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Coarse-grained model of titrating peptides interacting with lipid bilayers

Tesei, Giulio LU ; Vazdar, Mario and Lund, Mikael LU orcid (2018) In The Journal of chemical physics 149(24).
Abstract

Molecular-level computer simulations of peptide aggregation, translocation, and protonation at and in biomembranes are impeded by the large time and length scales involved. We present a computationally efficient, coarse-grained, and solvent-free model for the interaction between lipid bilayers and peptides. The model combines an accurate description of mechanical membrane properties with a new granular representation of the dielectric mismatch between lipids and the aqueous phase. All-atom force fields can be easily mapped onto the coarse-grained model, and parameters for coarse-grained monopeptides accurately extrapolate to membrane permeation free energies for the corresponding dipeptides and tripeptides. Acid-base equilibria of... (More)

Molecular-level computer simulations of peptide aggregation, translocation, and protonation at and in biomembranes are impeded by the large time and length scales involved. We present a computationally efficient, coarse-grained, and solvent-free model for the interaction between lipid bilayers and peptides. The model combines an accurate description of mechanical membrane properties with a new granular representation of the dielectric mismatch between lipids and the aqueous phase. All-atom force fields can be easily mapped onto the coarse-grained model, and parameters for coarse-grained monopeptides accurately extrapolate to membrane permeation free energies for the corresponding dipeptides and tripeptides. Acid-base equilibria of titratable amino acid residues are further studied using a constant-pH ensemble, capturing protonation state changes upon membrane translocation. Important differences between histidine, lysine, and arginine are observed, which are in good agreement with experimental observations.

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author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
The Journal of chemical physics
volume
149
issue
24
article number
244108
publisher
American Institute of Physics (AIP)
external identifiers
  • scopus:85059426028
  • pmid:30599743
ISSN
0021-9606
DOI
10.1063/1.5058234
language
English
LU publication?
yes
id
3083ab2b-ed25-42f7-a2b3-4e7948ee3685
date added to LUP
2019-01-11 12:38:35
date last changed
2021-08-18 04:25:16
@article{3083ab2b-ed25-42f7-a2b3-4e7948ee3685,
  abstract     = {<p>Molecular-level computer simulations of peptide aggregation, translocation, and protonation at and in biomembranes are impeded by the large time and length scales involved. We present a computationally efficient, coarse-grained, and solvent-free model for the interaction between lipid bilayers and peptides. The model combines an accurate description of mechanical membrane properties with a new granular representation of the dielectric mismatch between lipids and the aqueous phase. All-atom force fields can be easily mapped onto the coarse-grained model, and parameters for coarse-grained monopeptides accurately extrapolate to membrane permeation free energies for the corresponding dipeptides and tripeptides. Acid-base equilibria of titratable amino acid residues are further studied using a constant-pH ensemble, capturing protonation state changes upon membrane translocation. Important differences between histidine, lysine, and arginine are observed, which are in good agreement with experimental observations.</p>},
  author       = {Tesei, Giulio and Vazdar, Mario and Lund, Mikael},
  issn         = {0021-9606},
  language     = {eng},
  number       = {24},
  publisher    = {American Institute of Physics (AIP)},
  series       = {The Journal of chemical physics},
  title        = {Coarse-grained model of titrating peptides interacting with lipid bilayers},
  url          = {http://dx.doi.org/10.1063/1.5058234},
  doi          = {10.1063/1.5058234},
  volume       = {149},
  year         = {2018},
}