Crossref
journal-article
Springer Science and Business Media LLC
Nature Chemical Biology (297)
Authors
11
- Nathan R Zaccai (first)
- Bertie Chi (additional)
- Andrew R Thomson (additional)
- Aimee L Boyle (additional)
- Gail J Bartlett (additional)
- Marc Bruning (additional)
- Noah Linden (additional)
- Richard B Sessions (additional)
- Paula J Booth (additional)
- R Leo Brady (additional)
- Derek N Woolfson (additional)
References
49
Referenced
185
-
Liu, X., Fan, K. & Wang, W. The number of protein folds and their distribution over families in nature. Proteins 54, 491–499 (2004).
(
10.1002/prot.10514
) / Proteins by X Liu (2004) -
Levitt, M. Growth of novel protein structural data. Proc. Natl. Acad. Sci. USA 104, 3183–3188 (2007).
(
10.1073/pnas.0611678104
) / Proc. Natl. Acad. Sci. USA by M Levitt (2007) -
Grainger, B., Sadowski, M.I. & Taylor, W.R. Re-evaluating the “rules” of protein topology. J. Comput. Biol. 17, 1371–1384 (2010).
(
10.1089/cmb.2009.0265
) / J. Comput. Biol. by B Grainger (2010) -
Taylor, W.R., Chelliah, V., Hollup, S.M., MacDonald, J.T. & Jonassen, I. Probing the “dark matter” of protein fold space. Structure 17, 1244–1252 (2009).
(
10.1016/j.str.2009.07.012
) / Structure by WR Taylor (2009) -
Kuhlman, B. et al. Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364–1368 (2003).
(
10.1126/science.1089427
) / Science by B Kuhlman (2003) -
MacDonald, J.T., Maksimiak, K., Sadowski, M.I. & Taylor, W.R. De novo backbone scaffolds for protein design. Proteins 78, 1311–1325 (2010).
(
10.1002/prot.22651
) / Proteins by JT MacDonald (2010) -
Mason, J.M. & Arndt, K.M. Coiled coil domains: stability, specificity, and biological implications. ChemBioChem 5, 170–176 (2004).
(
10.1002/cbic.200300781
) / ChemBioChem by JM Mason (2004) -
Parry, D.A.D., Fraser, R.D.B. & Squire, J.M. Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structure. J. Struct. Biol. 163, 258–269 (2008).
(
10.1016/j.jsb.2008.01.016
) / J. Struct. Biol. by DAD Parry (2008) -
Crick, F.H.C. The packing of alpha-helices—simple coiled-coils. Acta Crystallogr. 6, 689–697 (1953).
(
10.1107/S0365110X53001964
) / Acta Crystallogr. by FHC Crick (1953) -
Walshaw, J. & Woolfson, D.N. Socket: a program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol. 307, 1427–1450 (2001).
(
10.1006/jmbi.2001.4545
) / J. Mol. Biol. by J Walshaw (2001) -
Woolfson, D.N. The design of coiled-coil structures and assemblies. Adv. Protein Chem. 70, 79–112 (2005).
(
10.1016/S0065-3233(05)70004-8
) / Adv. Protein Chem. by DN Woolfson (2005) -
Grigoryan, G. & Keating, A.E. Structural specificity in coiled-coil interactions. Curr. Opin. Struct. Biol. 18, 477–483 (2008).
(
10.1016/j.sbi.2008.04.008
) / Curr. Opin. Struct. Biol. by G Grigoryan (2008) -
Harbury, P.B., Plecs, J.J., Tidor, B., Alber, T. & Kim, P.S. High-resolution protein design with backbone freedom. Science 282, 1462–1467 (1998).
(
10.1126/science.282.5393.1462
) / Science by PB Harbury (1998) -
Nautiyal, S., Woolfson, D.N., King, D.S. & Alber, T. A designed heterotrimeric coiled-coil. Biochemistry 34, 11645–11651 (1995).
(
10.1021/bi00037a001
) / Biochemistry by S Nautiyal (1995) -
Grigoryan, G., Reinke, A.W. & Keating, A.E. Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 458, 859–864 (2009).
(
10.1038/nature07885
) / Nature by G Grigoryan (2009) -
Grigoryan, G. & DeGrado, W.F. Probing designability via a generalized model of helical bundle geometry. J. Mol. Biol. 405, 1079–1100 (2011).
(
10.1016/j.jmb.2010.08.058
) / J. Mol. Biol. by G Grigoryan (2011) -
Grigoryan, G. et al. Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science 332, 1071–1076 (2011).
