Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

Publication type:
Journal article
Metadata:
Autoren
  • Fabian Knoch
  • Ken Schaefer
  • Gregor Diezemann
  • Thomas Speck
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000424015400013&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1063/1.5010435
eISSN
1089-7690
Externe Identifier
  • Clarivate Analytics Document Solution ID: FU7ER
  • PubMed Identifier: 29390802
ISSN
0021-9606
Ausgabe der Veröffentlichung
4
Zeitschrift
JOURNAL OF CHEMICAL PHYSICS
Artikelnummer
ARTN 044109
Datum der Veröffentlichung
2018
Status
Published
Titel
Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
Sub types
  • Article
Ausgabe der Zeitschrift
148

Data source: Web of Science (Lite)

Other metadata sources:
Abstract
<jats:p>We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10−8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.</jats:p>
Autoren
  • Fabian Knoch
  • Ken Schäfer
  • Gregor Diezemann
  • Thomas Speck
DOI
10.1063/1.5010435
eISSN
1089-7690
ISSN
0021-9606
Ausgabe der Veröffentlichung
4
Zeitschrift
The Journal of Chemical Physics
Sprache
en
Online publication date
2018
Datum der Veröffentlichung
2018
Status
Published
Herausgeber
AIP Publishing
Herausgeber URL
http://dx.doi.org/10.1063/1.5010435
Datum der Datenerfassung
2023
Titel
Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
Ausgabe der Zeitschrift
148

Data source: Crossref

Abstract
We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10<sup>-8</sup>/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.
Addresses
  • Institut für Physik, Johannes Gutenberg Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany.
Autoren
  • Fabian Knoch
  • Ken Schäfer
  • Gregor Diezemann
  • Thomas Speck
DOI
10.1063/1.5010435
eISSN
1089-7690
Externe Identifier
  • PubMed Identifier: 29390802
Funding acknowledgements
  • Deutsche Forschungsgemeinschaft: TRR 146
  • Deutsche Forschungsgemeinschaft: DI693/3-1
Open access
false
ISSN
0021-9606
Ausgabe der Veröffentlichung
4
Zeitschrift
The Journal of chemical physics
Sprache
eng
Medium
Print
Paginierung
044109
Datum der Veröffentlichung
2018
Status
Published
Datum der Datenerfassung
2018
Titel
Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
148

Data source: Europe PubMed Central

Abstract
We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.
Autoren
  • Fabian Knoch
  • Ken Schäfer
  • Gregor Diezemann
  • Thomas Speck
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/29390802
DOI
10.1063/1.5010435
eISSN
1089-7690
Ausgabe der Veröffentlichung
4
Zeitschrift
J Chem Phys
Sprache
eng
Country
United States
Paginierung
044109
Datum der Veröffentlichung
2018
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2018
Titel
Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
148

Data source: PubMed

Abstract
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately $10^{-8}$/ns to $1$/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.
Autoren
  • Fabian Knoch
  • Ken Schäfer
  • Gregor Diezemann
  • Thomas Speck
Autoren-URL
http://arxiv.org/abs/1710.09699v1
Zeitschrift
J. Chem. Phys.
Schlüsselwörter
  • cond-mat.soft
  • cond-mat.soft
  • physics.bio-ph
  • q-bio.BM
Paginierung
044109
Datum der Veröffentlichung
2017
Herausgeber URL
http://dx.doi.org/10.1063/1.5010435
Datum der Datenerfassung
2017
Datum, an dem der Datensatz öffentlich gemacht wurde
2017
Titel
Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
Ausgabe der Zeitschrift
148

Files

1710.09699v1.pdf

Data source: arXiv

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