Aggregate geometry in amyloid fibril nucleation.
Irbäck, Anders LU
; Jonsson, Sigurdur
LU
; Linnemann, Niels
; Linse, Björn
and Wallin, Stefan
LU
(2013)
In Physical Review Letters
110(5).
- Abstract
- We present and study a minimal structure-based model for the self-assembly of peptides into ordered β-sheet-rich fibrils. The peptides are represented by unit-length sticks on a cubic lattice and interact by hydrogen bonding and hydrophobicity forces. Using Monte Carlo simulations with >10^{5} peptides, we show that fibril formation occurs with sigmoidal kinetics in the model. To determine the mechanism of fibril nucleation, we compute the joint distribution in length and width of the aggregates at equilibrium, using an efficient cluster move and flat-histogram techniques. This analysis, based on simulations with 256 peptides in which aggregates form and dissolve reversibly, shows that the main free-energy barriers that a nascent fibril... (More)
- We present and study a minimal structure-based model for the self-assembly of peptides into ordered β-sheet-rich fibrils. The peptides are represented by unit-length sticks on a cubic lattice and interact by hydrogen bonding and hydrophobicity forces. Using Monte Carlo simulations with >10^{5} peptides, we show that fibril formation occurs with sigmoidal kinetics in the model. To determine the mechanism of fibril nucleation, we compute the joint distribution in length and width of the aggregates at equilibrium, using an efficient cluster move and flat-histogram techniques. This analysis, based on simulations with 256 peptides in which aggregates form and dissolve reversibly, shows that the main free-energy barriers that a nascent fibril has to overcome are associated with changes in width. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/3559717
- author
- Irbäck, Anders
LU
; Jonsson, Sigurdur
LU
; Linnemann, Niels
; Linse, Björn
and Wallin, Stefan
LU
- organization
- publishing date
- 2013
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Physical Review Letters
- volume
- 110
- issue
- 5
- article number
- 058101
- publisher
- American Physical Society
- external identifiers
-
- wos:000314090300011
- pmid:23414048
- scopus:84873025905
- pmid:23414048
- ISSN
- 1079-7114
- DOI
- 10.1103/PhysRevLett.110.058101
- language
- English
- LU publication?
- yes
- id
- 84156d9e-1a4b-4763-a60a-cc458e54ba31 (old id 3559717)
- date added to LUP
- 2016-04-01 09:57:35
- date last changed
- 2023-01-01 23:53:06
@article{84156d9e-1a4b-4763-a60a-cc458e54ba31,
abstract = {{We present and study a minimal structure-based model for the self-assembly of peptides into ordered β-sheet-rich fibrils. The peptides are represented by unit-length sticks on a cubic lattice and interact by hydrogen bonding and hydrophobicity forces. Using Monte Carlo simulations with >10^{5} peptides, we show that fibril formation occurs with sigmoidal kinetics in the model. To determine the mechanism of fibril nucleation, we compute the joint distribution in length and width of the aggregates at equilibrium, using an efficient cluster move and flat-histogram techniques. This analysis, based on simulations with 256 peptides in which aggregates form and dissolve reversibly, shows that the main free-energy barriers that a nascent fibril has to overcome are associated with changes in width.}},
author = {{Irbäck, Anders and Jonsson, Sigurdur and Linnemann, Niels and Linse, Björn and Wallin, Stefan}},
issn = {{1079-7114}},
language = {{eng}},
number = {{5}},
publisher = {{American Physical Society}},
series = {{Physical Review Letters}},
title = {{Aggregate geometry in amyloid fibril nucleation.}},
url = {{https://lup.lub.lu.se/search/files/1425003/3562882.pdf}},
doi = {{10.1103/PhysRevLett.110.058101}},
volume = {{110}},
year = {{2013}},
}