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  Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors

Covino, R., Woodside, M. T., Hummer, G., Szabo, A., & Cossio, P. (2019). Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. The Journal of Chemical Physics, 151(15): 154115. doi:10.1063/1.5118362.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0004-F56F-C Version Permalink: http://hdl.handle.net/21.11116/0000-0004-F570-9
Genre: Journal Article

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 Creators:
Covino, Roberto1, Author              
Woodside, Michael T.2, Author
Hummer, Gerhard1, 3, Author              
Szabo, Attila4, Author
Cossio, Pilar1, 5, Author              
Affiliations:
1Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068292              
2Department of Physics, University of Alberta, Edmonton, Alberta, Canada, ou_persistent22              
3Insitute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany, ou_persistent22              
4Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Deseases, National Institute of Health, Bethesda, Maryland, USA, ou_persistent22              
5Biophysics of Tropical Deseases, Max Planck Tandem Group, University of Antioquia, Medellin, Colombia, ou_persistent22              

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 Abstract: In single-molecule force spectroscopy experiments, a biomolecule is attached to a force probe via polymer linkers and the total extension of the molecule plus apparatus is monitored as a function of time. In a typical unfolding experiment at constant force, the total extension jumps between two values that correspond to the folded and unfolded states of the molecule. For several biomolecular systems, the committor, which is the probability to fold starting from a given extension, has been used to extract the molecular activation barrier (a technique known as "committor inversion"). In this work, we study the influence of the force probe, which is much larger than the molecule being measured, on the activation barrier obtained by committor inversion. We use a two-dimensional framework in which the diffusion coefficient of the molecule and of the pulling device can differ. We systematically study the free energy profile along the total extension obtained from the committor by numerically solving the Onsager equation and using Brownian dynamics simulations. We analyze the dependence of the extracted barrier on the linker stiffness, molecular barrier height, and diffusion anisotropy and, thus, establish the range of validity of committor inversion. Along the way, we showcase the committor of 2-dimensional diffusive models and illustrate how it is affected by barrier asymmetry and diffusion anisotropy.

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Language(s): eng - English
 Dates: 2019-07-032019-09-292019-10-212019-10
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1063/1.5118362
BibTex Citekey: covino_molecular_2019
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Title: The Journal of Chemical Physics
  Other : J. Chem. Phys.
Source Genre: Journal
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Publ. Info: Woodbury, N.Y. : American Institute of Physics
Pages: - Volume / Issue: 151 (15) Sequence Number: 154115 Start / End Page: - Identifier: ISSN: 0021-9606
CoNE: https://pure.mpg.de/cone/journals/resource/954922836226