Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Integrating All-Atom and Coarse-Grained Simulations - Toward Understanding of IDPs at Surfaces

Hyltegren, Kristin LU ; Polimeni, Marco LU ; Skepö, Marie LU and Lund, Mikael LU orcid (2020) In Journal of Chemical Theory and Computation 16(3). p.1843-1853
Abstract

We present a scheme for transferring conformational degrees of freedom from all-atom (AA) simulations of an intrinsically disordered protein (IDP) to coarse-grained (CG) Monte Carlo (MC) simulations using conformational swap moves. AA simulations of a single histatin 5 peptide in water were used to obtain a structural ensemble, which is reweighted in a CGMC simulation in the presence of a negatively charged surface. For efficient sampling, the AA trajectory was condensed using two approaches: RMSD clustering (based on the root-mean-square difference in atom positions) and a "nalve" truncation, where only every 100th frame of the trajectory was included in the library. The results show that even libraries with few structures well... (More)

We present a scheme for transferring conformational degrees of freedom from all-atom (AA) simulations of an intrinsically disordered protein (IDP) to coarse-grained (CG) Monte Carlo (MC) simulations using conformational swap moves. AA simulations of a single histatin 5 peptide in water were used to obtain a structural ensemble, which is reweighted in a CGMC simulation in the presence of a negatively charged surface. For efficient sampling, the AA trajectory was condensed using two approaches: RMSD clustering (based on the root-mean-square difference in atom positions) and a "nalve" truncation, where only every 100th frame of the trajectory was included in the library. The results show that even libraries with few structures well reproduce the radius of gyration and interaction free energy as functions of the distance from the surface. We further observe that the surface slightly promotes the secondary structure of histatin 5 and more so if using explicit surface charges rather than smeared charges.

(Less)
Please use this url to cite or link to this publication:
author
; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Theory and Computation
volume
16
issue
3
pages
11 pages
publisher
The American Chemical Society (ACS)
external identifiers
  • scopus:85080889499
  • pmid:32036660
ISSN
1549-9618
DOI
10.1021/acs.jctc.9b01041
language
English
LU publication?
yes
id
55c92c81-bd03-4cfd-854c-d9824f1f5ac0
date added to LUP
2020-03-20 14:48:18
date last changed
2024-06-12 11:30:05
@article{55c92c81-bd03-4cfd-854c-d9824f1f5ac0,
  abstract     = {{<p>We present a scheme for transferring conformational degrees of freedom from all-atom (AA) simulations of an intrinsically disordered protein (IDP) to coarse-grained (CG) Monte Carlo (MC) simulations using conformational swap moves. AA simulations of a single histatin 5 peptide in water were used to obtain a structural ensemble, which is reweighted in a CGMC simulation in the presence of a negatively charged surface. For efficient sampling, the AA trajectory was condensed using two approaches: RMSD clustering (based on the root-mean-square difference in atom positions) and a "nalve" truncation, where only every 100th frame of the trajectory was included in the library. The results show that even libraries with few structures well reproduce the radius of gyration and interaction free energy as functions of the distance from the surface. We further observe that the surface slightly promotes the secondary structure of histatin 5 and more so if using explicit surface charges rather than smeared charges.</p>}},
  author       = {{Hyltegren, Kristin and Polimeni, Marco and Skepö, Marie and Lund, Mikael}},
  issn         = {{1549-9618}},
  language     = {{eng}},
  month        = {{03}},
  number       = {{3}},
  pages        = {{1843--1853}},
  publisher    = {{The American Chemical Society (ACS)}},
  series       = {{Journal of Chemical Theory and Computation}},
  title        = {{Integrating All-Atom and Coarse-Grained Simulations - Toward Understanding of IDPs at Surfaces}},
  url          = {{http://dx.doi.org/10.1021/acs.jctc.9b01041}},
  doi          = {{10.1021/acs.jctc.9b01041}},
  volume       = {{16}},
  year         = {{2020}},
}