Journal article
A stochastic reaction-diffusion model for protein aggregation on DNA
International journal of modern physics. C, Computational physics, physical computation, Vol.28(8), p.1750102
08/2017
Handle:
https://hdl.handle.net/2376/109500
Abstract
Vital functions of DNA, such as transcription and packaging, depend on the proper clustering of proteins on the double strand. The present study investigates how the interplay between DNA allostery and electrostatic interactions affects protein clustering. The statistical analysis of a simple but transparent computational model reveals two major consequences of this interplay. First, depending on the protein and salt concentration, protein filaments exhibit a bimodal DNA stiffening and softening behavior. Second, within a certain domain of the control parameters, electrostatic interactions can cause energetic frustration that forces proteins to assemble in rigid spiral configurations. Such spiral filaments might trigger both positive and negative supercoiling, which can ultimately promote gene compaction and regulate the promoter. It has been experimentally shown that bacterial histone-like proteins assemble in similar spiral patterns and/or exhibit the same bimodal behavior. The proposed model can, thus, provide computational insights into the physical mechanisms used by proteins to control the mechanical properties of the DNA.
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Details
- Title
- A stochastic reaction-diffusion model for protein aggregation on DNA
- Creators
- Nikolaos K Voulgarakis - Department of Mathematics and Statistics, Washington State University, Pullman, WA 99164, USA
- Publication Details
- International journal of modern physics. C, Computational physics, physical computation, Vol.28(8), p.1750102
- Academic Unit
- Mathematics and Statistics, Department of
- Identifiers
- 99900547044301842
- Language
- English
- Resource Type
- Journal article