Literature DB >> 16486329

Optimal target search on a fast-folding polymer chain with volume exchange.

Michael A Lomholt1, Tobias Ambjörnsson, Ralf Metzler.   

Abstract

We study the search process of a target on a rapidly folding polymer ("DNA") by an ensemble of particles ("proteins"), whose search combines 1D diffusion along the chain, Lévy type diffusion mediated by chain looping, and volume exchange. A rich behavior of the search process is obtained with respect to the physical parameters, in particular, for the optimal search.

Entities:  

Year:  2005        PMID: 16486329     DOI: 10.1103/PhysRevLett.95.260603

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  26 in total

1.  Physical aspects of precision in genetic regulation.

Authors:  Zvi Tamari; Naama Barkai; Itzhak Fouxon
Journal:  J Biol Phys       Date:  2010-11-19       Impact factor: 1.365

2.  Physical limits on cooperative protein-DNA binding and the kinetics of combinatorial transcription regulation.

Authors:  Nico Geisel; Ulrich Gerland
Journal:  Biophys J       Date:  2011-10-05       Impact factor: 4.033

3.  Generalized facilitated diffusion model for DNA-binding proteins with search and recognition states.

Authors:  Maximilian Bauer; Ralf Metzler
Journal:  Biophys J       Date:  2012-05-15       Impact factor: 4.033

4.  Dynamic strategies for target-site search by DNA-binding proteins.

Authors:  Mario A Díaz de la Rosa; Elena F Koslover; Peter J Mulligan; Andrew J Spakowitz
Journal:  Biophys J       Date:  2010-06-16       Impact factor: 4.033

Review 5.  Reaction-diffusion systems in intracellular molecular transport and control.

Authors:  Siowling Soh; Marta Byrska; Kristiana Kandere-Grzybowska; Bartosz A Grzybowski
Journal:  Angew Chem Int Ed Engl       Date:  2010-06-07       Impact factor: 15.336

6.  A quantitative study of lambda-phage SWITCH and its components.

Authors:  Chunbo Lou; Xiaojing Yang; Xili Liu; Bin He; Qi Ouyang
Journal:  Biophys J       Date:  2007-01-26       Impact factor: 4.033

7.  Facilitated diffusion with DNA coiling.

Authors:  Michael A Lomholt; Bram van den Broek; Svenja-Marei J Kalisch; Gijs J L Wuite; Ralf Metzler
Journal:  Proc Natl Acad Sci U S A       Date:  2009-05-06       Impact factor: 11.205

8.  How subdiffusion changes the kinetics of binding to a surface.

Authors:  Irwin M Zaid; Michael A Lomholt; Ralf Metzler
Journal:  Biophys J       Date:  2009-08-05       Impact factor: 4.033

9.  How DNA coiling enhances target localization by proteins.

Authors:  B van den Broek; M A Lomholt; S-M J Kalisch; R Metzler; G J L Wuite
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-06       Impact factor: 11.205

10.  Are DNA transcription factor proteins maxwellian demons?

Authors:  Longhua Hu; Alexander Y Grosberg; Robijn Bruinsma
Journal:  Biophys J       Date:  2008-05-02       Impact factor: 4.033

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