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Coiled-Coil Design: Updated and Upgraded

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Fibrous Proteins: Structures and Mechanisms

Part of the book series: Subcellular Biochemistry ((SCBI,volume 82))

Abstract

α-Helical coiled coils are ubiquitous protein-folding and protein-interaction domains in which two or more α-helical chains come together to form bundles. Through a combination of bioinformatics analysis of many thousands of natural coiled-coil sequences and structures, plus empirical protein engineering and design studies, there is now a deep understanding of the sequence-to-structure relationships for this class of protein architecture. This has led to considerable success in rational design and what might be termed in biro de novo design of simple coiled coils, which include homo- and hetero-meric parallel dimers, trimers and tetramers. In turn, these provide a toolkit for directing the assembly of both natural proteins and more complex designs in protein engineering, materials science and synthetic biology. Moving on, the increased and improved use of computational design is allowing access to coiled-coil structures that are rare or even not observed in nature, for example α-helical barrels, which comprise five or more α-helices and have central channels into which different functions may be ported. This chapter reviews all of these advances, outlining improvements in our knowledge of the fundamentals of coiled-coil folding and assembly, and highlighting new coiled coil-based materials and applications that this new understanding is opening up. Despite considerable progress, however, challenges remain in coiled-coil design, and the next decade promises to be as productive and exciting as the last.

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References

  • Ambroggio XI, Kuhlman B (2006) Design of protein conformational switches. Curr Opin Struct Biol 16(4):525–530

    Article  CAS  PubMed  Google Scholar 

  • Apgar JR, Gutwin KN, Keating AE (2008) Predicting helix orientation for coiled-coil dimers. Proteins 72(3):1048–1065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Armstrong CT, Vincent TL, Green PJ, Woolfson DN (2011) SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences. Bioinformatics 27(14):1908–1914

    Article  CAS  PubMed  Google Scholar 

  • Aronsson C, Danmark S, Zhou F, Oberg P, Enander K, Su H, Aili D (2015) Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties. Sci Rep:5

    Google Scholar 

  • Baker EG, Bartlett GJ, Crump MP, Sessions RB, Linden N, Faul CFJ, Woolfson DN (2015) Local and macroscopic electrostatic interactions in single alpha-helices. Nat Chem Biol 11(3):221–228

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bale JB, Park RU, Liu YX, Gonen S, Gonen T, Cascio D, King NP, Yeates TO, Baker D (2015) Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression. Protein Sci 24(10):1695–1701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Banwell EF, Abelardo ES, Adams DJ, Birchall MA, Corrigan A, Donald AM, Kirkland M, Serpell LC, Butler MF, Woolfson DN (2009) Rational design and application of responsive alpha-helical peptide hydrogels. Nat Mater 8(7):596–600

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D (2016) De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Science 352(6286):680–687

    Article  CAS  PubMed  Google Scholar 

  • Boyle AL, Woolfson DN (2011) De novo designed peptides for biological applications. Chem Soc Rev 40(8):4295–4306

    Article  CAS  PubMed  Google Scholar 

  • Boyle AL, Bromley EHC, Bartlett GJ, Sessions RB, Sharp TH, Williams CL, Curmi PMG, Forde NR, Linke H, Woolfson DN (2012) Squaring the circle in peptide assembly: from fibers to discrete nanostructures by de novo design. J Am Chem Soc 134(37):15457–15467

    Article  CAS  PubMed  Google Scholar 

  • Bromley EHC, Channon KJ (2011) Alpha-helical peptide assemblies: giving new function to designed structures. Prog Mol Biol Transl Sci 103:231–275

    Article  CAS  PubMed  Google Scholar 

  • Bromley EHC, Channon K, Moutevelis E, Woolfson DN (2008) Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems. ACS Chem Biol 3(1):38–50

    Article  CAS  PubMed  Google Scholar 

  • Bromley EHC, Sessions RB, Thomson AR, Woolfson DN (2009) Designed alpha-helical tectons for constructing multicomponent synthetic biological systems. J Am Chem Soc 131(3):928–930

    Article  CAS  PubMed  Google Scholar 

  • Brown JH, Cohen C, Parry DAD (1996) Heptad breaks in alpha-helical coiled coils: stutters and stammers. Proteins 26(2):134–145

    Article  CAS  PubMed  Google Scholar 

  • Burgess NC, Sharp TH, Thomas F, Wood CW, Thomson AR, Zaccai NR, Brady RL, Serpell LC, Woolfson DN (2015) Modular design of self-assembling peptide-based nanotubes. J Am Chem Soc 137(33):10554–10562

    Article  CAS  PubMed  Google Scholar 

  • Burton AJ, Thomas F, Agnew C, Hudson KL, Halford SE, Brady RL, Woolfson DN (2013) Accessibility, reactivity, and selectivity of side chains within a channel of de novo peptide assembly. J Am Chem Soc 135(34):12524–12527

    Article  CAS  PubMed  Google Scholar 

  • Burton AJ, Thomson AR, Dawson WM, Brady RL, Woolfson DN (2016) Installing hydrolytic activity into a completely de novo protein framework. Nat Chem 8(9):837–844.

