Coarse-grained model of titrating peptides interacting with lipid bilayers
Tesei, Giulio LU ; Vazdar, Mario and Lund, Mikael LU
(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.
(Less)
- author
- Tesei, Giulio
LU
; Vazdar, Mario
and Lund, Mikael
LU
- organization
- publishing date
- 2018
- 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
-
- pmid:30599743
- scopus:85059426028
- 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
- 2025-04-04 15:08:36
@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}},
}