Analysis of α-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation

Journal of Structural Biology

Volumn 137, Issue 1-2, 2002, Pages 54-64

  Strelkov, Sergei V ^a   Burkhard, Peter ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

Coiled coil; Computer program; Crick parameters; Heptad repeat; Protein conformation; Skips; Stutters

Indexed keywords

PROTEIN;

ALGORITHM; ALPHA HELIX; COMPUTER PROGRAM; CONFERENCE PAPER; GEOMETRY; PARAMETER; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; THREE DIMENSIONAL IMAGING;

EID: 0036445512     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.2002.4454     Document Type: Conference Paper

References (21)

1. Akey, D. L., Malashkevich, V. N., and Kim, P. S. (2001) Buried polar residues in coiled-coil interfaces. Biochemistry 40, 6352-6360.
2. Brown, J. H., Cohen, C., and Parry, D. A. (1996) Heptad breaks in alpha-helical coiled coils: Stutters and stammers. Proteins 26, 134-145.
3. Bullough, P. A., Hughson, F. M., Skehel, J. J., and Wiley, D. C. (1994) Structure of influenza haemagglutinin at the pH of membrane fusion. Nature 371, 37-43.
4. Burkhard, P., Kammerer, R. A., Steinmetz, M. O., Bourenkov, G. P., and Aebi, U. (2000) The coiled-coil trigger site of the rod domain of cortexillin I unveils a distinct network of inter- and intra-helical salt-bridges. Structure 8, 223-230.
5. Burkhard, P., Stetefeld, J., and Strelkov, S. V. (2001) Coiled coils: A highly versatile protein folding motif. Trends Cell. Biol. 11, 82-8.
6. CCP4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Cryst. D50, 760-763.
7. Chothia, C., Levitt, M., and Richardson, D. (1981) Helix to helix packing in proteins. J. Mol. Biol. 145, 215-250.
8. Crick, F. H. C. (1952) Is alpha-keratin a coiled coil? Nature 170, 882-883.
9. Crick, F. H. C. (1953) The Fourier transform of a coiled-coil. Acta Crystallogr. 6, 685-689.
10. Harbury, P. B., Kim, P. S., and Alber, T. (1994) Crystal structure of an isoleucine-zipper trimer. Nature 371, 80-83.
11. Junop, M. S., Modesti, M., Guarne, A., Ghirlando, R., Gellert, M., and Yang, W. (2000) Crystal structure of the Xrcc4 DNA repair protein and implications for end joining. EMBO J. 19, 5962-5970.
12. Lupas, A. (1996) Coiled coils: New structures and new functions. Trends Biochem. Sci. 21, 375-382.
13. Lupas, A. (1997) Predicting coiled-coil regions in proteins. Curr. Opin. Struct. Biol. 7, 388-393.
14. O'Shea, E. K., Klemm, J. D., Kim, P. S., and Alber, T. (1991) X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254, 539-544.
15. Seo, J., and Cohen, C. (1993) Pitch diversity in alpha-helical coiled coils. Proteins 15, 223-234.
16. Sibanda, B. L., Critchlow, S. E., Begun, J., Pei, X. Y., Jackson, S. P., Blundell, T. L., and Pellegrini, L. (2001) Crystal structure of an Xrcc4-DNA ligase IV complex. Nature Struct. Biol. 8, 1015-1019.
17. Strelkov, S. V., Herrmann, H., Geisler, N., Lustig, A., Ivaninskii, S., Zimbelmann, R., Burkhard, P., and Aebi, U. (2001) Divide-and-conquer crystallographic approach towards an atomic structure of intermediate filaments. J. Mol. Biol. 306, 773-781.
18. Strelkov, S. V., Herrmann, H., Geisler, N., Wedig, T., Zimbelmann, R., Aebi, U., and Burkhard, P. (2002) Conserved segments 1A and 2B of the intermediate filament dimer: Their atomic structures and role in filament assembly. EMBO J. 21, 1255-1266.
19. Tao, Y., Strelkov, S. V., Mesyanzhinov, V. V., and Rossmann, M. G. (1997) Structure of bacteriophage T4 fibritin: A segmented coiled coil and the role of the C-terminal domain. Structure 5, 789-798.
20. Walshaw, J., and Woolfson, D. N. (2001) Socket: A program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol. 307, 1427-1450.
21. Wilson, I. A., Skehel, J. J., and Wiley, D. C. (1981) Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 A resolution. Nature 289, 366-373.