CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

Wood, Christopher W.; Bruning, Marc; Ibarra, Amaurys Ávila; Bartlett, Gail J.; Thomson, Andrew; Sessions, Richard B.; Brady, R.L.; Woolfson, Derek N.

doi:10.1093/bioinformatics/btu502

Cited by 104 publications

(115 citation statements)

References 46 publications

(72 reference statements)

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“…Because of concerns over helix fraying, we discounted mutations near the termini and focused on those in the third heptad repeat. Using CCBuilder 38 and structural parameters from the crystal structures of a range of de novo coiled coils, 35,39 we generated in silico all-atom models for single, double and triple mutants as tetramers to heptamers (SI Table 1.1-1). Encouragingly, for 3 of the 5 sequences heptamer was predicted as the most-stable state.…”

Section: Rational Design Of Multiple Active Sitesmentioning

confidence: 99%

Installing hydrolytic activity into a completely de novo protein framework

et al. 2016

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Designing enzyme-like catalysts tests our understanding of sequence-tostructure/function relationships in proteins. Here, we install hydrolytic activity predictably into a completely de novo and thermo-stable -helical barrel, which comprises 7 helices arranged around an accessible channel. We show that the lumen of the barrel accepts 21 mutations to functional polar residues. The resulting variant, which has cysteine-histidine-glutamic acid triads on each helix, hydrolyses pnitrophenyl acetate with catalytic efficiencies matching the most-efficient redesigned hydrolases based on natural protein scaffolds. This is the first report of a functional catalytic triad engineered into a de novo protein framework. The flexibility of our system also allows the facile incorporation of unnatural side chains to improve activity and probe the catalytic mechanism. Such predictable and robust construction of truly de novo biocatalysts holds promise for applications in chemical and biochemical synthesis.(134 words)

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Section: Rational Design Of Multiple Active Sitesmentioning

confidence: 99%

Installing hydrolytic activity into a completely de novo protein framework

et al. 2016

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“…From the above dimensions and using the coiled-coil modeling program, CCBuilder 30 , we generated an in silico model of arrayed CC-Hex-T units. This model revealed spaces between the CC-Hex-T-based fibrils in the hydrated state.…”

Section: H-eiaqa Lkeiaka Lkeiawa Lkeiaqa Lk -Ohmentioning

confidence: 99%

Modular Design of Self-Assembling Peptide-Based Nanotubes

et al. 2015

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An ability to design peptide-based nanotubes (PNTs) rationally with defined and mutable internal channels would advance understanding of peptide self-assembly, and present new biomaterials for nanotechnology and medicine. PNTs have been made from Fmoc dipeptides, cyclic peptides, and lock-washer helical bundles. Here we show that blunt-ended α-helical barrelsi.e., pre-assembled bundles of α-helices with central channels-can be used as building blocks for PNTs. This approach is general and systematic, and uses a set of de novo helical bundles as standards. One of these bundles, a hexameric α-helical barrel, assembles into highly ordered PNTs, for which we have determined a structure by combining cryo-transmission electron microscopy, Xray fiber diffraction and model building. The structure reveals that the overall symmetry of the peptide module plays a critical role in ripening and ordering of the supramolecular assembly. PNTs based on pentameric, hexameric and heptameric α-helical barrels sequester hydrophobic dye within their lumens.

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“…A full model for human ezrin was initially generated by the I-TASSER server [44]. An ideal α-helical coiled-coil region was generated using the CCBuilder server [45]. These two models were used to supply the missing segments.…”

Section: Homology Modelingmentioning

confidence: 99%

Structural characterization suggests models for monomeric and dimeric forms of full-length ezrin

Phang

Harrop

Duff

et al. 2016

Biochemical Journal

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Ezrin is a member of the ERM (ezrin–radixin–moesin) family of proteins that have been conserved through metazoan evolution. These proteins have dormant and active forms, where the latter links the actin cytoskeleton to membranes. ERM proteins have three domains: an N-terminal FERM [band Four-point-one (4.1) ERM] domain comprising three subdomains (F1, F2, and F3); a helical domain; and a C-terminal actin-binding domain. In the dormant form, FERM and C-terminal domains form a stable complex. We have determined crystal structures of the active FERM domain and the dormant FERM:C-terminal domain complex of human ezrin. We observe a bistable array of phenylalanine residues in the core of subdomain F3 that is mobile in the active form and locked in the dormant form. As subdomain F3 is pivotal in binding membrane proteins and phospholipids, these transitions may facilitate activation and signaling. Full-length ezrin forms stable monomers and dimers. We used small-angle X-ray scattering to determine the solution structures of these species. As expected, the monomer shows a globular domain with a protruding helical coiled coil. The dimer shows an elongated dumbbell structure that is twice as long as the monomer. By aligning ERM sequences spanning metazoan evolution, we show that the central helical region is conserved, preserving the heptad repeat. Using this, we have built a dimer model where each monomer forms half of an elongated antiparallel coiled coil with domain-swapped FERM:C-terminal domain complexes at each end. The model suggests that ERM dimers may bind to actin in a parallel fashion.

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CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

Cited by 104 publications

References 46 publications

Installing hydrolytic activity into a completely de novo protein framework

Installing hydrolytic activity into a completely de novo protein framework

Modular Design of Self-Assembling Peptide-Based Nanotubes

Structural characterization suggests models for monomeric and dimeric forms of full-length ezrin

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