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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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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
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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
Design of self-assembly dipeptide hydrogels and machine learning via their chemical features
Li, F., Han, J., Cao, T., Lam, W., Fan, B., Tang, W., Chen, S., Fok, K. L., & Li, L. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1903376116 · Cited by 198
Accelerating the prediction and discovery of peptide hydrogels with human-in-the-loop
Xu, T., Wang, J., Zhao, S., Chen, D., Zhang, H., Fang, Y., Kong, N., Zhou, Z., Li, W., & Wang, H. (2023) · Nature Communications · doi:10.1038/s41467-023-39648-2 · Cited by 132
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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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