Literature DB >> 26590523

Shapes of dominant transition paths from single-molecule force spectroscopy.

Dmitrii E Makarov1.   

Abstract

Recent single molecule measurements of biomolecular folding achieved the time resolution sufficient for observation of individual transition paths. This note discusses several ways in which transition path ensembles can be statistically analyzed to extract a single, "typical" transition path. Analytical approximations derived here for such a transition path further allow one to estimate dynamical parameters (such as the intramolecular diffusion coefficient) directly from the transition path shapes.

Year:  2015        PMID: 26590523     DOI: 10.1063/1.4935706

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  9 in total

1.  Measuring the average shape of transition paths during the folding of a single biological molecule.

Authors:  Noel Q Hoffer; Krishna Neupane; Andrew G T Pyo; Michael T Woodside
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-05       Impact factor: 11.205

2.  Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation.

Authors:  Krishna Neupane; Feng Wang; Michael T Woodside
Journal:  Proc Natl Acad Sci U S A       Date:  2017-01-23       Impact factor: 11.205

3.  Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics.

Authors:  Alexander M Berezhkovskii; Dmitrii E Makarov
Journal:  J Chem Phys       Date:  2018-05-28       Impact factor: 3.488

4.  Mean Direct-Transit and Looping Times as Functions of the Potential Shape.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Phys Chem B       Date:  2017-05-17       Impact factor: 2.991

5.  A new insight into diffusional escape from a biased cylindrical trap.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2017-09-14       Impact factor: 3.488

6.  First passage, looping, and direct transition in expanding and narrowing tubes: Effects of the entropy potential.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2017-10-07       Impact factor: 3.488

7.  Probing Position-Dependent Diffusion in Folding Reactions Using Single-Molecule Force Spectroscopy.

Authors:  Daniel A N Foster; Rafayel Petrosyan; Andrew G T Pyo; Armin Hoffmann; Feng Wang; Michael T Woodside
Journal:  Biophys J       Date:  2018-04-10       Impact factor: 4.033

8.  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

9.  Inferring potential landscapes from noisy trajectories of particles within an optical feedback trap.

Authors:  J Shepard Bryan; Prithviraj Basak; John Bechhoefer; Steve Pressé
Journal:  iScience       Date:  2022-07-19
  9 in total

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