Impact of macromolecular crowding on DNA replication

Barak Akabayov, Sabine R. Akabayov, Seung-Joo Lee, Gerhard Wagner and Charles C. Richardson ()
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Barak Akabayov: Harvard Medical School
Sabine R. Akabayov: Harvard Medical School
Seung-Joo Lee: Harvard Medical School
Gerhard Wagner: Harvard Medical School
Charles C. Richardson: Harvard Medical School

Nature Communications, 2013, vol. 4, issue 1, 1-10

Abstract: Abstract Enzymatic activities in vivo occur in a crowded environment composed of many macromolecules. This environment influences DNA replication by increasing the concentration of the constituents, desolvation, decreasing the degrees of freedom for diffusion and hopping of proteins onto DNA, and enhancing binding equilibria and catalysis. However, the effect of macromolecular crowding on protein structure is poorly understood. Here we examine macromolecular crowding using the replication system of bacteriophage T7 and we show that it affects several aspects of DNA replication; the activity of DNA helicase increases and the sensitivity of DNA polymerase to salt is reduced. We also demonstrate, using small-angle X-ray scattering analysis, that the complex between DNA helicase and DNA polymerase/trx is far more compact in a crowded environment. The highest enzymatic activity corresponds to the most compact structure. Better knowledge of the effect of crowding on structure and activity will enhance mechanistic insight beyond information obtained from NMR and X-ray structures.

Date: 2013
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DOI: 10.1038/ncomms2620

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