In Silico Approaches to Design and Characterize Peptide-based Nanostructures

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KUMAR, Ashutosh, ed., Alok DHAWAN, ed.. Nanoparticle–Protein Corona : Biophysics to Biology. Cambridge: Royal Society of Chemistry, 2019, pp. 204-226. ISBN 978-1-78801-391-8. Available under: doi: 10.1039/9781788016308-00204
Zusammenfassung

Molecular dynamics (MD) simulations can show structural and dynamic details on an atomistic level in a native-like environment. Conventional atomistic MD simulations have been successfully applied to many problems, however, they often do not cover the necessary timescales to sufficiently explore conformational phase and reach convergence. In this study, we discuss two examples where we have employed atomistic simulations followed by either Hamiltonian replica exchange molecular dynamics (H-REMD) or coarse-grained (CG) simulations to identify the intrinsic details of nanostructure formation processes and the influence of various factors on them. We demonstrate that combining computational approaches or resolution levels is very useful to overcome the limitations of a single method, like pure atomistic simulations, while still keeping its advantages. However, it is very important to carefully select suitable methods, parameters and approaches to get meaningful results with sufficient accuracy.

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ISO 690GLOBISCH, Christoph, Marc ISELE, Christine PETER, Alok JAIN, 2019. In Silico Approaches to Design and Characterize Peptide-based Nanostructures. In: KUMAR, Ashutosh, ed., Alok DHAWAN, ed.. Nanoparticle–Protein Corona : Biophysics to Biology. Cambridge: Royal Society of Chemistry, 2019, pp. 204-226. ISBN 978-1-78801-391-8. Available under: doi: 10.1039/9781788016308-00204
BibTex
@incollection{Globisch2019Silic-46716,
  year={2019},
  doi={10.1039/9781788016308-00204},
  title={In Silico Approaches to Design and Characterize Peptide-based Nanostructures},
  isbn={978-1-78801-391-8},
  publisher={Royal Society of Chemistry},
  address={Cambridge},
  booktitle={Nanoparticle–Protein Corona : Biophysics to Biology},
  pages={204--226},
  editor={Kumar, Ashutosh and Dhawan, Alok},
  author={Globisch, Christoph and Isele, Marc and Peter, Christine and Jain, Alok}
}
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