A procedure for refining a coiled coil protein structure using x-ray fiber diffraction and modeling

Biophysical Journal

Volumn 83, Issue 4, 2002, Pages 1774-1783

  Briki, Fatma ^a   Doucet, Jean ^a   Etchebest, Catherine ^b  

^a UNIVERSITÉ PARIS SACLAY   (France)

^b INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

KERATIN;

ALGORITHM; ARTICLE; CALCULATION; DATA BASE; ENERGY; MOLECULAR DYNAMICS; PROTEIN DOMAIN; PROTEIN STRUCTURE; SIMULATION; X RAY DIFFRACTION;

EID: 0036787770     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)73943-X     Document Type: Article

References (30)

1. Bower, M. J., F. E. Cohen, and R. L. Dunbrack, Jr. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J. Mol. Biol. 267:1268-1282.
2. Burkhard, P., R. A. Kammerer, M. O. Steinmetz, G. P. Bourenkov, and U. Aebi. 2000. The coiled-coil trigger site of the rod domain of cortexillin I unveils a distinct network of interhelical and intrahelical salt bridges. Structure Fold. Des. 8:223-230.
3. Busson, B., F. Briki, and J. Doucet. 1999. Side-chain configurations in coiled coils revealed by the 5.15-A meridional reflection on hard alpha-keratin x-ray diffraction patterns. J. Struct. Biol. 125:1-10.
4. Busson, B., and J. Doucet. 1999. Modeling alpha-helical coiled coils: analytic relations between parameters. J. Struct. Biol. 127:16-21.
5. Coulombe, P. A., and E. Fuchs. 1990. Elucidating the early stages of keratin filament assembly. J. Cell Biol. 111:153-69.
6. Crick, F. H. C. 1953a. The Fourier transform of a coiled coil. Acta Crystallogr. 6:685-689.
7. Crick, F. H. C. 1953b. The packing of alpha-helices: simple coiled coils. Acta Crystallogr. 6:689-697.
8. Dowling, L. M., W. G. Crewther, and A. S. Inglis. 1986. The primary structure of component 8c-1, a subunit protein of intermediate filaments in wool keratin. Relationships with proteins from other intermediate filaments. Biochem. J. 236:695-703.
9. Dunbrack, R. L., Jr., and F. E. Cohen. 1997. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6:1661-1681.
10. Glover, J. N., and S. C. Harrison. 1995. Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature. 373:257-261.
11. Harbury, P. H., B. Tidor, and P. Kim. 1995. Repacking protein cores with backbone freedom: structure prediction for coiled coils. Proc. Natl. Acad. Sci. U.S.A. 92:8408-8412.
12. Herrling, J., and L. G. Sparrow. 1991. Interactions of intermediate filament proteins from wool. Intern. J. Biol. Macromol. 13:115-119.
13. Jones, T. A. 1985. Interactive computer graphics. Methods Comp. Methods Enzymol. 115:157-171.
14. Kahn, R., R. Fourme, A. Gader, J. Janin, C. Dumas, and D. Andre. 1982. Macromolecular crystallography with synchrotron radiation: photographic data collection and polarization correction. J. Appl. Crystallogr. 15:330-337.
15. Koehl, P., and M. Delarue. 1994. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239:249-275.
16. Kreis, T., and R. Vale. 1999. Guidebook to the Cytoskeletal and Motor Proteins. Oxford University Press, Oxford.
17. Kreplak, L., J. Doucet, and F. Briki. 2001. Unraveling double stranded alpha-helical coiled coils: an x-ray diffraction study on hard alpha-keratin fibers. Biopolymers. 58:526-533.
18. Lavery, R., I. Parker, and J. Kendrick. 1986. A general approach to the optimization of the conformation of ring molecules with an application to valinomycin. J. Biomol. Struct. Dyn. 4:443-462.
19. Lavery, R., K. Zakrzewska, and H. Sklenar. 1995. Junction minimization of nucleic acids. Comp. Phys. Commun. 91:135-138.
20. MacKenzie, K. R., J. H. Prestegard, and D. M. Engelman. 1996. Leucine side-chain rotamers in a glycophorin A transmembrane peptide as revealed by three-bond carbon-carbon couplings and 13C chemical shifts. J. Biomol. NMR. 7:256-260.
21. MacKenzie, K. R., J. H. Prestegard, and D. M. Engelman. 1997. A transmembrane helix dimer: structure and implications. Science. 276: 131-133.
22. O'Shea, E. K., J. D. Klemm, P. S. Kim, and T. Alber. 1991. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science. 254:539-544.
23. Parry, D. A. D., and R. D. B. Fraser. 1985. Intermediate filament structure. I. Analysis of IF protein sequence data. Intern. J. Biol. Macromol. 7:203-213.
24. Parry, D. A. D., and P. M. Steinert. 1995. Intermediate Fiilament Structure. Springer Verlag, Heidelberg, Germany.
25. Parry, D. A. D., A. C. Steven, and P. M. Steinert. 1985. The coiled coil molecules of intermediate filaments consist of two parallel chains in exact axial register. Biochem. Biophys. Res. Commun. 127:1012-1018.
26. Seo, J., and C. Cohen. 1993. Pitch diversity in alpha-helical coiled coils. Proteins: Struct., Funct., Genet. 15:223-234.
27. Sparrow, L. G., C. P. Robinson, D. T. W. MacMahon, and M. R. Rubira. 1989. The amino acid sequence of component 7c, a type II intermediate filament protein from wool. Biochem. J. 261:1015-1022.
28. Tufféry, P., C. Etchebest, and S. Hazout. 1997. Prediction of protein side chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space. Protein Eng. 10:361-372.
29. van Gunsteren, W. F., and H. J. C. Berendsefn. 1987. Groningen Molecular Simulation (GROMOS), the Netherlands.
30. Zakrzewska, K., and A. Pullman. 1985. Optimized monopole expansions for the representation of the electrostatic properties of polypeptide and proteins. J. Comp. Chem. 6:265-273.