    Google Scholar 

  • Channon K, Bromley EHC, Woolfson DN (2008) Synthetic biology through biomolecular design and engineering. Curr Opin Struct Biol 18(4):491–498

    Article  CAS  PubMed  Google Scholar 

  • Chothia C, Levitt M, Richardson D (1981) Helix to helix packing in proteins. J Mol Biol 145(1):215–250

    Article  CAS  PubMed  Google Scholar 

  • Crick FHC (1953a) The Fourier transform of a coiled-coil. Acta Crystallogr 6(8-9):685–689

    Article  CAS  Google Scholar 

  • Crick FHC (1953b) The packing of alpha-helices – simple coiled-coils. Acta Crystallogr 6(8-9):689–697

    Article  CAS  Google Scholar 

  • Crooks RO, Baxter D, Panek AS, Lubben AT, Mason JM (2016) Deriving heterospecific self-assembling protein-protein interactions using a computational interactome screen. J Mol Biol 428(2):385–398

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dasgupta A, Mondal JH, Das D (2013) Peptide hydrogels. RSC Adv 3(24):9117–9149

    Article  CAS  Google Scholar 

  • Davey JA, Chica RA (2012) Multistate approaches in computational protein design. Protein Sci 21(9):1241–1252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Delorenzi M, Speed T (2002) An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics 18(4):617–625

    Article  CAS  PubMed  Google Scholar 

  • Diss ML, Kennan AJ (2008) Heterotrimeric coiled coils with core residue urea side chains. J Org Chem 73(24):9752–9755

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong CJ, Beis K, Nesper J, Brunkan-LaMontagne AL, Clarke BR, Whitfield C, Naismith JH (2006) Wza the translocon for E-coli capsular polysaccharides defines a new class of membrane protein. Nature 444(7116):226–229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong H, Paramonov SE, Hartgerink JD (2008) Self-assembly of alpha-helical coiled coil nanofibers. J Am Chem Soc 130(41):13691–13695

    Article  CAS  PubMed  Google Scholar 

  • Egelman EH, Xu C, DiMaio F, Magnotti E, Modlin C, Yu X, Wright E, Baker D, Conticello VP (2015) Structural plasticity of helical nanotubes based on coiled-coil assemblies. Structure 23(2):280–289

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eshaghi S, Niegowski D, Kohl A, Molina DM, Lesley SA, Nordlund P (2006) Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution. Science 313(5785):354–357

    Article  CAS  PubMed  Google Scholar 

  • Fairman R, Chao HG, Lavoie TB, Villafranca JJ, Matsueda GR, Novotny J (1996) Design of heterotetrameric coiled coils: evidence for increased stabilization by Glu(-)-Lys(+) ion pair interactions. Biochemistry 35(9):2824–2829

    Article  CAS  PubMed  Google Scholar 

  • Feldmeier K, Hocker B (2013) Computational protein design of ligand binding and catalysis. Curr Opin Chem Biol 17(6):929–933

    Article  CAS  PubMed  Google Scholar 

  • Fletcher JM, Boyle AL, Bruning M, Bartlett GJ, Vincent TL, Zaccai NR, Armstrong CT, Bromley EHC, Booth PJ, Brady RL, Thomson AR, Woolfson DN (2012) A basis set of de novo coiled-coil peptide oligomers for rational protein design and synthetic biology. ACS Synth Biol 1(6):240–250

    Article  CAS  PubMed  Google Scholar 

  • Fletcher JM, Harniman RL, Barnes FRH, Boyle AL, Collins A, Mantell J, Sharp TH, Antognozzi M, Booth PJ, Linden N, Miles MJ, Sessions RB, Verkade P, Woolfson DN (2013) Self-assembling cages from coiled-coil peptide modules. Science 340(6132):595–599

    Article  CAS  PubMed  Google Scholar 

  • Fong JH, Keating AE, Singh M (2004) Predicting specificity in bZIP coiled-coil protein interactions. Genome Biol 5(2): R11

    Google Scholar 

  • Ghirlanda G, Lear JD, Ogihara NL, Eisenberg D, DeGrado WF (2002) A hierarchic approach to the design of hexameric helical barrels. J Mol Biol 319(1):243–253

