Cooperative effects on binding of proteins to DNA

Nechipurenko, Yu. D.; Gursky, G. V.

doi:10.1016/0301-4622(86)85025-6

Cited by 37 publications

(12 citation statements)

References 16 publications

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“…Note, that the dotted and dashed curves in Figure 1 were obtained also by the numerical solution of SDE (Nechipurenko & Gurski, 1986).The procedure of finding the dependence of the mean number of ligands adsorbed on DNA on the dimensionless ligand concentration (adsorption isotherms, Figure 1) is such. Initially Equation (4) is rewritten in the dimensionless form…”

Section: Resultsmentioning

confidence: 99%

“…Against a background of a number of works devoted to the theoretical calculation of the mean number of ligands adsorbed on DNA (Crothers, 1968;McGhee & Von Hippel, 1974;Nechipurenko & Gurski, 1986;Zasedatelev, Gurski, & Volkenshtejn, 1971), the number of works concerned with the influence of a noise on the ligand adsorption on DNA is relatively small (Arakelyan, Babayan, & Potikyan, 2000;Babayan, Potikyan, Arakelyan, & Kazaryan, 2001;Jovanovich & Nechipurenko, 1990;Nechipurenko & Gursky, 2003). At the same time, it is well known that under the influence of the noise the character of adsorption may radically change.…”

Section: Introductionmentioning

confidence: 97%

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Isotherm of ligand adsorption on DNA at multiplicative noise

Arakelyan

Harutyunyan

Andriasyan

et al. 2012

Journal of Biomolecular Structure and Dynamics

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Fluctuations of the number of ligands adsorbed on macromolecules are considered in the case when the number of ligands in the solution fluctuates under the action of fluctuations of the external medium (external noise). For the case of small filling, the multiplicative type of stochastic differential equation is obtained, describing the time variation of the number of ligands adsorbed on macromolecules. The isotherm of adsorption of ligands on DNA is obtained. It is shown that at small ligand concentrations, for some relations between adsorption parameters and the intensity of the external noise, no macromolecule adsorption of ligands takes place.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Isotherm of ligand adsorption on DNA at multiplicative noise

Arakelyan

Harutyunyan

Andriasyan

et al. 2012

Journal of Biomolecular Structure and Dynamics

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“…In order to describe the interaction of a small molecule (in this study, H + ) with infinite polymers, a number of mathematical models [14][15][16][17][18] has been developed. The matrix method [19] has been proposed to calculate the equilibrium constants which govern the binding of small molecules to a short sequence of equivalent sites (oligomer).…”

Section: Introductionmentioning

confidence: 99%

Spectrometric study of the folding process of i-motif-forming DNA sequences upstream of the c-kit transcription initiation site

Bucek¹,

Gargallo²,

Kudrev³

2010

Analytica Chimica Acta

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“…Once a pair of dimers is formed, a third dimer binds DNA non-cooperatively (45,46). Such interactions may be described by the extended MvH model, where two different orientations of the bound proteins are taken into account (47,48). The f -mer assembly model provides a further generalization.…”

Section: Construction Of the Basic Matrix Modelsmentioning

confidence: 99%

General transfer matrix formalism to calculate DNA–protein–drug binding in gene regulation: application to O R operator of phage λ

Teif

2007

Nucleic Acids Research

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The transfer matrix methodology is proposed as a systematic tool for the statistical–mechanical description of DNA–protein–drug binding involved in gene regulation. We show that a genetic system of several cis-regulatory modules is calculable using this method, considering explicitly the site-overlapping, competitive, cooperative binding of regulatory proteins, their multilayer assembly and DNA looping. In the methodological section, the matrix models are solved for the basic types of short- and long-range interactions between DNA-bound proteins, drugs and nucleosomes. We apply the matrix method to gene regulation at the OR operator of phage λ. The transfer matrix formalism allowed the description of the λ-switch at a single-nucleotide resolution, taking into account the effects of a range of inter-protein distances. Our calculations confirm previously established roles of the contact CI–Cro–RNAP interactions. Concerning long-range interactions, we show that while the DNA loop between the OR and OL operators is important at the lysogenic CI concentrations, the interference between the adjacent promoters PR and PRM becomes more important at small CI concentrations. A large change in the expression pattern may arise in this regime due to anticooperative interactions between DNA-bound RNA polymerases. The applicability of the matrix method to more complex systems is discussed.

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Cooperative effects on binding of proteins to DNA

Cited by 37 publications

References 16 publications

Isotherm of ligand adsorption on DNA at multiplicative noise

Isotherm of ligand adsorption on DNA at multiplicative noise

Spectrometric study of the folding process of i-motif-forming DNA sequences upstream of the c-kit transcription initiation site

General transfer matrix formalism to calculate DNA–protein–drug binding in gene regulation: application to O R operator of phage λ

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