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Direct observation of external force mediated conformational dynamics of IHF bound Holliday junction

Abstract

We have investigated isomerization dynamics and plausible energy landscape of 4-way Holliday junctions (4WHJs) bound to integration host factor (IHF, a DNA binding protein) considering the effect of applied external force, by single-molecule FRET methods. Slowing down of the forward as well as the backward rates of isomerization process of the protein bound 4WHJ have been observed under the influence of an external force that indicates an imposed restriction on the conformational switching. This has also been reflected by an increase in rigidity as observed from the increase in single-molecule FRET (smFRET)-anisotropy values (0.270 ± 0.012 to 0.360 ± 0.008). The application of an external force has assisted the conformational transitions to share the unstacked open structure intermediate, with different rate-limiting steps and induced huge variation in the energy landscape. Furthermore, the associated landscape of the 4WHJ is visualized in terms of rarely interconverting states embedded into the two isoforms using nonlinear dynamics analysis that shows the chaoticity of the system increases at intermediate force (0.4 to 1.6 pN). The identification of chaos in our investigation provides useful information in comprehensively explaining the origin of the complex behavior of the system, that effectively helps to perceive the dynamics of IHF bound 4WHJs under the influence of external force, and also demonstrated the applicability of nonlinear dynamics analysis in the field of biology.

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Publication details

The article was received on 21 Aug 2017, accepted on 01 Nov 2017 and first published on 01 Nov 2017


Article type: Paper
DOI: 10.1039/C7FD00184C
Citation: Faraday Discuss., 2017, Accepted Manuscript
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    Direct observation of external force mediated conformational dynamics of IHF bound Holliday junction

    S. C. Bera, T. Paul, A. N. S. Iyengar and P. P. Mishra, Faraday Discuss., 2017, Accepted Manuscript , DOI: 10.1039/C7FD00184C

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