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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. 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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3. Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs

   https://doi.org/10.1073/pnas.1903910116  

   Hughes, Spencer A. ; Wang, Fengbin ; Wang, Shengyuan ; Kreutzberger, Mark A. ; Osinski, Tomasz ; Orlova, Albina ; Wall, Joseph S. ; Zuo, Xiaobing ; Egelman, Edward H. ; Conticello, Vincent P. ( July 2019 , Proceedings of the National Academy of Sciences)

   null (Ed.)

   Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release. 

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4. Building structured, functional materials inspired by nature: Using peptides, peptoids, and polymerizations

   https://doi.org/10.1002/pol.20230651  

   Montz, Brian J. ; Emrick, Todd ( December 2023 , Journal of Polymer Science)

   The assembly of peptide and peptide‐inspired building blocks into functional, well‐defined, multi‐length scale materials represents an exciting, rapidly expanding research field that bridges the principles of polymer science and engineering with a tremendous breadth of biomolecular interactions. The advantageous features of peptides, including their biocompatibility, functional diversity, and high purity, are complemented by the breadth of potential applications that may arise from their resultant structures and assemblies. Applications in biology (tissue scaffolding and drug conjugation), electronics (electron and/or ion‐conduction), and membranes (ion capture and ultrafiltration) represent a few of many examples where such biologically rich materials hold potential for enabling new routes to enhanced materials performance. Achieving successful solution and interfacial assembly techniques for peptides and other peptidomimetic materials requires obtaining a deep understanding of their design principles and limitations, as well as their amenability to structure formation when subjected to a variety of environmental conditions, such as pH, solvent, and temperature, to which such assembly methods may be exquisitely sensitive. This review especially focuses on mechanisms and the product of oligo‐ and polypeptide assembly, often resulting in the formation of extended, wire‐like structures obtained by solution methods, with inclusion of peptoid‐based structures and the complementary roles of polymerizations and step‐by‐step synthetic methods. Moreover, we describe relationships between naturally occurring peptide‐based structures, such asGeobacter pili, that in turn inspire self‐assembly of peptide‐based structures, composites with polymer materials, and assemblies therefrom.

    

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5. Structural basis of protein condensation on microtubules underlying branching microtubule nucleation

   https://doi.org/10.1038/s41467-023-39176-z  

   Guo, Changmiao ; Alfaro-Aco, Raymundo ; Zhang, Chunting ; Russell, Ryan W. ; Petry, Sabine ; Polenova, Tatyana ( June 2023 , Nature Communications)

   Targeting protein for Xklp2 (TPX2) is a key factor that stimulates branching microtubule nucleation during cell division. Upon binding to microtubules (MTs), TPX2 forms condensates via liquid-liquid phase separation, which facilitates recruitment of microtubule nucleation factors and tubulin. We report the structure of the TPX2 C-terminal minimal active domain (TPX2^α5-α7) on the microtubule lattice determined by magic-angle-spinning NMR. We demonstrate that TPX2^α5-α7forms a co-condensate with soluble tubulin on microtubules and binds to MTs between two adjacent protofilaments and at the intersection of four tubulin heterodimers. These interactions stabilize the microtubules and promote the recruitment of tubulin. Our results reveal that TPX2^α5-α7is disordered in solution and adopts a folded structure on MTs, indicating that TPX2^α5-α7undergoes structural changes from unfolded to folded states upon binding to microtubules. The aromatic residues form dense interactions in the core, which stabilize folding of TPX2^α5-α7on microtubules. This work informs on how the phase-separated TPX2^α5-α7behaves on microtubules and represents an atomic-level structural characterization of a protein that is involved in a condensate on cytoskeletal filaments.

    

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