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. 2015 Dec 15;44(1):63–74. doi: 10.1093/nar/gkv1091

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© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — A switch in the MTERF1 superhelical topology. (A) In recognition mode, unbiased MD simulations show that MTERF1 populates a high pitch state consistent being bound to unwound (high pitch) DNA. The DNA is not shown for clarity. To show the expected range of B-DNA pitch, horizontal lines mark the average structure of B-DNA (black) plus one, two and three standard deviations (grey, red, blue, respectively). A vertical guide is placed at 7 Å to represent B-DNA radius compatibility. (B) In the absence of DNA, apo MTERF1 samples a wide range of superhelical conformations, extending into the range compatible with B-DNA. (C) In search mode, the superhelical dynamics of MTERF1 are suppressed by B-DNA with a much narrower distribution of both pitch and radius. Compared with holo-specific, the small increase in radius of holo-nonspecific is likely caused by the decrease in pitch. Snapshots of MTERF1 were selected evenly from concatenated trajectories of the respective ensembles; the N-terminus is towards the top.