    Article  CAS  PubMed  Google Scholar 

  • Ghosh I, Hamilton AD, Regan L (2000) Antiparallel leucine zipper-directed protein reassembly: application to the green fluorescent protein. J Am Chem Soc 122(23):5658–5659

    Article  CAS  Google Scholar 

  • Gonzalez L, Woolfson DN, Alber T (1996) Buried polar residues and structural specificity in the GCN4 leucine zipper. Nat Struct Biol 3(12):1011–1018

    Article  CAS  PubMed  Google Scholar 

  • Gradisar H, Jerala R (2011) De novo design of orthogonal peptide pairs forming parallel coiled-coil heterodimers. J Pept Sci 17(2):100–106

    Article  CAS  PubMed  Google Scholar 

  • Gradisar H, Bozic S, Doles T, Vengust D, Hafner-Bratkovic I, Mertelj A, Webb B, Sali A, Klavzar S, Jerala R (2013) Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nat Chem Biol 9(6):362–366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grigoryan G, DeGrado WF (2011) Probing designability via a generalized model of helical bundle geometry. J Mol Biol 405(4):1079–1100

    Article  CAS  PubMed  Google Scholar 

  • Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, Willis L, Drndic M, Kikkawa JM, DeGrado WF (2011) Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science 332(6033):1071–1076

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gruber M, Lupas AN (2003) Historical review: another 50th anniversary – new periodicities in coiled coils. Trends Biochem Sci 28(12):679–685

    Article  CAS  PubMed  Google Scholar 

  • Gurnon DG, Whitaker JA, Oakley MG (2003) Design and characterization of a homodimeric antiparallel coiled coil. J Am Chem Soc 125(25):7518–7519

    Article  CAS  PubMed  Google Scholar 

  • Hadley EB, Gellman SH (2006) An antiparallel alpha-helical coiled-coil model system for rapid assessment of side-chain recognition at the hydrophobic interface. J Am Chem Soc 128(51):16444–16445

    Article  CAS  PubMed  Google Scholar 

  • Hadley EB, Testa OD, Woolfson DN, Gellman SH (2008) Preferred side-chain constellations at antiparallel coiled-coil interfaces. Proc Natl Acad Sci U S A 105(2):530–535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harbury PB, Zhang T, Kim PS, Alber T (1993) A switch between 2-stranded, 3-stranded and 4-stranded coiled coils in Gcn4 leucine-zipper mutants. Science 262(5138):1401–1407

    Article  CAS  PubMed  Google Scholar 

  • Harbury PB, Kim PS, Alber T (1994) Crystal-structure of an isoleucine-zipper trimer. Nature 371(6492):80–83

    Article  CAS  PubMed  Google Scholar 

  • Harbury PB, Tidor B, Kim PS (1995) Repacking protein cores with backbone freedom – structure prediction for coiled coils. Proc Natl Acad Sci U S A 92(18):8408–8412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS (1998) High-resolution protein design with backbone freedom. Science 282(5393):1462–1467

    Article  CAS  PubMed  Google Scholar 

  • Hartmann MD, Ridderbusch O, Zeth K, Albrecht R, Testa O, Woolfson DN, Sauer G, Dunin-Horkawicz S, Lupas AN, Alvarez BH (2009) A coiled-coil motif that sequesters ions to the hydrophobic core. Proc Natl Acad Sci U S A 106(40):16950–16955

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hicks MR, Holberton DV, Kowalczyk C, Woolfson DN (1997) Coiled-coil assembly by peptides with non-heptad sequence motifs. Fold Des 2(3):149–158

    Article  CAS  PubMed  Google Scholar 

  • Hicks MR, Walshaw J, Woolfson DN (2002) Investigating the tolerance of coiled-coil peptides to nonheptad sequence inserts. J Struct Biol 137(1-2):73–81

    Article  CAS  PubMed  Google Scholar 

  • Hol WGJ, Vanduijnen PT, Berendsen HJC (1978) Alpha-helix dipole and properties of proteins. Nature 273(5662):443–446

    Article  CAS  PubMed  Google Scholar 

  • Huang PS, Oberdorfer G, Xu CF, Pei XY, Nannenga BL, Rogers JM, DiMaio F, Gonen T, Luisi B, Baker D (2014) High thermodynamic stability of parametrically designed helical bundles. Science 346(6208):481–485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hume J, Sun J, Jacquet R, Renfrew PD, Martin JA, Bonneau R, Gilchrist ML, Montclare JK (2014) Engineered coiled-coil protein microfibers. Biomacromolecules 15(10):3503–3510

    Article  CAS  PubMed  Google Scholar 

  • Joh NH, Wang T, Bhate MP, Acharya R, Wu YB, Grabe M, Hong M, Grigoryan G, DeGrado WF (2014) De novo design of a transmembrane Zn2+-transporting four-helix bundle. Science 346(6216):1520-1524.

    Google Scholar 

  • Kaplan JB, Reinke AW, Keating AE (2014) Increasing the affinity of selective bZIP-binding peptides through surface residue redesign. Protein Sci 23(7):940–953

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kashiwada A, Hiroaki H, Kohda D, Nango M, Tanaka T (2000) Design of a heterotrimeric alpha-helical bundle by hydrophobic core engineering. J Am Chem Soc 122(2):212–215

    Article  CAS  Google Scholar 

  • King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, Andre I, Gonen T, Yeates TO, Baker D (2012) Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 336(6085):1171–1174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, Yeates TO, Baker D (2014) Accurate design of co-assembling multi-component protein nanomaterials. Nature 510(7503):103–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kiyokawa T, Kanaori K, Tajima K, Kawaguchi M, Mizuno T, Oku JI, Tanaka T (2004) Selective formation of AAB- and ABC-type heterotrimeric alpha-helical coiled coils. Chem Eur J 10(14):3548–3554

    Article  CAS  PubMed  Google Scholar 

  • Kocar V, Abram SB, Doles T, Basic N, Gradisar H, Pisanski T, Jerala R (2015) TOPOFOLD, the designed modular biomolecular folds: polypeptide-based molecular origami nanostructures following the footsteps of DNA. Wiley Interdiscip Rev Nanomed Nanobiotechnol 7(2):218–237

    Article  CAS  PubMed  Google Scholar 

  • Kong L, Askes SHC, Bonnet S, Kros A, Campbell F (2016) Temporal control of membrane fusion through photolabile PEGylation of liposome membranes. Angew Chem Int Ed 55(4):1396–1400

    Article  CAS  Google Scholar 

  • Koronakis V, Sharff A, Koronakis E, Luisi B, Hughes C (2000) Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Nature 405(6789):914–919

    Article  CAS  PubMed  Google Scholar 

  • Litowski JR, Hodges RS (2002) Designing heterodimeric two-stranded alpha-helical coiled-coils – effects of hydrophobicity and alpha-helical propensity on protein folding, stability, and specificity. J Biol Chem 277(40):37272–37279

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Zheng Q, Deng Y, Cheng C-S, Kallenbach NR, Lu M (2006a) A seven-helix coiled coil. Proc Natl Acad Sci U S A 103(42):15457–15462

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu J, Zheng Q, Deng YQ, Kallenbach NR, Lu M (2006b) Conformational transition between four and five-stranded phenylalanine zippers determined by a local packing interaction. J Mol Biol 361(1):168–179

    Article  CAS  PubMed  Google Scholar 

  • Lizatovic R, Aurelius O, Stenstrom O, Drakenberg T, Akke M, Logan DT, Andre I (2016) A de novo designed coiled-coil peptide with a reversible pH-induced oligomerization switch.

    Google Scholar 

  • Lovejoy B, Choe S, Cascio D, McRorie DK, Degrado WF, Eisenberg D (1993) Crystal-structure of a synthetic triple-stranded alpha-helical bundle. Science 259(5099):1288–1293

    Article  CAS  PubMed  Google Scholar 

  • Lumb KJ, Kim PS (1998) A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil (vol 34, pg 8642, 1995). Biochemistry 37(37):13042–13042

    Article  CAS  PubMed  Google Scholar 

  • Lupas A (1996a) Coiled coils: new structures and new functions. Trends Biochem Sci 21(10):375–382

    Article  CAS  PubMed  Google Scholar 

  • Lupas A (1996b) Prediction and analysis of coiled-coil structures. Methods Enzymol 266:513–525

    Article  CAS  PubMed  Google Scholar 

  • Lupas AN, Gruber M (2005) The structure of alpha-helical coiled coils. Adv Protein Chem 70:37–78

    Article  CAS  PubMed  Google Scholar 

  • Lupas A, Vandyke M, Stock J (1991) Predicting coiled coils from protein sequences. Science 252(5009):1162–1164

    Article  CAS  PubMed  Google Scholar 

  • Magliery TJ (2015) Protein stability: computation, sequence statistics, and new experimental methods. Curr Opin Struct Biol 33:161–168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malashkevich VN, Kammerer RA, Efimov VP, Schulthess T, Engel J (1996) The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel? Science 274(5288):761–765

    Article  CAS  PubMed  Google Scholar 

  • Marsden HR, Elbers NA, Bomans PHH, Sommerdijk NAJM, Kros A (2009) A reduced SNARE model for membrane fusion. Angew Chem Int Ed 48(13):2330–2333

    Article  CAS  Google Scholar 

  • Marsden HR, Tomatsu I, Kros A (2011) Model systems for membrane fusion. Chem Soc Rev 40(3):1572–1585

    Article  CAS  PubMed  Google Scholar 

  • McClain DL, Woods HL, Oakley MG (2001) Design and characterization of a heterodimeric coiled coil that forms exclusively with an antiparallel relative helix orientation. J Am Chem Soc 123(13):3151–3152

    Article  CAS  PubMed  Google Scholar 

  • McDonnell AV, Jiang T, Keating AE, Berger B (2006) Paircoil2: improved prediction of coiled coils from sequence. Bioinformatics 22(3):356–358

    Article  CAS  PubMed  Google Scholar 

  • Mizuno T, Suzuki K, Imai T, Kitade Y, Furutani Y, Kudou M, Oda M, Kandori H, Tsumoto K, Tanaka T (2009) Manipulation of protein-complex function by using an engineered heterotrimeric coiled-coil switch. Org Biomol Chem 7(15):3102–3111

    Article  CAS  Google Scholar 

  • Mocny CS, Pecoraro VL (2015) De novo protein design as a methodology for synthetic bioinorganic chemistry. Acc Chem Res 48(8):2388–2396

    Article  CAS  PubMed  Google Scholar 

  • Moll JR, Ruvinov SB, Pastan I, Vinson C (2001) Designed heterodimerizing leucine zippers with a range of pIs and stabilities up to 10(-15) M. Protein Sci 10(3):649–655

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Monera OD, Zhou NE, Kay CM, Hodges RS (1993) Comparison of antiparallel and parallel 2-stranded alpha-helical coiled-coils – design, synthesis, and characterization. J Biol Chem 268(26):19218–19227

    CAS  PubMed  Google Scholar 

  • Monera OD, Kay CM, Hodges RS (1994) Electrostatic interactions control the parallel and antiparallel orientation of alpha-helical chains in 2-stranded alpha-helical coiled-coils. Biochemistry 33(13):3862–3871

    Article  CAS  PubMed  Google Scholar 

  • Mora NL, Bahreman A, Valkenier H, Li HY, Sharp TH, Sheppard DN, Davis AP, Kros A (2016) Targeted anion transporter delivery by coiled-coil driven membrane fusion. Chem Sci 7(3):1768–1772

    Article  CAS  Google Scholar 

  • Moutevelis E, Woolfson DN (2009) A periodic table of coiled-coil protein structures. J Mol Biol 385(3):726–732

    Article  CAS  PubMed  Google Scholar 

  • Myszka DG, Chaiken IM (1994) Design and characterization of an intramolecular antiparallel coiled-coil peptide. Biochemistry 33(9):2363–2372

    Article  CAS  PubMed  Google Scholar 

  • Nautiyal S, Alber T (1999) Crystal structure of a designed, thermostable; heterotrimeric coiled coil. Protein Sci 8(1):84–90

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nautiyal S, Woolfson DN, King DS, Alber T (1995) A designed heterotrimeric coiled-coil. Biochemistry 34(37):11645–11651

    Article  CAS  PubMed  Google Scholar 

  • Negron C, Keating AE (2013) Multistate protein design using CLEVER and CLASSY. Methods Enzymol 523:171–190

    Article  CAS  PubMed  Google Scholar 

  • Negron C, Keating AE (2014) A set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit. J Am Chem Soc 136(47):16544–16556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Norn CH, Andre I (2016) Computational design of protein self-assembly. Curr Opin Struct Biol 39:39–45

    Article  CAS  PubMed  Google Scholar 

  • Oakley MG, Hollenbeck JJ (2001) The design of antiparallel coiled coils. Curr Opin Struct Biol 11(4):450–457

    Article  CAS  PubMed  Google Scholar 

  • Offer G, Sessions R (1995) Computer modeling of the alpha-helical coiled-coil – packing of side-chains in the inner-core. J Mol Biol 249(5):967–987

    Article  CAS  PubMed  Google Scholar 

  • Offer G, Hicks MR, Woolfson DN (2002) Generalized Crick equations for modeling noncanonical coiled coils. J Struct Biol 137(1-2):41–53

    Article  CAS  PubMed  Google Scholar 

  • Ogihara NL, Weiss MS, Degrado WF, Eisenberg D (1997) The crystal structure of the designed trimeric coiled coil coil-V(a)L(d): implications for engineering crystals and supramolecular assemblies. Protein Sci 6(1):80–88

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oshaben KM, Salari R, McCaslin DR, Chong LT, Horne WS (2012) The native GCN4 leucine-zipper domain does not uniquely specify a dimeric oligomerization state. Biochemistry 51(47):9581–9591

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • O’Shea EK, Klemm JD, Kim PS, Alber T (1991) X-ray structure of the Gcn4 leucine zipper, a 2-stranded, parallel coiled coil. Science 254(5031):539–544

