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α/β coiled coils.

<div class='caption-title'>The green area marks the estimated boundaries of periodicities accessible to α-helical coiled coils. It is centered around the periodicity of unperturbed α-helices, about 3.63 residues per turn. Higher values than 3.63 lead to right-handed and lower values to left-handed supercoiling. The effects of consecutive insertions of stammers (3 residues) or stutters (4 residues) into a heptad pattern are shown by blue and green lines, respectively. The red lines correspond to the insertion of 1 to 6 residues into the heptad periodicity and their progressive delocalization over neighboring heptads. For example, an insertion of 4 residues is accommodated as 11 residues over 3 turns (11/3), when delocalized over one heptad, or as 18/5, when delocalized over two. Insertions of 1 or 5 residues have to be delocalized over two heptads, resulting in periodicities of 15/4 or 19/5 (which could also be brought about by consecutive stutters – following the green line from 7/2 over 11/3 over 15/4 to 19/5). Insertions of 3 can be accommodated as 10/3, at the very edge of the green area, although in the known examples the α-helices are distorted due to the strong left-handed supercoiling which could be avoided by further delocalization. For insertions of 2 or 6 residues (dashed lines) a strong delocalization would be required to reach the green lawn of accessible periodicities. However, for all constructs in this paper, this is not observed. Via the formation of β-layers these insertions sustain the heptad periodicity as unperturbed as possible.</div>
<div class='caption-title'>(A) The structure of the Actinobacillus OMP100 stalk construct is aligned with (B) its sequence and a periodicity plot. The area of the stammer is highlighted in pink, the three residues of the β-layer by a grey bar. This bar points to the β region of the Ramachandran plot (D), where all nine β-layer residues of the trimer are found. The close-ups show the (C) side and (E) top view in stereo, highlighting the β-layer interactions. The trimer is colored by chain, GCN4 adaptors in grey. The plot is smoothed over a window of three residues to mask local fluctuations. Empty regions of the Ramachandran plot are cropped.</div>
<div class='caption-title'>(A) The sequences and structures of the GCN4-fusion constructs are shown together with (B) a Ramachandran plot of their backbone torsion angles and (C, D) their periodicities. In the structures, the inserts between the GCN4 adaptors are drawn with thick lines. Disturbances in the α-helical segments are highlighted in pink; the stutter in the A6 structure and the stammer in the T96 structure are also highlighted in pink in panels C and D. In the periodicity plots, all proteins are aligned on the β-layer and their coiled-coil registers are indicated. The plots are shown separately for β-layers forming nonads (C) and hexads (D). A glitch in the periodicity caused by the g/c position preceding β-layers in hexads is highlighted in pink in panel D. As in the previous figure, the periodicity plots are smoothed over a three-residue sliding window. The Ramachandran plot in panel B includes all structures except the kinked grey A9b structure; all residues of the β-layers are shown as red dots and all other residues as black dots. Again, empty regions of the Ramachandran plot are cropped.</div>
Hartmann MD, Mendler CT, Bassler J, Karamichali I, Ridderbusch O, Lupas AN, Hernandez Alvarez B
OpenAccess logo Elife 5 (2016)
Related entries: 5app, 5apq, 5aps, 5apt, 5apu, 5apv, 5apw, 5apx, 5apy

Cited: 16 times
EuropePMC logo PMID: 26771248

Abstract

Coiled coils are the best-understood protein fold, as their backbone structure can uniquely be described by parametric equations. This level of understanding has allowed their manipulation in unprecedented detail. They do not seem a likely source of surprises, yet we describe here the unexpected formation of a new type of fiber by the simple insertion of two or six residues into the underlying heptad repeat of a parallel, trimeric coiled coil. These insertions strain the supercoil to the breaking point, causing the local formation of short β-strands, which move the path of the chain by 120° around the trimer axis. The result is an α/β coiled coil, which retains only one backbone hydrogen bond per repeat unit from the parent coiled coil. Our results show that a substantially novel backbone structure is possible within the allowed regions of the Ramachandran space with only minor mutations to a known fold.

