The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35
Open accessAbstract
Understanding the early steps of aggregation at atomic detail might be crucial for the rational design of therapeutics preventing diseases associated with amyloid deposits. In this paper, aggregation of the heptapeptide GNNQQNY, from the N-terminal prion-determining domain of the yeast protein Sup35, was studied by 20 molecular dynamics runs for a total simulation time of 20 μs. The simulations generate in-register parallel packing of GNNQQNY β-strands that is consistent with x-ray diffraction and Fourier transform infrared data. The statistically preferred aggregation pathway does not correspond to a purely downhill profile of the energy surface because of the presence of enthalpic barriers that originate from out-of-register interactions. The parallel β-sheet arrangement is favored over the antiparallel because of side-chain contacts; in particular, stacking interactions of the tyrosine rings and hydrogen bonds between amide groups. No ordered aggregation was found in control simulations with the mutant sequence SQNGNQQRG in accord with experimental data and the strong sequence dependence of aggregation.
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Molecular dynamics simulations and novel drug discovery
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Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock–lock mechanism
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Interpreting the Aggregation Kinetics of Amyloid Peptides
Pellarin, R., & Caflisch, A. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.05.033 · Cited by 254
Self-citationPrediction of aggregation prone regions of therapeutic proteins
Chennamsetty, N., Voynov, V., Kayser, V., Helk, B., & Trout, B. L. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp911706q · Cited by 200
Qiao, Q., Bowman, G. R., & Huang, X. (2013) · Journal of the American Chemical Society · doi:10.1021/ja403147m · Cited by 182
Metadata
- Authors
- Gsponer, J., Haberthür, U., & Caflisch, A.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2003-04-16
- Volume
- 100
- Issue
- 9
- Pages
- 5154-5159
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2143678630
- Cited by
- 264
- References
- 30
- FWCI
- 7.61
- Type
- journal article
- Language
- en
- Open access
- green
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- Gsponer, J., Haberthür, U., & Caflisch, A. (2003). The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0835307100
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