    Article  PubMed  Google Scholar 

  • O’Shea EK, Lumb KJ, Kim PS (1993) Peptide velcro – design of a heterodimeric coiled-coil. Curr Biol 3(10):658–667

    Article  PubMed  Google Scholar 

  • Padilla JE, Colovos C, Yeates TO (2001) Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments. Proc Natl Acad Sci U S A 98(5):2217–2221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pagel K, Koksch B (2008) Following polypeptide folding and assembly with conformational switches. Curr Opin Chem Biol 12(6):730–739

    Article  CAS  PubMed  Google Scholar 

  • Pandya MJ, Cerasoli E, Joseph A, Stoneman RG, Waite E, Woolfson DN (2004) Sequence and structural duality: designing peptides to adopt two stable conformations. J Am Chem Soc 126(51):17016–17024

    Article  CAS  PubMed  Google Scholar 

  • Patterson DP, Su M, Franzmann TM, Sciore A, Skiniotis G, Marsh ENG (2014) Characterization of a highly flexible self-assembling protein system designed to form nanocages. Protein Sci 23(2):190–199

    Article  CAS  PubMed  Google Scholar 

  • Payandeh J, Pai EF (2006) A structural basis for Mg2+ homeostasis and the CorA translocation cycle. EMBO J 25(16):3762–3773

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Plecs JJ, Harbury PB, Kim PS, Alber T (2004) Structural test of the parameterized-backbone method for protein design. J Mol Biol 342(1):289–297

    Article  CAS  PubMed  Google Scholar 

  • Potapov V, Kaplan JB, Keating AE (2015) Data-driven prediction and design of bZIP coiled-coil interactions. PLoS Comput Biol 11(2) UNSP e1004046

    Google Scholar 

  • Quinlan RA, Bromley EH, Pohl E (2015) A silk purse from a sow’s ear – bioinspired materials based on alpha-helical coiled coils. Curr Opin Cell Biol 32:131–137

    Article  CAS  PubMed  Google Scholar 

  • Rackham OJL, Madera M, Armstrong CT, Vincent TL, Woolfson DN, Gough J (2010) The evolution and structure prediction of coiled coils across all genomes. J Mol Biol 403(3):480–493

    Article  CAS  PubMed  Google Scholar 

  • Ramisch S, Lizatovic R, Andre I (2015) Exploring alternate states and oligomerization preferences of coiled-coils by de novo structure modeling. Proteins 83(2):235–247

    Article  PubMed  CAS  Google Scholar 

  • Regan L, Caballero D, Hinrichsen MR, Virrueta A, Williams DM, O’Hern CS (2015) Protein design: past, present, and future. Biopolymers 104(4):334–350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reinke AW, Grant RA, Keating AE (2010) A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering. J Am Chem Soc 132(17):6025–6031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Root BC, Pellegrino LD, Crawford ED, Kokona B, Fairman R (2009) Design of a heterotetrameric coiled coil. Protein Sci 18(2):329–336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rose PW, Prlic A, Bi CX, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne PE, Burley SK (2015) The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res 43(D1):D345–D356

    Article  PubMed  Google Scholar 

  • Sastri NP, Viskovska M, Hyser JM, Tanner MR, Horton LB, Sankaran B, Prasad BVV, Estes MK (2014) Structural plasticity of the coiled-coil domain of rotavirus NSP4. J Virol 88(23):13602–13612

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schnarr NA, Kennan AJ (2002) Peptide tic-tac-toe: heterotrimeric coiled-coil specificity from steric matching of multiple hydrophobic side chains. J Am Chem Soc 124(33):9779–9783

    Article  CAS  PubMed  Google Scholar 

  • Schwenen LLG, Hubrich R, Milovanovic D, Geil B, Yang J, Kros A, Jahn R, Steinem C (2015) Resolving single membrane fusion events on planar pore-spanning membranes. Sci Rep 5

    Google Scholar 

  • Sharp TH, Bruning M, Mantell J, Sessions RB, Thomson AR, Zaccai NR, Brady RL, Verkade P, Woolfson DN (2012) Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design. Proc Natl Acad Sci U S A 109(33):13266–13271

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sinclair JC (2013) Constructing arrays of proteins. Curr Opin Chem Biol 17(6):946–951

    Article  CAS  PubMed  Google Scholar 

  • Sinclair JC, Davies KM, Venien-Bryan C, Noble MEM (2011) Generation of protein lattices by fusing proteins with matching rotational symmetry. Nat Nanotechnol 6(9):558–562

    Article  CAS  PubMed  Google Scholar 

  • Slope LN, Peacock AFA (2016) De novo design of xeno-metallo coiled coils. Chem Asian J 11(5):660–666

