Scholar]
  4. Harbury P. B., Zhang T., Kim P. S., Alber T. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science. 1993 Nov 26;262(5138):1401–1407. doi: 10.1126/science.8248779. [DOI] [PubMed] [Google Scholar]
  5. Janin J., Miller S., Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol. 1988 Nov 5;204(1):155–164. doi: 10.1016/0022-2836(88)90606-7. [DOI] [PubMed] [Google Scholar]
  6. Lewis M., Chang G., Horton N. C., Kercher M. A., Pace H. C., Schumacher M. A., Brennan R. G., Lu P. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science. 1996 Mar 1;271(5253):1247–1254. doi: 10.1126/science.271.5253.1247. [DOI] [PubMed] [Google Scholar]
  7. Lovejoy B., Choe S., Cascio D., McRorie D. K., DeGrado W. F., Eisenberg D. Crystal structure of a synthetic triple-stranded alpha-helical bundle. Science. 1993 Feb 26;259(5099):1288–1293. doi: 10.1126/science.8446897. [DOI] [PubMed] [Google Scholar]
  8. Malashkevich V. N., Kammerer R. A., Efimov V. P., Schulthess T., Engel J. The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel? Science. 1996 Nov 1;274(5288):761–765. doi: 10.1126/science.274.5288.761. [DOI] [PubMed] [Google Scholar]
  9. Matthews B. W. Solvent content of protein crystals. J Mol Biol. 1968 Apr 28;33(2):491–497. doi: 10.1016/0022-2836(68)90205-2. [DOI] [PubMed] [Google Scholar]
  10. McLachlan A. D., Stewart M. Tropomyosin coiled-coil interactions: evidence for an unstaggered structure. J Mol Biol. 1975 Oct 25;98(2):293–304. doi: 10.1016/s0022-2836(75)80119-7. [DOI] [PubMed] [Google Scholar]
  11. Merritt E. A., Murphy M. E. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):869–873. doi: 10.1107/S0907444994006396. [DOI] [PubMed] [Google Scholar]
  12. Monera O. D., Zhou N. E., Kay C. M., Hodges R. S. Comparison of antiparallel and parallel two-stranded alpha-helical coiled-coils. Design, synthesis, and characterization. J Biol Chem. 1993 Sep 15;268(26):19218–19227. [PubMed] [Google Scholar]
  13. O'Neil K. T., DeGrado W. F. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science. 1990 Nov 2;250(4981):646–651. doi: 10.1126/science.2237415. [DOI] [PubMed] [Google Scholar]
  14. O'Shea E. K., Klemm J. D., Kim P. S., Alber T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science. 1991 Oct 25;254(5031):539–544. doi: 10.1126/science.1948029. [DOI] [PubMed] [Google Scholar]
  15. Ponder J. W., Richards F. M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol. 1987 Feb 20;193(4):775–791. doi: 10.1016/0022-2836(87)90358-5. [DOI] [PubMed] [Google Scholar]
  16. Weis W. I., Drickamer K. Trimeric structure of a C-type mannose-binding protein. Structure. 1994 Dec 15;2(12):1227–1240. doi: 10.1016/S0969-2126(94)00124-3. [DOI] [PubMed] [Google Scholar]
  17. Wendt H., Berger C., Baici A., Thomas R. M., Bosshard H. R. Kinetics of folding of leucine zipper domains. Biochemistry. 1995 Mar 28;34(12):4097–4107. doi: 10.1021/bi00012a028. [DOI] [PubMed] [Google Scholar]
  18. Wilson I. A., Skehel J. J., Wiley D. C. Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution. Nature. 1981 Jan 29;289(5796):366–373. doi: 10.1038/289366a0. [DOI] [PubMed] [Google Scholar]
  19. Yan Y., Winograd E., Viel A., Cronin T., Harrison S. C., Branton D. Crystal structure of the repetitive segments of spectrin. Science. 1993 Dec 24;262(5142):2027–2030. doi: 10.1126/science.8266097. [DOI] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES