Structural analysis of the β‐sheet edge of peptide self‐assembly using a model protein
- 12 February 2021
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 89 (7), 845-852
- https://doi.org/10.1002/prot.26063
Abstract
Peptides and proteins self‐assemble into β‐sheet‐rich fibrils, amyloid, which extends its structure by incorporating peptide/protein molecules from solution. At the elongation edge, the peptide/protein molecule binds to the edge of the amyloid β‐sheet. Such processes are transient and elusive when observing molecular details by experimental methods. We used a model protein system, peptide self‐assembly mimic (PSAM), which mimics an amyloid‐like structure within a globular protein by capping both edges of single‐layer β sheet (SLB) with certain domains. We constructed a PSAM variant that lacks the capping domain on the C‐terminal side to observe the structure of the β‐sheet edge of the peptide self‐assembly. This variant, which we termed PSAM‐edge, proved to be soluble with a monomeric form. Urea‐induced unfolding experiments revealed that PSAM‐edge displayed two‐state cooperative unfolding, indicating the N‐terminal capping domain and extended SLB folded as one unit. The crystal structure showed that SLB was almost completely structured except for a few terminal residues. A molecular dynamics simulation results revealed that the SLB structure was retained while the C‐terminal four residues fluctuated, which was consistent with the crystal structure. Our findings indicate that SLB is stable even when one side of the β‐sheet edge is exposed to a solvent. This stability may prevent the dissociation of the attached peptide from the peptide self‐assembly. Because of the scarcity of SLB proteins with exposed β‐sheet edges in nature, successful construction of the PSAM‐edge expands our understanding of protein folding and design.Keywords
Funding Information
- Asahi Glass Foundation
- Kurita Water and Environment Foundation
- NOVARTIS Foundation (Japan) for the Promotion of Science
- Sumitomo Foundation (na)
This publication has 36 references indexed in Scilit:
- Structural Analysis of the G-Box Domain of the Microcephaly Protein CPAP Suggests a Role in Centriole ArchitectureStructure, 2013
- Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephalyeLife, 2013
- Minimalist design of water-soluble cross-β architectureProceedings of the National Academy of Sciences of the United States of America, 2010
- PHENIX: a comprehensive Python-based system for macromolecular structure solutionActa Crystallographica Section D-Biological Crystallography, 2010
- Aromatic Cross-Strand Ladders Control the Structure and Stability of β-Rich Peptide Self-Assembly MimicsJournal of Molecular Biology, 2008
- High-Resolution Structure of a Self-Assembly-Competent Form of a Hydrophobic Peptide Captured in a Soluble β-Sheet ScaffoldJournal of Molecular Biology, 2008
- β-Strand Flipping and Slipping Triggered by Turn Replacement Reveal the Opportunistic Nature of β-Strand PairingJournal of the American Chemical Society, 2007
- Atomic structures of peptide self-assembly mimicsProceedings of the National Academy of Sciences of the United States of America, 2006
- Coot: model-building tools for molecular graphicsActa Crystallographica Section D-Biological Crystallography, 2004
- [20] Processing of X-ray diffraction data collected in oscillation modeMethods in Enzymology, 1997