    Article  CAS  PubMed  Google Scholar 

  • Steinkruger JD, Bartlett GJ, Hadley EB, Fay L, Woolfson DN, Gellman SH (2012a) The d′-d-d′ vertical triad is less discriminating than the a′-a-a′ vertical triad in the antiparallel coiled-coil dimer motif. J Am Chem Soc 134(5):2626–2633

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steinkruger JD, Bartlett GJ, Woolfson DN, Gellman SH (2012b) Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils. J Am Chem Soc 134(38):15652–15655

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Strelkov SV, Burkhard P (2002) Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation. J Struct Biol 137(1-2):54–64

    Article  CAS  PubMed  Google Scholar 

  • Sun L, Young LN, Zhang XZ, Boudko SP, Fokine A, Zbornik E, Roznowski AP, Molineux IJ, Rossmann MG, Fane BA (2014) Icosahedral bacteriophage Phi X174 forms a tail for DNA transport during infection. Nature 505(7483):432–435

    Article  CAS  PubMed  Google Scholar 

  • Surkont J, Diekmann Y, Ryder PV, Pereira-Leal JB (2015) Coiled-coil length: size does matter. Proteins 83(12):2162–2169

    Article  CAS  PubMed  Google Scholar 

  • Tanaka Y, Sasaki T, Kumagai I, Yasutake Y, Yao M, Tanaka I, Tsumoto K (2007) Molecular properties of two proteins homologous to PduO-Type ATP: cob(I)alamin adenosyltransferase from Sulfolobus tokodaii. Proteins 68(2):446–457

    Article  CAS  PubMed  Google Scholar 

  • Taylor WR, Chelliah V, Hollup SM, MacDonald JT, Jonassen I (2009) Probing the “Dark Matter” of protein fold space. Structure 17(9):1244–1252

    Article  CAS  PubMed  Google Scholar 

  • Tebo AG, Pecoraro VL (2015) Artificial metalloenzymes derived from three-helix bundles. Curr Opin Chem Biol 25:65–70

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Testa OD, Moutevelis E, Woolfson DN (2009) CC plus: a relational database of coiled-coil structures. Nucleic Acids Res 37:D315-D322.

    Google Scholar 

  • Thomas F, Boyle AL, Burton AJ, Woolfson DN (2013) A set of de novo designed parallel heterodimeric coiled coils with quantified dissociation constants in the micromolar to sub-nanomolar regime. J Am Chem Soc 135(13):5161–5166

    Article  CAS  PubMed  Google Scholar 

  • Thomas F, Burgess NC, Thomson AR, Woolfson DN (2016) Controlling the assembly of coiled-coil peptide nanotubes. Angew Chem Int Ed 55(3):987–991

    Article  CAS  Google Scholar 

  • Thompson KE, Bashor CJ, Lim WA, Keating AE (2012) SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains. ACS Synth Biol 1(4):118–129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomson AR, Wood CW, Burton AJ, Bartlett GJ, Sessions RB, Brady RL, Woolfson DN (2014) Computational design of water-soluble alpha-helical barrels. Science 346(6208):485–488

    Article  CAS  PubMed  Google Scholar 

  • Trigg J, Gutwin K, Keating AE, Berger B (2011) Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone. PLoS One 6(8) e23519

    Google Scholar 

  • Versluis F, Dominguez J, Voskuhl J, Kros A (2013a) Coiled-coil driven membrane fusion: zipper-like vs. non-zipper-like peptide orientation. Faraday Discuss 166:349–359

    Article  CAS  PubMed  Google Scholar 

  • Versluis F, Voskuhl J, van Kolck B, Zope H, Bremmer M, Albregtse T, Kros A (2013b) In situ modification of plain liposomes with lipidated coiled coil forming peptides induces membrane fusion. J Am Chem Soc 135(21):8057–8062

    Article  CAS  PubMed  Google Scholar 

  • Vincent TL, Green PJ, Woolfson DN (2013) LOGICOIL-multi-state prediction of coiled-coil oligomeric state. Bioinformatics 29(1):69–76

    Article  CAS  PubMed  Google Scholar 

  • Vostrikov VV, Mote KR, Verardi R, Veglia G (2013) Structural dynamics and topology of phosphorylated phospholamban homopentamer reveal its role in the regulation of calcium transport. Structure 21(12):2119–2130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wagner N, Ashkenasy G (2009) Systems chemistry: logic gates, arithmetic units, and network motifs in small networks. Chem-Eur J 15(7):1765–1775

    Article  CAS  PubMed  Google Scholar 

  • Walshaw J, Woolfson DN (2001a) Open-and-shut cases in coiled-coil assembly: alpha-sheets and alpha-cylinders. Protein Sci 10(3):668–673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Walshaw J, Woolfson DN (2001b) SOCKET: a program for identifying and analysing coiled-coil motifs within protein structures. J Mol Biol 307(5):1427–1450

