Theory of site-specific DNA-protein interactions in the presence of conformational fluctuations of DNA binding domains.

Biophysical Journal
Rajamanickam Murugan

Abstract

We develop a theory that explains how the thermally driven conformational fluctuations in the DNA binding domains (DBDs) of the DNA binding proteins (DBPs) are effectively coupled to the one-dimensional searching dynamics of DBPs for their cognate sites on DNA. We show that the rate gammaopt, associated with the flipping of conformational states of DBDs beyond which the maximum search efficiency of DBPs is achieved, varies with the one-dimensional sliding length L as gammaopt proportional, L(-2) and with the number of roadblock protein molecules present on the same DNA m as gammaopt proportional, m2. The required free energy barrier ERTO associated with this flipping transition seems to be varying with L as ERTO proportional, variant ln L2. When the barrier height associated with the conformational flipping of DBDs is comparable with that of the thermal free energy, then the possible value of L under in vivo conditions seems to be L<or=70 bps.

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Citations

May 6, 2011·Proceedings of the National Academy of Sciences of the United States of America·Huan-Xiang Zhou
Jun 8, 2012·Proceedings of the National Academy of Sciences of the United States of America·Levani ZandarashviliJunji Iwahara
Nov 8, 2012·PLoS Computational Biology·Rajamanickam Murugan, Gabriel Kreiman
Dec 17, 2014·The Journal of Chemical Physics·Lin Liu, Kaifu Luo
Sep 2, 2015·Proceedings of the National Academy of Sciences of the United States of America·Levani ZandarashviliJunji Iwahara
Feb 3, 2012·Current Opinion in Structural Biology·Krystyna Zakrzewska, Richard Lavery
Feb 16, 2013·Transcription·Junji Iwahara, Yaakov Levy
Sep 29, 2011·Biophysical Journal·Rajamanickam Murugan, Gabriel Kreiman
Dec 20, 2014·The Journal of Physical Chemistry. B·Athi N NaganathanSwaathiratna Suresh
Jun 15, 2016·Nucleic Acids Research·Jiangguo LinHong Wang
Jul 8, 2011·Journal of the American Chemical Society·Athi N Naganathan, Modesto Orozco
Oct 17, 2013·The Journal of Physical Chemistry. B·Athi N Naganathan, Modesto Orozco
Apr 14, 2016·PloS One·Gnanapragasam Niranjani, Rajamanickam Murugan
Dec 8, 2017·Nucleic Acids Research·Massimo Cencini, Simone Pigolotti
May 24, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·R Murugan
Jul 23, 2015·Physical Biology·Jérôme Cartailler, Jürgen Reingruber
Mar 28, 2019·Molecular Biology Reports·Abbasali EmamjomehAmir Khodavirdipour
Mar 17, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Michael C DeSantisY M Wang

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