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Are DNA transcription factor proteins maxwellian demons?
Biophys J. 2008 Aug;95(3):1151-6. doi: 10.1529/biophysj.108.129825. Epub 2008 May 2.
2
Facilitated diffusion on confined DNA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Feb;85(2 Pt 1):021919. doi: 10.1103/PhysRevE.85.021919. Epub 2012 Feb 22.
3
Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.
Biophys J. 2004 Dec;87(6):4021-35. doi: 10.1529/biophysj.104.050765. Epub 2004 Oct 1.
4
Generalized theory of site-specific DNA-protein interactions.
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Jul;76(1 Pt 1):011901. doi: 10.1103/PhysRevE.76.011901. Epub 2007 Jul 2.
5
Mechanism of DNA compaction by yeast mitochondrial protein Abf2p.
Biophys J. 2004 Mar;86(3):1632-9. doi: 10.1016/S0006-3495(04)74231-9.
6
How does a protein search for the specific site on DNA: The role of disorder.
Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Aug;74(2 Pt 1):021903. doi: 10.1103/PhysRevE.74.021903. Epub 2006 Aug 3.
7
Packaging effects on site-specific DNA-protein interactions.
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jun;79(6 Pt 1):061920. doi: 10.1103/PhysRevE.79.061920. Epub 2009 Jun 19.
8
Facilitated diffusion of DNA-binding proteins: Simulation of large systems.
J Chem Phys. 2006 Jul 7;125(1):014906. doi: 10.1063/1.2211614.
9
Protein sliding and hopping kinetics on DNA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Feb;83(2 Pt 1):021907. doi: 10.1103/PhysRevE.83.021907. Epub 2011 Feb 16.
10
How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.
Bioessays. 2016 Jul;38(7):605-12. doi: 10.1002/bies.201600005. Epub 2016 May 19.

引用本文的文献

1
Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA.
Proc Natl Acad Sci U S A. 2021 Jun 8;118(23). doi: 10.1073/pnas.2102621118.
2
Quantifying the two-state facilitated diffusion model of protein-DNA interactions.
Nucleic Acids Res. 2019 Jun 20;47(11):5530-5538. doi: 10.1093/nar/gkz308.
3
Mitotic chromosome binding predicts transcription factor properties in interphase.
Nat Commun. 2019 Jan 30;10(1):487. doi: 10.1038/s41467-019-08417-5.
4
Mechanisms of Protein Search for Targets on DNA: Theoretical Insights.
Molecules. 2018 Aug 22;23(9):2106. doi: 10.3390/molecules23092106.
5
Rad4 recognition-at-a-distance: Physical basis of conformation-specific anomalous diffusion of DNA repair proteins.
Prog Biophys Mol Biol. 2017 Aug;127:93-104. doi: 10.1016/j.pbiomolbio.2016.12.004. Epub 2016 Dec 8.
7
Coordinated Expression of Phosphoinositide Metabolic Genes during Development and Aging of Human Dorsolateral Prefrontal Cortex.
PLoS One. 2015 Jul 13;10(7):e0132675. doi: 10.1371/journal.pone.0132675. eCollection 2015.
8
Real sequence effects on the search dynamics of transcription factors on DNA.
Sci Rep. 2015 Jul 8;5:10072. doi: 10.1038/srep10072.
9
On the Possibility of Facilitated Diffusion of Dendrimers Along DNA.
J Phys Chem B. 2015 Jun 11;119(23):6894-904. doi: 10.1021/acs.jpcb.5b02090. Epub 2015 Jun 2.
10
Modeling Viral Capsid Assembly.
Adv Chem Phys. 2014;155:1-68. doi: 10.1002/9781118755815.ch01.

本文引用的文献

1
How a protein searches for its specific site on DNA: the role of intersegment transfer.
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Nov;76(5 Pt 1):051909. doi: 10.1103/PhysRevE.76.051909. Epub 2007 Nov 9.
2
Probing transcription factor dynamics at the single-molecule level in a living cell.
Science. 2007 May 25;316(5828):1191-4. doi: 10.1126/science.1141967.
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How does a protein search for the specific site on DNA: The role of disorder.
Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Aug;74(2 Pt 1):021903. doi: 10.1103/PhysRevE.74.021903. Epub 2006 Aug 3.
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Single molecule measurements of repressor protein 1D diffusion on DNA.
Phys Rev Lett. 2006 Jul 28;97(4):048302. doi: 10.1103/PhysRevLett.97.048302. Epub 2006 Jul 27.
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Optimal target search on a fast-folding polymer chain with volume exchange.
Phys Rev Lett. 2005 Dec 31;95(26):260603. doi: 10.1103/PhysRevLett.95.260603. Epub 2005 Dec 22.
7
How proteins search for their specific sites on DNA: the role of DNA conformation.
Biophys J. 2006 Apr 15;90(8):2731-44. doi: 10.1529/biophysj.105.078162. Epub 2006 Feb 3.
8
Target search of N sliding proteins on a DNA.
Biophys J. 2005 Aug;89(2):895-902. doi: 10.1529/biophysj.104.057612. Epub 2005 May 20.
9
Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.
Biophys J. 2004 Dec;87(6):4021-35. doi: 10.1529/biophysj.104.050765. Epub 2004 Oct 1.
10
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.
Science. 2004 Jul 16;305(5682):386-9. doi: 10.1126/science.1097064.

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