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J Am Chem Soc. 2015 Oct 14;137(40):13041-8. doi: 10.1021/jacs.5b07898. Epub 2015 Sep 29.

Associative Interactions in Crowded Solutions of Biopolymers Counteract Depletion Effects.

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Institute for Molecules and Materials, Radboud University , 6525 AJ, Nijmegen, The Netherlands.
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , 9747 AG Groningen, The Netherlands.
Graduate School of Biostudies & The Hakubi Center for Advanced Research, Kyoto University , 606-8501 Kyoto, Japan.
Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu 9, E-40 28040 Madrid, Spain.


The cytosol of Escherichia coli is an extremely crowded environment, containing high concentrations of biopolymers which occupy 20-30% of the available volume. Such conditions are expected to yield depletion forces, which strongly promote macromolecular complexation. However, crowded macromolecule solutions, like the cytosol, are very prone to nonspecific associative interactions that can potentially counteract depletion. It remains unclear how the cytosol balances these opposing interactions. We used a FRET-based probe to systematically study depletion in vitro in different crowded environments, including a cytosolic mimic, E. coli lysate. We also studied bundle formation of FtsZ protofilaments under identical crowded conditions as a probe for depletion interactions at much larger overlap volumes of the probe molecule. The FRET probe showed a more compact conformation in synthetic crowding agents, suggesting strong depletion interactions. However, depletion was completely negated in cell lysate and other protein crowding agents, where the FRET probe even occupied slightly more volume. In contrast, bundle formation of FtsZ protofilaments proceeded as readily in E. coli lysate and other protein solutions as in synthetic crowding agents. Our experimental results and model suggest that, in crowded biopolymer solutions, associative interactions counterbalance depletion forces for small macromolecules. Furthermore, the net effects of macromolecular crowding will be dependent on both the size of the macromolecule and its associative interactions with the crowded background.

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