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General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.

ABSTRACT: 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 O(R) operator of phage lambda. The transfer matrix formalism allowed the description of the lambda-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 O(R) and O(L) operators is important at the lysogenic CI concentrations, the interference between the adjacent promoters P(R) and P(RM) 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.

SUBMITTER: Teif VB

PROVIDER: S-EPMC1920246 | biostudies-other | 2007

REPOSITORIES: biostudies-other

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General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.

Teif Vladimir B VB

Nucleic acids research 20070525 11

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 ...[more]

PMID: 17526526

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Project description:PURPOSE:An extended phase graph framework (EPG-X) for modeling systems with exchange or magnetization transfer (MT) is proposed. THEORY:EPG-X models coupled two-compartment systems by describing each compartment with separate phase graphs that exchange during evolution periods. There are two variants: EPG-X(BM) for systems governed by the Bloch-McConnell equations, and EPG-X(MT) for the pulsed MT formalism. For the MT case, the "bound" protons have no transverse components, so their phase graph consists of only longitudinal states. METHODS:The EPG-X model was validated against steady-state solutions and isochromat-based simulation of gradient-echo sequences. Three additional test cases were investigated: (i) MT effects in multislice turbo spin-echo; (ii) variable flip angle gradient-echo imaging of the type used for MR fingerprinting; and (iii) water exchange in multi-echo spin-echo T2 relaxometry. RESULTS:EPG-X was validated successfully against isochromat based transient simulations and known steady-state solutions. EPG-X(MT) simulations matched in-vivo measurements of signal attenuation in white matter in multislice turbo spin-echo images. Magnetic resonance fingerprinting-style experiments with a bovine serum albumin (MT) phantom showed that the data were not consistent with a single-pool model, but EPG-X(MT) could be used to fit the data well. The EPG-X(BM) simulations of multi-echo spin-echo T2 relaxometry suggest that exchange could lead to an underestimation of the myelin-water fraction. CONCLUSIONS:The EPG-X framework can be used for modeling both steady-state and transient signal response of systems exhibiting exchange or MT. This may be particularly beneficial for relaxometry approaches that rely on characterizing transient rather than steady-state sequences. Magn Reson Med 80:767-779, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Dataset Information

General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.

Publications

General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.

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