Coiled coils 9-to-5: rational de novo design of α-helical barrels with tunable oligomeric states

The rational design of linear peptides that assemble controllably and predictably in water is challenging. Short sequences must encode unique target structures and avoid alternative states. However, the non-covalent forces that stabilize and discriminate between states are weak. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentameric to nonameric barrels are accessed by varying the residue at one of the h sites. In peptides with four L/I–K–E–I–A–x–Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.

The table below summarises the geometric issues observed across the polymeric chains and their t to the electron density. The red, orange, yellow and green segments of the lower bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction is indicated below the corresponding segment, with a dot representing fractions <=5% The upper red bar (where present) indicates the fraction of residues that have poor t to the electron density. The numeric value is given above the bar.

Mol Chain Length
Quality of chain

O
There are 2 unique types of molecules in this entry. The entry contains 2460 atoms, of which 0 are hydrogens and 0 are deuteriums.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms.
Molecule 1 is a protein called CC-Type2-(TgLaId)4-W19BrPhe.. 3 Residue-property plots i O These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The rst graphic for a chain summarises the proportions of the various outlier classes displayed in the second graphic. The second graphic shows the sequence view annotated by issues in geometry and electron density. Residues are color-coded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dot above a residue indicates a poor t to the electron density (RSRZ > 2). Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present in the sample, but not in the model, are shown in grey.
Chain E: ACE0 Y19 NH231 • Molecule 1: CC-Type2-(TgLaId)4-W19BrPhe. Xtriage's analysis on translational NCS is as follows: The analyses of the Patterson function reveals a signicant o-origin peak that is 25.60 % of the origin peak, indicating pseudo-translational symmetry. The chance of nding a peak of this or larger height randomly in a structure without pseudo-translational symmetry is equal to 3.0745e-03. The detected translational NCS is most likely also responsible for the elevated intensity ratio. There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers. Continued on next page...

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes
All (10) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude.
Atom-1 Atom-2 Interatomic distance (Å) Clash overlap (Å) In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain as a percentile score with respect to all X-ray entries followed by that with respect to entries of similar resolution.
The Analysed column shows the number of residues for which the backbone conformation was analysed, and the total number of residues.
Mol Chain Analysed Favoured Allowed Outliers Percentiles There are no Ramachandran outliers to report.

Protein sidechains i O
In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all X-ray entries followed by that with respect to entries of similar resolution.
The Analysed column shows the number of residues for which the sidechain conformation was analysed, and the total number of residues. There are no protein residues with a non-rotameric sidechain to report.

Mol Chain Analysed Rotameric Outliers Percentiles
Sometimes sidechains can be ipped to improve hydrogen bonding and reduce clashes. There are no such sidechains identied.

RNA i O
There are no RNA molecules in this entry.

5.4
Non-standard residues in protein, DNA, RNA chains i O 10 non-standard protein/DNA/RNA residues are modelled in this entry.
In the following table, the Counts columns list the number of bonds (or angles) for which Mogul statistics could be retrieved, the number of bonds (or angles) that are observed in the model and the number of bonds (or angles) that are dened in the Chemical Component Dictionary. The Link column lists molecule types, if any, to which the group is linked. The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles). There are no chirality outliers.

Mol Type Chain Res Link
There are no torsion outliers.
There are no ring outliers.
No monomer is involved in short contacts.