Self-assembling dipeptides : including solvent degrees of freedom in a coarse-grained model

Villa, Alessandra; van der Vegt, Nico F. A.; Peter, Christine

Self-assembling dipeptides : including solvent degrees of freedom in a coarse-grained model

Dateien

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Datum

2009

Autor:innen

Villa, Alessandra

van der Vegt, Nico F. A.

Peter, Christine

DOI (zitierfähiger Link)

https://doi.org/10.1039/b818146m

Sammlungen

Chemie

Publikationstyp

Zeitschriftenartikel

Publikationsstatus

Published

Erschienen in

Physical chemistry chemical physics : PCCP. 2009, 11(12), pp. 2068-2076. ISSN 1463-9076. eISSN 1463-9084. Available under: doi: 10.1039/b818146m

Zusammenfassung

In the previous paper [A. Villa, C. Peter, N. F. A. van der Vegt, Phys. Chem. Chem. Phys., 2009, DOI: ], a strategy to develop a solvent-free coarse-grained model for peptides is outlined which is based on an atomistic (force field) description. The coarse-grained model is designed such that it correctly captures the conformational flexibility of the molecules and reproduces the interaction between peptides in aqueous solution. In the present paper, we revisit this model and present a method to devise nonbonded interactions such that also the coarse-grained level maintains explicit solvent degrees of freedom. In this new approach we rely on a structure-based coarse graining methodology which preserves the solvation structure around the peptides in combination with a method to devise nonbonded potentials between peptide beads in a way that the peptide-peptide interaction in water is represented correctly and that results in the correct thermodynamic association behavior. The outlined coarse graining strategy provides us with two (one implicit- and one explicit-solvent) models that are well suited for multiscale-simulation and scale-bridging purposes. We show that this is a powerful tool to efficiently simulate long time-scale and large length-scale biomolecular processes such as peptide self-assembly. In combination with an efficient backmapping methodology we can obtain well-equilibrated atomistic structures of the resulting aggregates.

Fachgebiet (DDC)

540 Chemie

Zitieren

ISO 690

VILLA, Alessandra, Nico F. A. VAN DER VEGT, Christine PETER, 2009. Self-assembling dipeptides : including solvent degrees of freedom in a coarse-grained model. In: Physical chemistry chemical physics : PCCP. 2009, 11(12), pp. 2068-2076. ISSN 1463-9076. eISSN 1463-9084. Available under: doi: 10.1039/b818146m

BibTex

@article{Villa2009Selfa-40232,
  year={2009},
  doi={10.1039/b818146m},
  title={Self-assembling dipeptides : including solvent degrees of freedom in a coarse-grained model},
  number={12},
  volume={11},
  issn={1463-9076},
  journal={Physical chemistry chemical physics : PCCP},
  pages={2068--2076},
  author={Villa, Alessandra and van der Vegt, Nico F. A. and Peter, Christine}
}

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