Monte Carlo studies of protein aggregation
Jonsson, Sigurdur LU ; Staneva, Iskra LU ; Mohanty, Sandipan LU and Irbäck, Anders LU
(2012)
25th Workshop on Computer Simulation Studies in Condensed Matter Physics
34.
p.49-54
- Abstract
- The disease-linked amyloid beta (A beta) and alpha-synuclein (alpha S) proteins are both fibril-forming and natively unfolded in free monomeric form. Here, we discuss two recent studies, where we used extensive implicit solvent all-atom Monte Carlo (MC) simulations to elucidate the conformational ensembles sampled by these proteins. For alpha S, we somewhat unexpectedly observed two distinct phases, separated by a clear free-energy barrier. The presence of the barrier makes alpha S, with 140 residues, a challenge to simulate. By using a two-step simulation procedure based on flat-histogram techniques, it was possible to alleviate this problem. The barrier may in part explain why fibril formation is much slower for alpha S than it is for A... (More)
- The disease-linked amyloid beta (A beta) and alpha-synuclein (alpha S) proteins are both fibril-forming and natively unfolded in free monomeric form. Here, we discuss two recent studies, where we used extensive implicit solvent all-atom Monte Carlo (MC) simulations to elucidate the conformational ensembles sampled by these proteins. For alpha S, we somewhat unexpectedly observed two distinct phases, separated by a clear free-energy barrier. The presence of the barrier makes alpha S, with 140 residues, a challenge to simulate. By using a two-step simulation procedure based on flat-histogram techniques, it was possible to alleviate this problem. The barrier may in part explain why fibril formation is much slower for alpha S than it is for A beta. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/3577806
- author
- Jonsson, Sigurdur
LU
; Staneva, Iskra
LU
; Mohanty, Sandipan
LU
and Irbäck, Anders
LU
- organization
- publishing date
- 2012
- type
- Chapter in Book/Report/Conference proceeding
- publication status
- published
- subject
- keywords
- protein misfolding, protein aggregation, amyloid
- host publication
- Physics Procedia
- volume
- 34
- pages
- 49 - 54
- publisher
- Elsevier
- conference name
- 25th Workshop on Computer Simulation Studies in Condensed Matter Physics
- conference dates
- 2012-02-20 - 2012-02-24
- external identifiers
-
- wos:000314152800008
- scopus:85013130546
- ISSN
- 1875-3892
- DOI
- 10.1016/j.phpro.2012.05.008
- language
- English
- LU publication?
- yes
- id
- ef5cf631-98d0-423f-a82a-cf81fb3d43f9 (old id 3577806)
- date added to LUP
- 2016-04-01 12:55:12
- date last changed
- 2022-12-11 07:14:30
@inproceedings{ef5cf631-98d0-423f-a82a-cf81fb3d43f9,
abstract = {{The disease-linked amyloid beta (A beta) and alpha-synuclein (alpha S) proteins are both fibril-forming and natively unfolded in free monomeric form. Here, we discuss two recent studies, where we used extensive implicit solvent all-atom Monte Carlo (MC) simulations to elucidate the conformational ensembles sampled by these proteins. For alpha S, we somewhat unexpectedly observed two distinct phases, separated by a clear free-energy barrier. The presence of the barrier makes alpha S, with 140 residues, a challenge to simulate. By using a two-step simulation procedure based on flat-histogram techniques, it was possible to alleviate this problem. The barrier may in part explain why fibril formation is much slower for alpha S than it is for A beta.}},
author = {{Jonsson, Sigurdur and Staneva, Iskra and Mohanty, Sandipan and Irbäck, Anders}},
booktitle = {{Physics Procedia}},
issn = {{1875-3892}},
keywords = {{protein misfolding; protein aggregation; amyloid}},
language = {{eng}},
pages = {{49--54}},
publisher = {{Elsevier}},
title = {{Monte Carlo studies of protein aggregation}},
url = {{http://dx.doi.org/10.1016/j.phpro.2012.05.008}},
doi = {{10.1016/j.phpro.2012.05.008}},
volume = {{34}},
year = {{2012}},
}