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arXiv · 1010.3247

Protein sliding and hopping kinetics on DNA

Michael C. DeSantis·Je-Luen Li·Y. M. Wang
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Abstract

Using Monte-Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (1) in each diffusion trajectory, a protein makes on average hundreds of alternating slides and hops with a mean sliding time of several tens of ms; (2) sliding dominates the root mean square displacement of fast diffusion trajectories, whereas hopping dominates slow ones; (3) flow and variations in salt concentration have limited effects on hopping kinetics, while in vivo DNA configuration is not expected to influence sliding kinetics; furthermore, (4) the rate of occurrence for hops longer than 200 nm agrees with experimental data for EcoRV proteins.

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Michael C. DeSantis, Je-Luen Li, Y. M. Wang. 2011-07-22. Protein sliding and hopping kinetics on DNA. https://doi.org/10.1016/j.bpj.2010.12.1268

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