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1. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials

   https://doi.org/10.1038/s41467-020-20689-w.  

   Wang F, Gnewou O (January 2021, Nature communications)

   null (Ed.)

   The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili. 

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2. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials

   https://doi.org/10.1038/s41467-020-20689-w  

   Wang, Fengbin; Gnewou, Ordy; Modlin, Charles; Beltran, Leticia C.; Xu, Chunfu; Su, Zhangli; Juneja, Puneet; Grigoryan, Gevorg; Egelman, Edward H.; Conticello, Vincent P. (January 2021, Nature Communications)

   Abstract The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili. 

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3. Phenol-soluble modulins PSMα3 and PSMβ2 form nanotubes that are cross-α amyloids

   https://doi.org/10.1073/pnas.2121586119  

   Kreutzberger, Mark A.; Wang, Shengyuan; Beltran, Leticia C.; Tuachi, Abraham; Zuo, Xiaobing; Egelman, Edward H.; Conticello, Vincent P. (May 2022, Proceedings of the National Academy of Sciences)

   Phenol-soluble modulins (PSMs) are peptide-based virulence factors that play significant roles in the pathogenesis of staphylococcal strains in community-associated and hospital-associated infections. In addition to cytotoxicity, PSMs display the propensity to self-assemble into fibrillar species, which may be mediated through the formation of amphipathic conformations. Here, we analyze the self-assembly behavior of two PSMs, PSMα3 and PSMβ2, which are derived from peptides expressed by methicillin-resistant Staphylococcus aureus (MRSA), a significant human pathogen. In both cases, we observed the formation of a mixture of self-assembled species including twisted filaments, helical ribbons, and nanotubes, which can reversibly interconvert in vitro. Cryo–electron microscopy structural analysis of three PSM nanotubes, two derived from PSMα3 and one from PSMβ2, revealed that the assemblies displayed remarkably similar structures based on lateral association of cross-α amyloid protofilaments. The amphipathic helical conformations of PSMα3 and PSMβ2 enforced a bilayer arrangement within the protofilaments that defined the structures of the respective PSMα3 and PSMβ2 nanotubes. We demonstrate that, similar to amyloids based on cross-β protofilaments, cross-α amyloids derived from these PSMs display polymorphism, not only in terms of the global morphology (e.g., twisted filament, helical ribbon, and nanotube) but also with respect to the number of protofilaments within a given peptide assembly. These results suggest that the folding landscape of PSM derivatives may be more complex than originally anticipated and that the assemblies are able to sample a wide range of supramolecular structural space. 

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4. Near-atomic-resolution structure of J-aggregated helical light-harvesting nanotubes

   https://doi.org/10.1038/s41557-023-01432-6  

   Deshmukh, Arundhati P.; Zheng, Weili; Chuang, Chern; Bailey, Austin D.; Williams, Jillian A.; Sletten, Ellen M.; Egelman, Edward H.; Caram, Justin R. (February 2024, Nature Chemistry)

   Cryo-electron microscopy has delivered a resolution revolution for biological self-assemblies, yet only a handful of structures have been solved for synthetic supramolecular materials. Particularly for chromophore supramolecular aggregates, high-resolution structures are necessary for understanding and modulating the long-range excitonic coupling. Here, we present a 3.3 Å structure of prototypical biomimetic light-harvesting nanotubes derived from an amphiphilic cyanine dye (C8S3-Cl). Helical 3D reconstruction directly visualizes the chromophore packing that controls the excitonic properties. Our structure clearly shows a brick layer arrangement, revising the previously hypothesized herringbone arrangement. Furthermore, we identify a new non-biological supramolecular motif—interlocking sulfonates—that may be responsible for the slip-stacked packing and J-aggregate nature of the light-harvesting nanotubes. This work shows how independently obtained native-state structures complement photophysical measurements and will enable accurate understanding of (excitonic) structure–function properties, informing materials design for light-harvesting chromophore aggregates. 

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5. Rationally seeded computational protein design of ɑ-helical barrels

   https://doi.org/10.1038/s41589-024-01642-0  

   Albanese, Katherine I; Petrenas, Rokas; Pirro, Fabio; Naudin, Elise A; Borucu, Ufuk; Dawson, William M; Scott, D Arne; Leggett, Graham J; Weiner, Orion D; Oliver, Thomas_A A; et al (August 2024, Nature Chemical Biology)

   Abstract Computational protein design is advancing rapidly. Here we describe efficient routes starting from validated parallel and antiparallel peptide assemblies to design two families of α-helical barrel proteins with central channels that bind small molecules. Computational designs are seeded by the sequences and structures of defined de novo oligomeric barrel-forming peptides, and adjacent helices are connected by loop building. For targets with antiparallel helices, short loops are sufficient. However, targets with parallel helices require longer connectors; namely, an outer layer of helix–turn–helix–turn–helix motifs that are packed onto the barrels. Throughout these computational pipelines, residues that define open states of the barrels are maintained. This minimizes sequence sampling, accelerating the design process. For each of six targets, just two to six synthetic genes are made for expression inEscherichia coli. On average, 70% of these genes express to give soluble monomeric proteins that are fully characterized, including high-resolution structures for most targets that match the design models with high accuracy. 

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