Reviews - 5apz mentioned but not cited (1)

  1. The Structure and Topology of α-Helical Coiled Coils. Lupas AN, Bassler J, Dunin-Horkawicz S. Subcell Biochem 82 95-129 (2017)

Articles - 5apz mentioned but not cited (1)

  1. α/β coiled coils. Hartmann MD, Mendler CT, Bassler J, Karamichali I, Ridderbusch O, Lupas AN, Hernandez Alvarez B. Elife 5 e11861 (2016)


Reviews citing this publication (2)

  1. The accommodation index measures the perturbation associated with insertions and deletions in coiled-coils: Application to understand signaling in histidine kinases. Schmidt NW, Grigoryan G, DeGrado WF. Protein Sci 26 414-435 (2017)
  2. Decoding the role of coiled-coil motifs in human prion-like proteins. Behbahanipour M, García-Pardo J, Ventura S. Prion 15 143-154 (2021)

Articles citing this publication (12)

  1. Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p. Khazina E, Weichenrieder O. Elife 7 e34960 (2018)
  2. A library of coiled-coil domains: from regular bundles to peculiar twists. Szczepaniak K, Bukala A, da Silva Neto AM, Ludwiczak J, Dunin-Horkawicz S. Bioinformatics 36 5368-5376 (2021)
  3. A multidomain connector links the outer membrane and cell wall in phylogenetically deep-branching bacteria. von Kügelgen A, van Dorst S, Alva V, Bharat TAM. Proc Natl Acad Sci U S A 119 e2203156119 (2022)
  4. Chirality transmission in macromolecular domains. Pandey S, Mandal S, Danielsen MB, Brown A, Hu C, Christensen NJ, Kulakova AV, Song S, Brown T, Jensen KJ, Wengel J, Lou C, Mao H. Nat Commun 13 76 (2022)
  5. Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p. Furano AV, Jones CE, Periwal V, Callahan KE, Walser JC, Cook PR. PLoS Genet 16 e1008991 (2020)
  6. Functions of Gle1 are governed by two distinct modes of self-association. Mason AC, Wente SR. J Biol Chem 295 16813-16825 (2020)
  7. Insights into the molecular diversity of Plasmodium vivax merozoite surface protein-3γ (pvmsp3γ), a polymorphic member in the msp3 multi-gene family. Kuamsab N, Putaporntip C, Pattanawong U, Jongwutiwes S. Sci Rep 10 10977 (2020)
  8. Borna Disease Virus 1 Phosphoprotein Forms a Tetramer and Interacts with Host Factors Involved in DNA Double-Strand Break Repair and mRNA Processing. Tarbouriech N, Chenavier F, Kawasaki J, Bachiri K, Bourhis JM, Legrand P, Freslon LL, Laurent EMN, Suberbielle E, Ruigrok RWH, Tomonaga K, Gonzalez-Dunia D, Horie M, Coyaud E, Crépin T. Viruses 14 2358 (2022)
  9. Characterisation of sequence-structure-function space in sensor-effector integrators of phytochrome-regulated diguanylate cyclases. Böhm C, Gourinchas G, Zweytick S, Hujdur E, Reiter M, Trstenjak S, Sensen CW, Winkler A. Photochem Photobiol Sci 21 1761-1779 (2022)
  10. The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans. Farci D, Graça AT, Iesu L, de Sanctis D, Piano D. J Biol Chem 299 102784 (2023)
  11. research-article Preface. Pecoraro VL. Methods Enzymol 580 xvii-xxii (2016)
  12. Single-molecule experiments reveal the elbow as an essential folding guide in SMC coiled-coil arms. Freitag M, Jaklin S, Padovani F, Radzichevici E, Zernia S, Schmoller KM, Stigler J. Biophys J 121 4702-4713 (2022)


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