    Article  CAS  PubMed  Google Scholar 

  • Walshaw J, Woolfson DN (2003) Extended knobs-into-holes packing in classical and complex coiled-coil assemblies. J Struct Biol 144(3):349–361

    Article  CAS  PubMed  Google Scholar 

  • Walther D, Eisenhaber F, Argos P (1996) Principles of helix-helix packing in proteins: the helical lattice superposition model. J Mol Biol 255(3):536–553

    Article  CAS  PubMed  Google Scholar 

  • Wood CW, Bruning M, Ibarra AA, Bartlett GJ, Thomson AR, Sessions RB, Brady RL, Woolfson DN (2014) CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies. Bioinformatics 30(21):3029–3035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Woolfson DN (2005) The design of coiled-coil structures and assemblies. Adv Protein Chem 70:79–112

    Article  CAS  PubMed  Google Scholar 

  • Woolfson DN, Alber T (1995) Predicting oligomerization states of coiled coils. Protein Sci 4(8):1596–1607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Woolfson DN, Mahmoud ZN (2010) More than just bare scaffolds: towards multi-component and decorated fibrous biomaterials. Chem Soc Rev 39(9):3464–3479

    Article  CAS  PubMed  Google Scholar 

  • Woolfson DN, Bartlett GJ, Bruning M, Thomson AR (2012) New currency for old rope: from coiled-coil assemblies to alpha-helical barrels. Curr Opin Struct Biol 22(4):432–441

    Article  CAS  PubMed  Google Scholar 

  • Woolfson DN, Bartlett GJ, Burton AJ, Heal JW, Niitsu A, Thomson AR, Wood CW (2015) De novo protein design: how do we expand into the universe of possible protein structures? Curr Opin Struct Biol 33:16–26

    Article  CAS  PubMed  Google Scholar 

  • Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP (2013) Rational design of helical nanotubes from self-aof coiled-coil lock washers. J Am Chem Soc 135(41):15565–15578

    Article  CAS  PubMed  Google Scholar 

  • Yoshizumi A, Fletcher JM, Yu ZX, Persikov AV, Bartlett GJ, Boyle AL, Vincent TL, Woolfson DN, Brodsky B (2011) Designed coiled coils promote folding of a recombinant bacterial collagen. J Biol Chem 286(20):17512–17520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zaccai NR, Chi B, Thomson AR, Boyle AL, Bartlett GJ, Bruning M, Linden N, Sessions RB, Booth PJ, Brady RL, Woolfson DN (2011) A de novo peptide hexamer with a mutable channel. Nat Chem Biol 7(12):935–941

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng TT, Voskuhl J, Versluis F, Zope HR, Tomatsu I, Marsden HR, Kros A (2013) Controlling the rate of coiled coil driven membrane fusion. Chem Commun 49(35):3649–3651

    Article  CAS  Google Scholar 

  • Zheng TT, Bulacu M, Daudey G, Versluis F, Voskuhl J, Martelli G, Raap J, Sevink GJA, Kros A, Boyle AL (2016) A non-zipper-like tetrameric coiled coil promotes membrane fusion. RSC Adv 6(10):7990–7998

    Article  CAS  Google Scholar 

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Acknowledgements

I thank Gail Bartlett, James Ross and Drew Thomson for help with making some of the figures. I would like to thank current and past members of my research group who have added, both knowingly or unwittingly, to my understanding and knowledge of coiled-coil folding, assembly and design. I am grateful to the European Research Council (340764) for funding, and to the Royal Society and the Wolfson Foundation for the gift of a Royal Society Wolfson Research Merit Award.

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  1. School of Chemistry, University of Bristol, BS8 1TS, Bristol, UK

    Derek N. Woolfson

  2. School of Biochemistry, University of Bristol, BS8 1TD, Bristol, UK

    Derek N. Woolfson

  3. BrisSynBio, Life Sciences Building, University of Bristol, BS8 1TQ, Bristol, UK

    Derek N. Woolfson

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Correspondence to Derek N. Woolfson .

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  1. Institute of Fundamental Sciences and Riddet Institute, Massey University, Palmerston North, New Zealand

    David A.D. Parry

  2. Muscle Contraction Group, School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom

    John M. Squire

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Woolfson, D.N. (2017). Coiled-Coil Design: Updated and Upgraded. In: Parry, D., Squire, J. (eds) Fibrous Proteins: Structures and Mechanisms. Subcellular Biochemistry, vol 82. Springer, Cham. https://doi.org/10.1007/978-3-319-49674-0_2

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