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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)



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)



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