Journal
JOURNAL OF MOLECULAR BIOLOGY
Volume 361, Issue 2, Pages 268-285Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2006.06.005
Keywords
lattice model; exact enumeration; Monte Carlo sampling; conformational entropy; self-avoiding lattice polygon
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Funding
- NIAID NIH HHS [R01 AI054830] Funding Source: Medline
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Topoisomerases may unknot by recognizing specific DNA juxtapositions. The physical basis of this hypothesis is investigated by considering single-loop conformations in a coarse-grained polymer model. We determine the statistical relationship between the local geometry of a juxtaposition of two chain segments and whether the loop is knotted globally, and ascertain how the knot/unknot topology is altered by a topoisomerase-like segment passage at the juxtaposition. Segment passages at a free juxtaposition tend to increase knot probability. In contrast, segment passages at a hooked juxtaposition cause more transitions from knot to unknot than vice versa, resulting in a steady-state knot probability far lower than that at topological equilibrium. The reduction in knot population by passing chain segments through a hooked juxtaposition is more prominent for loops of smaller sizes, n, but remains significant even for larger loops: steady-state knot probability is only similar to 2%, and similar to 5% of equilibrium, respectively, for n = 100 and 500 in the model. An exhaustive analysis of similar to 6000 different juxtaposition geometries indicates that the ability of a segment passage to unknot correlates strongly with the juxtaposition's hookedness. Remarkably, and consistent with experiments on type-2 topoisomerases from different organisms, the unknotting potential of a juxtaposition geometry in our polymer model correlates almost perfectly with its corresponding decatenation potential. These quantitative findings suggest that it is possible for topoisomerases to disentangle by acting selectively on juxtapositions with hooked geometries. (c) 2006 Elsevier Ltd. All rights reserved.
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