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Chromatin configuration affects the dynamics and distribution of a transiently interacting protein

A. Amitai
doi: https://doi.org/10.1101/246231
A. Amitai
1Department of Chemical Engineering; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139
2Ragon Institute of MGH, MIT, & Harvard, Cambridge, MA 02139.
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Abstract

We present a theoretical study of the interaction between a protein (diffusing particle) with chromatin (polymer chain). Each monomer is a trap where a particle can transiently bind. We derive novel formulas for the transition rate between monomer sites, given a specific polymer configuration, and find that a particle is likely to rapidly rebind many times to its release site, before moving to another. The reattachment probability is larger when the local density around the release site is smaller. Interestingly, for an equilibrated polymer, the transition probability decays as a power-law for close monomer-to-monomer distances and reaches an asymptotic value for faraway ones. By computing the transition rate between monomers, we show that the problem of facilitated search by a protein can be mapped to a continuous time Markov chain, which we solve. Our findings suggest that proteins may be locally trapped for a time much longer than their dissociation time, while their overall motion is ergodic. Our results are corroborated by Brownian simulations.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 10, 2018.
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Chromatin configuration affects the dynamics and distribution of a transiently interacting protein
A. Amitai
bioRxiv 246231; doi: https://doi.org/10.1101/246231
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Chromatin configuration affects the dynamics and distribution of a transiently interacting protein
A. Amitai
bioRxiv 246231; doi: https://doi.org/10.1101/246231

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