Classes of fast and specific search mechanisms for proteins on DNA

2011/04/05 by M Sheinman, M. Sheinman, O. Bénichou +5 · 4 citations
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Class (philosophy) #DNA #Diffusion and Search Dynamics #Focus (optics) #Mechanism (biology) #Origins and Evolution of Life #Transcription (linguistics) #Transcription factor #cond-mat.soft #physics.bio-ph #q-bio.BM #q-bio.SC #stochastic dynamics and bifurcation

paper · pdf · doi:10.1088/0034-4885/75/2/026601

published as Rep. Prog. Phys. 75 (2012) 026601 · 65 pages, 23 figures

arxiv created 2011/04/05 · openalex publication_date 2012/01/24 · arxiv updated 2015/03/18 · openalex created_date 2016/06/24 · openalex updated_date 2026/08/05

Abstract

Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.

Citations

• The Ribosome Is a Ribozyme
• The effects of intersegmental transfers on target location by proteins
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• The Combinations of Haemoglobin with Oxygen and with Carbon Monoxide. I

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• Finite-range viscoelastic subdiffusion in disordered systems with inclusion of inertial effects
• Intracellular Facilitated Diffusion: Searchers, Crowders, and Blockers