Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Facilitated diffusion framework for transcription factor search with
  conformational changes   Cellular responses often require the fast activation or repression of
specific genes, which depends on Transcription Factors (TFs) that have to
quickly find the promoters of these genes within a large genome. Transcription
Factors (TFs) search for their DNA promoter target by alternating between bulk
diffusion and sliding along the DNA, a mechanism known as facilitated
diffusion. We study a facilitated diffusion framework with switching between
three search modes: a bulk mode and two sliding modes triggered by
conformational changes between two protein conformations. In one conformation
(search mode) the TF interacts unspecifically with the DNA backbone resulting
in fast sliding. In the other conformation (recognition mode) it interacts
specifically and strongly with DNA base pairs leading to slow displacement.
From the bulk, a TF associates with the DNA at a random position that is
correlated with the previous dissociation point, which implicitly is a function
of the DNA structure. The target affinity depends on the conformation. We
derive exact expressions for the mean first passage time (MFPT) to bind to the
promoter and the conditional probability to bind before detaching when arriving
at the promoter site. We systematically explore the parameter space and compare
various search scenarios. We compare our results with experimental data for the
dimeric Lac repressor search in E.Coli bacteria. We find that a coiled DNA
conformation is absolutely necessary for a fast MFPT. With frequent spontaneous
conformational changes, a fast search time is achieved even when a TF becomes
immobilized in the recognition state due to the specific bindings. We find a
MFPT compatible with experimental data in presence of a specific TF-DNA
interaction energy that has a Gaussian distribution with a large variance.

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The categories of this paper are: hep-ex
22
The categories of this paper are: chao-dyn
9
The categories of this paper are: nlin
25
The categories of this paper are: patt-sol
14
The categories of this paper are: math-ph
31
The categories of this paper are: ao-sci
5
The categories of this paper are: gr-qc
11
The categories of this paper are: hep-lat
0
The categories of this paper are: hep-ph
33
The categories of this paper are: plasm-ph
30
The categories of this paper are: q-alg
2
The categories of this paper are: math
13
The categories of this paper are: quant-ph
24
The categories of this paper are: dg-ga
6
The categories of this paper are: astro-ph
3
The categories of this paper are: physics