Journal ArticleDOI
Cooperative effects on binding of proteins to DNA
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TLDR
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 ligand on the lattice at high levels of occupancy.About:
This article is published in Biophysical Chemistry.The article was published on 1986-08-01. It has received 38 citations till now. The article focuses on the topics: Cooperativity & Cooperative binding.read more
Citations
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Journal ArticleDOI
Condensed DNA: condensing the concepts.
TL;DR: A brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube and main theoretical approaches for the description of these systems are presented.
Book ChapterDOI
Thermodynamics of ligand-nucleic acid interactions.
TL;DR: An assessment of the basis for the stability and specificity of ligand-or protein-DNA interactions requires quantitative studies of these interactions as a function of a range of solution variables.
Journal ArticleDOI
General transfer matrix formalism to calculate DNA–protein–drug binding in gene regulation: application to OR operator of phage λ
TL;DR: It is shown 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, and the effects of a range of inter-protein distances.
Journal ArticleDOI
Statistical-mechanical lattice models for protein-DNA binding in chromatin.
Vladimir B. Teif,Karsten Rippe +1 more
TL;DR: The theoretical framework for lattice models of histone-DNA interactions in chromatin is presented and the (competitive) DNA binding of other chromosomal proteins and transcription factors are investigated.
Journal ArticleDOI
A lattice model for transcription factor access to nucleosomal DNA.
TL;DR: In this paper, a DNA lattice model was developed for describing ligand binding in the presence of a nucleosome, which takes into account intermediate states, in which DNA is partially unwrapped from the histone octamer.
References
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Journal ArticleDOI
On the Nature of Allosteric Transitions: A Plausible Model
TL;DR: "It is certain that all bodies whatsoever, though they have no sense, yet they have perception, and whether the body be alterant or alterec, evermore a perception precedeth operation; for else all bodies would be like one to another."
Journal ArticleDOI
Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice.
TL;DR: The results indicate that the binding of any non-interacting ligand covering more than one lattice residue results in non- linear (convex downward) Scatchard plots, and the introduction of positive ligand-ligand co-operativity antagonizes this non-linearity, and eventually leads to plots of the opposite curvature.
Journal ArticleDOI
Calculation of binding isotherms for heterogeneous polymers.
TL;DR: The purpose of this paper is to point out that problems of this type are readily solved with good accuracy by use of random‐number methods on a high‐speed digital computer.
Journal ArticleDOI
Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice: A model for ligand-ougonucleotide interactions
TL;DR: It is shown that irreversible binding cannot be viewed as a limiting case of reversible binding, and expressions for the extent of irreversible binding are derived.
Journal ArticleDOI
Equilibrium studies of ethidium--polynucleotide interactions.
TL;DR: The data reveal a switch of poly[d(I-C)] to a form able to bind ethidium more effectively, with allowance both for cooperativity of binding and for a structural switch of the helix to a different form which binds the drug more effectively.