(
10.1126/science.1198841
) / Science by G Grigoryan (2011) -
Lupas, A.N. & Gruber, M. The structure of alpha-helical coiled coils. Adv. Protein Chem. 70, 37–78 (2005).
(
10.1016/S0065-3233(05)70003-6
) / Adv. Protein Chem. by AN Lupas (2005) -
Moutevelis, E. & Woolfson, D.N. A periodic table of coiled-coil protein structures. J. Mol. Biol. 385, 726–732 (2009).
(
10.1016/j.jmb.2008.11.028
) / J. Mol. Biol. by E Moutevelis (2009) -
Liu, J. et al. A seven-helix coiled coil. Proc. Natl. Acad. Sci. USA 103, 15457–15462 (2006).
(
10.1073/pnas.0604871103
) / Proc. Natl. Acad. Sci. USA by J Liu (2006) -
Koronakis, V., Sharff, A., Koronakis, E., Luisi, B. & Hughes, C. Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Nature 405, 914–919 (2000).
(
10.1038/35016007
) / Nature by V Koronakis (2000) -
Walshaw, J. & Woolfson, D.N. Open-and-shut cases in coiled-coil assembly: alpha-sheets and alpha-cylinders. Protein Sci. 10, 668–673 (2001).
(
10.1110/ps.36901
) / Protein Sci. by J Walshaw (2001) -
Walshaw, J. & Woolfson, D.N. Extended knobs-into-holes packing in classical and complex coiled-coil assemblies. J. Struct. Biol. 144, 349–361 (2003).
(
10.1016/j.jsb.2003.10.014
) / J. Struct. Biol. by J Walshaw (2003) -
Ghirlanda, G., Lear, J.D., Ogihara, N.L., Eisenberg, D. & DeGrado, W.F. A hierarchic approach to the design of hexameric helical barrels. J. Mol. Biol. 319, 243–253 (2002).
(
10.1016/S0022-2836(02)00233-4
) / J. Mol. Biol. by G Ghirlanda (2002) -
Donald, J.E. et al. Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion. Proc. Natl. Acad. Sci. USA 108, 3958–3963 (2011).
(
10.1073/pnas.1019668108
) / Proc. Natl. Acad. Sci. USA by JE Donald (2011) -
North, B., Summa, C.M., Ghirlanda, G. & DeGrado, W.F. D(n)-symmetrical tertiary templates for the design of tubular proteins. J. Mol. Biol. 311, 1081–1090 (2001).
(
10.1006/jmbi.2001.4900
) / J. Mol. Biol. by B North (2001) -
Armstrong, C.T., Vincent, T.L., Green, P.J. & Woolfson, D.N. SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences. Bioinformatics 27, 1908–1914 (2011).
(
10.1093/bioinformatics/btr299
) / Bioinformatics by CT Armstrong (2011) -
Harbury, P.B., Zhang, T., Kim, P.S. & Alber, T. A switch between 2-stranded, 3-stranded and 4-stranded coiled coils in GCN4 leucine-zipper mutants. Science 262, 1401–1407 (1993).
(
10.1126/science.8248779
) / Science by PB Harbury (1993) -
O'Shea, E.K., Lumb, K.J. & Kim, P.S. Peptide 'Velcro'—design of a heterodimeric coiled-coil. Curr. Biol. 3, 658–667 (1993).
(
10.1016/0960-9822(93)90063-T
) / Curr. Biol. by EK O'Shea (1993) -
Bromley, E.H.C., Sessions, R.B., Thomson, A.R. & Woolfson, D.N. Designed alpha-helical tectons for constructing multicomponent synthetic biological systems. J. Am. Chem. Soc. 131, 928–930 (2009).
(
10.1021/ja804231a
) / J. Am. Chem. Soc. by EHC Bromley (2009) -
Reinke, A.W., Grant, R.A. & Keating, A.E. A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering. J. Am. Chem. Soc. 132, 6025–6031 (2010).
(
10.1021/ja907617a
) / J. Am. Chem. Soc. by AW Reinke (2010) -
Strelkov, S.V. & Burkhard, P. Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation. J. Struct. Biol. 137, 54–64 (2002).
(
10.1006/jsbi.2002.4454
) / J. Struct. Biol. by SV Strelkov (2002) -
Woolfson, D.N. & Alber, T. Predicting oligomerization states of coiled coils. Protein Sci. 4, 1596–1607 (1995).
(
10.1002/pro.5560040818
) / Protein Sci. by DN Woolfson (1995) -
Berman, H., Henrick, K., Nakamura, H. & Markley, J.L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35, D301–D303 (2007).
