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Hidden complexity in the isomerization dynamics of Holliday junctions

Nature Chemistry volume 4, pages 907–914 (2012)Cite this article

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Abstract

A plausible consequence of the rugged folding energy landscapes inherent to biomolecules is that there may be more than one functionally competent folded state. Indeed, molecule-to-molecule variations in the folding dynamics of enzymes and ribozymes have recently been identified in single-molecule experiments, but without systematic quantification or an understanding of their structural origin. Here, using concepts from glass physics and complementary clustering analysis, we provide a quantitative method to analyse single-molecule fluorescence resonance energy transfer (smFRET) data, thereby probing the isomerization dynamics of Holliday junctions, which display such heterogeneous dynamics over a long observation time (Tobs ≈ 40 s). We show that the ergodicity of Holliday junction dynamics is effectively broken and that their conformational space is partitioned into a folding network of kinetically disconnected clusters. Theory suggests that the persistent heterogeneity of Holliday junction dynamics is a consequence of internal multiloops with varying sizes and flexibilities frozen by Mg2+ ions. An annealing experiment using Mg2+ pulses lends support to this idea by explicitly showing that interconversions between trajectories with different patterns can be induced.

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Figure 1: Holliday junction dynamics probed with smFRET experiments and their analysis using a conventional ensemble averaging method.
Figure 2: Molecule-to-molecule variation (or molecular heterogeneity) manifested in the time traces of isomerization dynamics of Holliday junctions.
Figure 3: Probing ergodicity breaking.
Figure 4: Partitioning the molecules into distinct clusters.
Figure 5: Structural model to account for the origin of molecule-to-molecule variation in the Holliday junction dynamics.
Figure 6: Mg2+ pulse experiments to reset the molecular population in conformational space.

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Acknowledgements

This work was supported in part by grants from the National Research Foundation of Korea (2010-0000602 to C.H.), the Creative Research Initiatives (Physical Genetics Laboratory, 2009-0081562 to S.H.) and the National Science Foundation (grant CHE 09-14033 to D.T.).

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Authors and Affiliations

  1. School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 130-722, Korea

    Changbong Hyeon & Jeseong Yoon

  2. Department of Physics and Astronomy, Seoul National University, Seoul, 151-747, Korea

    Jinwoo Lee & Sungchul Hohng

  3. Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, 20742, USA

    D. Thirumalai

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  1. Changbong Hyeon
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Contributions

J.L. and S.H. carried out smFRET measurements on Holliday junctions under varying Mg2+ concentrations and Mg2+ pulse. C.H. carried out the smFRET data analysis. J.Y. carried out all-atom molecular dynamics simulations to determine the radial distribution of Mg2+ ions around the Holliday junctions. C.H. and D.T. conceived and directed the project, and prepared the manuscript.

Corresponding authors

Correspondence to Changbong Hyeon or D. Thirumalai.

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Hyeon, C., Lee, J., Yoon, J. et al. Hidden complexity in the isomerization dynamics of Holliday junctions. Nature Chem 4, 907–914 (2012). https://doi.org/10.1038/nchem.1463

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