PMID: 3768466Aug 1, 1986Paper

Cooperative effects on binding of proteins to DNA

Biophysical Chemistry
Y D Nechipurenko, Georgii V Gursky

Abstract

Equations are derived for description of cooperative binding of large ligands to a homogeneous polynucleotide lattice for a wide variety of binding models. Both short- and long-range interactions between nearest-neighbour bound ligands are taken into account. It is shown that cooperative binding of ligand at high levels of occupancy can be described with good accuracy by the equation derived for the noncooperative binding of the same ligand with an apparent binding constant Keff. A new method is proposed for the analysis of cooperative binding isotherms. It is based on a comparison of the asymptotic behavior of cooperative and noncooperative binding isotherms in the limit when the occupancy of lattice by ligand approaches the saturation level of binding. It is demonstrated that cooperative effects mediated by direct contact between bound ligands can be divided into two classes depending on whether dimeric species or aggregates of unrestricted size are formed by bound ligands on the lattice at high levels of occupancy. These two classes can be easily distinguished on strictly empirical grounds. In particular, if interligand interactions favor the formation of dimeric species on DNA, Keff approximately a 1/2 where a is the interl...Continue Reading

Citations

Apr 1, 1997·Journal of Biomolecular Structure & Dynamics·A N SurovayaC Zimmer
Nov 23, 2000·Journal of Biomolecular Structure & Dynamics·V ArakelyanG Potikyan
May 4, 2001·Journal of Biomolecular Structure & Dynamics· Nechipurenko YuDI R Nabiev
Jul 30, 2002·Journal of Biomolecular Structure & Dynamics·Valeri B ArakelyanTigran S Haroutiunian
Aug 20, 2004·Journal of Biomolecular Structure & Dynamics·V B ArakelyanT S Haroutunyan
Jul 4, 2008·Journal of Biomolecular Structure & Dynamics·Dmitri Y Lando, Yury D Nechipurenko
Jun 19, 2012·Journal of Biomolecular Structure & Dynamics·Valeri ArakelyanHakob Arakelyan
Jul 9, 2011·Briefings in Bioinformatics·Vladimir B Teif, Karsten Rippe
Oct 21, 2010·Biophysical Journal·Vladimir B TeifKarsten Rippe
Aug 8, 2018·Journal of Biomolecular Structure & Dynamics·Y V StirmanovY D Nechipurenko
Mar 10, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Vladimir B Teif, Karsten Rippe
May 29, 2015·Biopolymers·Manana Melikishvili, Michael G Fried
Jul 20, 2010·Progress in Biophysics and Molecular Biology·Vladimir B Teif, Klemen Bohinc

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