The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly
Open accessAbstract
Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system.
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Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Coarse Grained Model for Semiquantitative Lipid Simulations
Marrink, S. J., de Vries, A. H., & Mark, A. E. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp036508g · Cited by 2,257
Cited by
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Tao, K., Levin, A., Adler-Abramovich, L., & Gazit, E. (2016) · Chemical Society Reviews · doi:10.1039/c5cs00889a · Cited by 482
Fan, Z., Sun, L., Huang, Y., Wang, Y., & Zhang, M. (2016) · Nature Nanotechnology · doi:10.1038/nnano.2015.312 · Cited by 369
Prebiotic Peptides: Molecular Hubs in the Origin of Life
Frenkel-Pinter, M., Samanta, M., Ashkenasy, G., & Leman, L. J. (2020) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00664 · Cited by 354
Two decades of Martini: Better beads, broader scope
Marrink, S. J., Monticelli, L., Melo, M. N., Alessandri, R., Tieleman, D. P., & Souza, P. C. T. (2023) · WIREs Computational Molecular Science · doi:10.1002/wcms.1620 · Cited by 255
Metadata
- Authors
- Frederix, P. W. J. M., Ulijn, R. V., Hunt, N. T., & Tuttle, T.
- Venue
- The Journal of Physical Chemistry Letters
- Publisher
- American Chemical Society (ACS)
- Published
- 2011-09-06
- Volume
- 2
- Issue
- 19
- Pages
- 2380-2384
- ISSN
- 1948-7185 (ISSN-L)
- OpenAlex
- W2067258309
- Cited by
- 256
- References
- 2
- FWCI
- 2.10
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Frederix, P. W. J. M., Ulijn, R. V., Hunt, N. T., & Tuttle, T. (2011). Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly. The Journal of Physical Chemistry Letters. https://doi.org/10.1021/jz2010573
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