Testing Kinetic Identities Involving Transition-Path Properties Using Single-Molecule Folding Trajectories

The Journal of Physical Chemistry. B
Krishna NeupaneMichael T Woodside

Abstract

Recent advances in single-molecule assays have allowed individual transition paths during the folding of single molecules to be observed directly. We used the transition paths of DNA hairpins having different sequences, measured with high-resolution optical tweezers, to test theoretical relations between the properties of the transition paths and the folding kinetics. We showed that folding and unfolding rates were related to the average transition-path times, as expected from theory, for all hairpins studied. We also found that the probability distribution of transition-path occupancies agreed with the profile of the average velocity along the transition paths for each of the hairpins, as expected theoretically. Finally, we used the latter result to show that the committor probability recovered from the velocity profile matches the committor measured empirically. These results validate the proposed kinetic identities.

References

Apr 25, 2002·Annual Review of Physical Chemistry·Peter G BolhuisPhillip L Geissler
Jul 23, 2004·The Journal of Chemical Physics·Gerhard Hummer
Apr 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Robert B Best, Gerhard Hummer
Dec 31, 2005·Physical Review Letters·William J GreenleafSteven M Block
Apr 12, 2006·Physical Review Letters·Olga K DudkoAttila Szabo
Apr 12, 2006·Proceedings of the National Academy of Sciences of the United States of America·Michael T WoodsideSteven M Block
Nov 13, 2008·Annual Review of Physical Chemistry·Weinan E, Eric Vanden-Eijnden
Jul 9, 2009·Proceedings of the National Academy of Sciences of the United States of America·Hoi Sung ChungWilliam A Eaton
Jul 24, 2010·The Journal of Chemical Physics·Srabanti Chaudhury, Dmitrii E Makarov
Jun 10, 2011·Nucleic Acids Research·Krishna NeupaneMichael T Woodside
Oct 25, 2013·Nature·Hoi Sung Chung, William A Eaton
Jun 5, 2014·Annual Review of Biophysics·Michael T Woodside, Steven M Block
Jun 4, 2015·Proceedings of the National Academy of Sciences of the United States of America·Ajay P ManuelMichael T Woodside
Jun 26, 2015·Proceedings of the National Academy of Sciences of the United States of America·Hao YuMichael T Woodside
Jul 17, 2015·Physical Review Letters·Katherine TruexWilliam A Eaton
Jul 21, 2015·Current Opinion in Structural Biology·Dustin B Ritchie, Michael T Woodside
Aug 12, 2015·The Journal of Physical Chemistry Letters·Krishna NeupaneMichael T Woodside
Sep 26, 2015·Science·Hoi Sung ChungWilliam A Eaton
Nov 23, 2015·The Journal of Chemical Physics·Dmitrii E Makarov
Jan 25, 2017·Proceedings of the National Academy of Sciences of the United States of America·Krishna NeupaneMichael T Woodside
Jun 6, 2018·The Journal of Chemical Physics·Alexander M Berezhkovskii, Dmitrii E Makarov

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Citations

Apr 7, 2019·Proceedings of the National Academy of Sciences of the United States of America·Noel Q HofferMichael T Woodside
Mar 24, 2021·The Journal of Chemical Physics·Grace H Taumoefolau, Robert B Best
Aug 22, 2018·The Journal of Physical Chemistry. B·David De SanchoVictor Muñoz
Aug 14, 2020·The Journal of Physical Chemistry Letters·David VoráčArtem Ryabov
Sep 5, 2018·The Journal of Physical Chemistry. B·Eduardo MedinaDmitrii E Makarov
Apr 10, 2019·The Journal of Physical Chemistry. B·Alexander M BerezhkovskiiSergey M Bezrukov
Jan 17, 2019·The Journal of Physical Chemistry. B·Rohit Satija, Dmitrii E Makarov

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