ArticleProceedings of the National Academy of Sciences of the United States of America2006
Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- The Intrinsic UV-Visible Fluorescence of Peptides Widely Used for Studying Amyloid Aggregation Devoid of Aromatic Residues.International journal of molecular sciences · 2026Article
- Molecular dynamics study of the helix-to-disorder transition in short antimicrobial peptides from Urodacus yaschenkoi.European biophysics journal : EBJ · 2025Article
- An N-terminal acidic β-sheet domain is responsible for the metal-accumulation properties of amyloid-β protofibrils: a molecular dynamics study.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2024Article
- Lung endothelium, tau, and amyloids in health and disease.Physiological reviews · 2024Review
- Identification of a Steric Zipper Motif in the Amyloidogenic Core of Human Cystatin C and Its Use for the Design of Self-Assembling Peptides.International journal of molecular sciences · 2022Article
- A theoretical study of polymorphism in VQIVYK fibrils.Biophysical journal · 2021Article
- Energetics Underlying Twist Polymorphisms in Amyloid Fibrils.The journal of physical chemistry. B · 2018Article
- The centriolar protein CPAP G-box: an amyloid fibril in a single domain.Biochemical Society transactions · 2015Review
- The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Article
- Molecular modeling to investigate the binding of Congo red toward GNNQQNY protofibril and in silico virtual screening for the identification of new aggregation inhibitors.Journal of molecular modeling · 2013Article
- Conformational stability of fibrillar amyloid-beta oligomers via protofilament pair formation - a systematic computational study.PloS one · 2013Article
- Unique example of amyloid aggregates stabilized by main chain H-bond instead of the steric zipper: molecular dynamics study of the amyloidogenic segment of amylin wild-type and mutants.Journal of molecular modeling · 2012Article
- Insight into the stability of cross-β amyloid fibril from VEALYL short peptide with molecular dynamics simulation.PloS one · 2012Article
- Free cholesterol induces higher β-sheet content in Aβ peptide oligomers by aromatic interaction with Phe19.PloS one · 2012Article
- Spontaneous formation of twisted Aβ(16-22) fibrils in large-scale molecular-dynamics simulations.Biophysical journal · 2011Article
- Can molecular dynamics simulations assist in design of specific inhibitors and imaging agents of amyloid aggregation? Structure, stability and free energy predictions for amyloid oligomers of VQIVYK, MVGGVV and LYQLEN.Journal of molecular modeling · 2011Article
- Structural complexity of a composite amyloid fibril.Journal of the American Chemical Society · 2011Article
- Role of hydration force in the self-assembly of collagens and amyloid steric zipper filaments.Journal of the American Chemical Society · 2011Article
- A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35.PLoS computational biology · 2011Article
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3 authors.
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Abstract
The structural characterization of amyloid fibers is one of the most investigated areas in structural biology. The structural motif, denoted as steric zipper, recently discovered for the peptide GNNQQNY [Nelson, R., Sawaya, M. R., Balbirnie, M., Madsen, A. O., Riekel, C., Grothe, R. & Eisenberg, D. (2005) Nature 435, 773-778], is expected to exert strong influence in this field. To obtain further insights into the features of this unique structural motif, we report several molecular dynamics simulations of various GNNQQNY aggregates. Our analyses show that even pairs of beta-sheets composed of a limited number of beta-strands are stable in the 20-ns time interval considered, which suggests that steric zipper interactions at a beta-sheet-beta-sheet interface strongly contribute to the stability of these aggregates. Moreover, although the basic features of side chain-side chain interactions are preserved in the simulation, the backbone structure undergoes significant variations. Upon equilibration, a significant twist of the beta-strands that compose the beta-sheets is observed. These results demonstrate that the occurrence of steric zipper interactions is compatible with flat and twisted beta-sheets. Molecular dynamics simulations carried out on two pairs of beta-sheets, separated in the crystal state by a hydrated interface, lead to interesting results. The two pairs of sheets, while twisting, associate through stable peptide-peptide interactions. These findings provide insight into the mechanism that leads to the formation of higher aggregates. On these bases, it is possible to reconcile the crystallographic and the EM data on the size of the basic GNNQQNY fiber unit.
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