(
10.1093/nar/gkl971
) / Nucleic Acids Res. by H Berman (2007) -
Opella, S.J. et al. Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy. Nat. Struct. Biol. 6, 374–379 (1999).
(
10.1038/7610
) / Nat. Struct. Biol. by SJ Opella (1999) -
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 274, 761–765 (1996).
(
10.1126/science.274.5288.761
) / Science by VN Malashkevich (1996) -
Liu, J., Yong, W., Deng, Y.Q., Kallenbach, N.R. & Lu, M. Atomic structure of a tryptophan-zipper pentamer. Proc. Natl. Acad. Sci. USA 101, 16156–16161 (2004).
(
10.1073/pnas.0405319101
) / Proc. Natl. Acad. Sci. USA by J Liu (2004) -
Jeoung, J.H., Pippig, D.A., Martins, B.M., Wagener, N. & Dobbek, H. HTHP: A novel class of hexameric, tyrosine-coordinated heme proteins. J. Mol. Biol. 368, 1122–1131 (2007).
(
10.1016/j.jmb.2007.02.079
) / J. Mol. Biol. by JH Jeoung (2007) -
Dong, C. et al. Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein. Nature 444, 226–229 (2006).
(
10.1038/nature05267
) / Nature by C Dong (2006) -
Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. & Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–730 (2009).
(
10.1038/nature08026
) / Nature by M Mueller (2009) -
Demeler, B. UltraScan—a comprehensive data analysis software package for analytical ultracentrifugation experiments. in Modern Analytical Ultracentrifugation: Techniques and Methods (eds. Scott, D.J. & Harding, S.E.) 210–229 (Royal Society of Chemistry, 2005).
(
10.1039/9781847552617-00210
) -
Collaborative Computational Project, Number 4. The CCP4 suite—programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).
(
10.1107/S0907444994003112
) -
Sheldrick, G.M. A short history of SHELX. Acta Crystallogr. A 64, 112–122 (2008).
(
10.1107/S0108767307043930
) / Acta Crystallogr. A by GM Sheldrick (2008) -
Perrakis, A., Harkiolaki, M., Wilson, K.S. & Lamzin, V.S. ARP/wARP and molecular replacement. Acta Crystallogr. D Biol. Crystallogr. 57, 1445–1450 (2001).
(
10.1107/S0907444901014007
) / Acta Crystallogr. D Biol. Crystallogr. by A Perrakis (2001) -
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
(
10.1107/S0907444904019158
) / Acta Crystallogr. D Biol. Crystallogr. by P Emsley (2004) -
Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).
(
10.1107/S0907444996012255
) / Acta Crystallogr. D Biol. Crystallogr. by GN Murshudov (1997) -
Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
(
10.1107/S0907444909052925
) / Acta Crystallogr. D Biol. Crystallogr. by PD Adams (2010) -
McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
(
10.1107/S0021889807021206
) / J. Appl. Crystallogr. by AJ McCoy (2007) -
Testa, O.D., Moutevelis, E. & Woolfson, D.N. CC+: a relational database of coiled-coil structures. Nucleic Acids Res. 37, D315–D322 (2009).
(
10.1093/nar/gkn675
) / Nucleic Acids Res. by OD Testa (2009)
Dates
Type | When |
---|---|
Created | 13 years, 9 months ago (Oct. 30, 2011, 2:39 p.m.) |
Deposited | 2 years, 2 months ago (June 10, 2023, 4:39 p.m.) |
Indexed | 2 weeks, 5 days ago (Aug. 6, 2025, 9:05 a.m.) |
Issued | 13 years, 9 months ago (Oct. 30, 2011) |
Published | 13 years, 9 months ago (Oct. 30, 2011) |
Published Online | 13 years, 9 months ago (Oct. 30, 2011) |
Published Print | 13 years, 8 months ago (Dec. 1, 2011) |
@article{Zaccai_2011, title={A de novo peptide hexamer with a mutable channel}, volume={7}, ISSN={1552-4469}, url={http://dx.doi.org/10.1038/nchembio.692}, DOI={10.1038/nchembio.692}, number={12}, journal={Nature Chemical Biology}, publisher={Springer Science and Business Media LLC}, author={Zaccai, Nathan R and Chi, Bertie and Thomson, Andrew R and Boyle, Aimee L and Bartlett, Gail J and Bruning, Marc and Linden, Noah and Sessions, Richard B and Booth, Paula J and Brady, R Leo and Woolfson, Derek N}, year={2011}, month=oct, pages={935–941} }