Cryo-EM structure of a catalytic amyloid fibril

Heerde, Thomas; Bansal, Akanksha; Schmidt, Matthias; Fändrich, Marcus

doi:10.1038/s41598-023-30711-y

Cited by 11 publications

(6 citation statements)

References 39 publications

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“…Additionally, IIQ fibrils were observed to assemble into structures reaching lengths of ∼400 nm, widths of ∼50 nm, and thicknesses of ∼20 nm, a size much larger than the dimensions of the oligomers as shown by XRD, suggesting that the oligomers undergo further assembly into higher-ordered structures. Similar scenarios have also been observed in the literature. ,, …”

Section: Resultssupporting

confidence: 89%

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Computation-Driven Rational Design of Self-Assembled Short Peptides for Catalytic Hydrogen Production

Yang,

Wang,

et al. 2024

J. Am. Chem. Soc.

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Self-assembling peptides represent a captivating area of study in nanotechnology and biomaterials. This interest is largely driven by their unique properties and the vast application potential across various fields such as catalytic functions. However, design complexities, including high-dimensional sequence space and structural diversity, pose significant challenges in the study of such systems. In this work, we explored the possibility of self-assembled peptides to catalyze the hydrolysis of hydrosilane for hydrogen production using ab initio calculations and carried out wet-lab experiments to confirm the feasibility of these catalytic reactions under ambient conditions. Further, we delved into the nuanced interplay between sequence, structural conformation, and catalytic activity by combining modeling with experimental techniques such as transmission electron microscopy and nuclear magnetic resonance and proposed a dual mode of the microstructure of the catalytic center. Our results reveal that although research in this area is still at an early stage, the development of self-assembled peptide catalysts for hydrogen production has the potential to provide a more sustainable and efficient alternative to conventional hydrogen production methods. In addition, this work also demonstrates that a computation-driven rational design supplemented by experimental validation is an effective protocol for conducting research on functional self-assembled peptides.

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Section: Resultssupporting

confidence: 89%

“…Similar scenarios have also been observed in the literature. 49,52,53 Modes I and II Are Possible Catalytically Active Site Configurations. ssNMR was employed to characterize the histidine chemical shift and the possible protonation states.…”

Section: Ab Initio Calculations Reveal the Possibility Ofmentioning

confidence: 99%

Computation-Driven Rational Design of Self-Assembled Short Peptides for Catalytic Hydrogen Production

Yang,

Wang,

et al. 2024

J. Am. Chem. Soc.

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“…4a ). A increased tilt of the peptide molecules at outer radial positions was recently observed in a catalytically active peptide fibril 30 , suggesting that the altered tilt helps to compensate the higher torsional strain at outer radial positions.…”

Section: Discussionmentioning

confidence: 78%

Cryo-EM structure and polymorphic maturation of a viral transduction enhancing amyloid fibril

et al. 2023

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Amyloid fibrils have emerged as innovative tools to enhance the transduction efficiency of retroviral vectors in gene therapy strategies. In this study, we used cryo-electron microscopy to analyze the structure of a biotechnologically engineered peptide fibril that enhances retroviral infectivity. Our findings show that the peptide undergoes a time-dependent morphological maturation into polymorphic amyloid fibril structures. The fibrils consist of mated cross-β sheets that interact by the hydrophobic residues of the amphipathic fibril-forming peptide. The now available structural data help to explain the mechanism of retroviral infectivity enhancement, provide insights into the molecular plasticity of amyloid structures and illuminate the thermodynamic basis of their morphological maturation.

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“…A histidine triad in related enzymes such as CA coordinates Zn 2+ to which H 2 O and substrate are subsequently bound . High-resolution structures of catalytic amyloids with peptides sequences derived from IHIHIQI showed similar catalytic triads. , Furthermore, molecular modeling of IHIHIQI amyloids also exhibits this triad . However, a fourth histidine in CA acts as a proton shuttle that is essential for catalysis. , Interestingly, ab initio calculations with IHIHIQI amyloids showed a fourth histidine as a proton acceptor during catalysis similar to CA .…”

Section: Resultsmentioning

confidence: 95%

Metal Ions Can Modulate the Self-Assembly and Activity of Catalytic Peptide Amyloids

Duran-Meza,

Araya-Secchi,

Romero-Hasler

et al. 2024

Langmuir

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Rational design of peptides has become a powerful tool to produce self-assembled nanostructures with the ability to catalyze different chemical reactions, paving the way to develop minimalistic enzyme-like nanomaterials. Catalytic amyloid-like assemblies have emerged among the most versatile and active, but they often require additional factors for activity. Elucidating how these factors influence the structure and activity is key for the design. Here, we showed that biologically relevant metal ions can guide and modulate the self-assembly of a small peptide into diverse amyloid architectures. The morphology and catalytic activity of the resulting fibrils were tuned by the specific metal ion decorating the surface, whereas X-ray structural analysis of the amyloids showed ion-dependent shape sizes. Molecular dynamics simulations showed that the metals can strongly affect the local conformational space, which can trigger major rearrangements of the fibrils. Our results demonstrate that the conformational landscape of catalytic amyloids is broad and tunable by external factors, which can be critical for future design strategies.

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Cryo-EM structure of a catalytic amyloid fibril

Cited by 11 publications

References 39 publications

Computation-Driven Rational Design of Self-Assembled Short Peptides for Catalytic Hydrogen Production

Computation-Driven Rational Design of Self-Assembled Short Peptides for Catalytic Hydrogen Production

Cryo-EM structure and polymorphic maturation of a viral transduction enhancing amyloid fibril

Metal Ions Can Modulate the Self-Assembly and Activity of Catalytic Peptide Amyloids

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