Literature DB >> 33087575

Broad distributions of transition-path times are fingerprints of multidimensionality of the underlying free energy landscapes.

Rohit Satija1, Alexander M Berezhkovskii2, Dmitrii E Makarov3,4.   

Abstract

Recent single-molecule experiments have observed transition paths, i.e., brief events where molecules (particularly biomolecules) are caught in the act of surmounting activation barriers. Such measurements offer unprecedented mechanistic insights into the dynamics of biomolecular folding and binding, molecular machines, and biological membrane channels. A key challenge to these studies is to infer the complex details of the multidimensional energy landscape traversed by the transition paths from inherently low-dimensional experimental signals. A common minimalist model attempting to do so is that of one-dimensional diffusion along a reaction coordinate, yet its validity has been called into question. Here, we show that the distribution of the transition path time, which is a common experimental observable, can be used to differentiate between the dynamics described by models of one-dimensional diffusion from the dynamics in which multidimensionality is essential. Specifically, we prove that the coefficient of variation obtained from this distribution cannot possibly exceed 1 for any one-dimensional diffusive model, no matter how rugged its underlying free energy landscape is: In other words, this distribution cannot be broader than the single-exponential one. Thus, a coefficient of variation exceeding 1 is a fingerprint of multidimensional dynamics. Analysis of transition paths in atomistic simulations of proteins shows that this coefficient often exceeds 1, signifying essential multidimensionality of those systems.

Keywords:  force spectroscopy; protein folding; single molecules; transition paths

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Year:  2020        PMID: 33087575      PMCID: PMC7959536          DOI: 10.1073/pnas.2008307117

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  46 in total

1.  From transition paths to transition states and rate coefficients.

Authors:  Gerhard Hummer
Journal:  J Chem Phys       Date:  2004-01-08       Impact factor: 3.488

Review 2.  Protein folding transition path times from single molecule FRET.

Authors:  Hoi Sung Chung; William A Eaton
Journal:  Curr Opin Struct Biol       Date:  2017-11-05       Impact factor: 6.809

3.  Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: a case study of polymer cyclization.

Authors:  Ryan R Cheng; Dmitrii E Makarov
Journal:  J Chem Phys       Date:  2011-02-28       Impact factor: 3.488

4.  Communication: Does force spectroscopy of biomolecules probe their intrinsic dynamic properties?

Authors:  Dmitrii E Makarov
Journal:  J Chem Phys       Date:  2014-12-28       Impact factor: 3.488

5.  Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity.

Authors:  Toshifumi Mori; Shinji Saito
Journal:  J Phys Chem B       Date:  2016-11-03       Impact factor: 2.991

6.  Dynamic distance disorder in proteins is caused by trapping.

Authors:  Guobin Luo; Ioan Andricioaei; X Sunney Xie; Martin Karplus
Journal:  J Phys Chem B       Date:  2006-05-18       Impact factor: 2.991

7.  Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.

Authors:  Ralf Metzler; Jae-Hyung Jeon; Andrey G Cherstvy; Eli Barkai
Journal:  Phys Chem Chem Phys       Date:  2014-11-28       Impact factor: 3.676

Review 8.  Reconstructing folding energy landscapes by single-molecule force spectroscopy.

Authors:  Michael T Woodside; Steven M Block
Journal:  Annu Rev Biophys       Date:  2014       Impact factor: 12.981

9.  Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape.

Authors:  William M Jacobs; Eugene I Shakhnovich
Journal:  J Phys Chem B       Date:  2018-08-22       Impact factor: 2.991

10.  Decoding the pattern of photon colors in single-molecule FRET.

Authors:  Irina V Gopich; Attila Szabo
Journal:  J Phys Chem B       Date:  2009-08-06       Impact factor: 2.991

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  3 in total

1.  Broad distributions of transition-path times are fingerprints of multidimensionality of the underlying free energy landscapes.

Authors:  Rohit Satija; Alexander M Berezhkovskii; Dmitrii E Makarov
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-21       Impact factor: 11.205

2.  Estimating transition path times and shapes from single-molecule photon trajectories: A simulation analysis.

Authors:  Grace H Taumoefolau; Robert B Best
Journal:  J Chem Phys       Date:  2021-03-21       Impact factor: 3.488

3.  The Effect of Time Resolution on Apparent Transition Path Times Observed in Single-Molecule Studies of Biomolecules.

Authors:  Dmitrii E Makarov; Alexander Berezhkovskii; Gilad Haran; Eli Pollak
Journal:  J Phys Chem B       Date:  2022-10-04       Impact factor: 3.466

  3 in total

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