Book chapter
[19] Analysis of site-specific interaction parameters in protein-DNA complexes
Methods in Enzymology, pp.405-425
Elsevier Science & Technology
1992
DOI: 10.1016/0076-6879(92)10021-5
PMID: 1584044
Abstract
This chapter discusses the analysis of site-specific interaction parameters in protein–DNA complexes. The chapter presents examples to illustrate the nonlinear least-squares analyses for estimation of site-specific interaction parameters. The examples are from studies that have been carried out in laboratory during the past few years. Most of the studies have been carried out on the λcI repressor operator system. The least-squares approach to parameter estimation makes three assumptions: (1) all error in the data can be ascribed to the dependent variable; (2) there are no systematic errors in the data; and (3) the random errors of the data conform to a Gaussian distribution. Least-squares analysis is a numerical technique for choosing an optimal set of parameters, α, for a function, G, that describes a set of data points, Xi and Yi. The chapter describes the application of nonlinear least-squares techniques for data obtained using footprint titration, filter binding, gel chromatography, and mobility shift techniques for analyzing the site-specific binding of proteins to multiple sites on DNA. Most of the applications are discussed in the chapter using a common model system—namely, the binding of bacteriophage λ cI repressor to the right operator region (OR).
Details
- Title: Subtitle
- [19] Analysis of site-specific interaction parameters in protein-DNA complexes
- Creators
- Kenneth S KoblanDavid L BainDorothy BeckettMadeline A SheaGary K Ackers
- Resource Type
- Book chapter
- Publication Details
- Methods in Enzymology, pp.405-425
- Publisher
- Elsevier Science & Technology
- DOI
- 10.1016/0076-6879(92)10021-5
- PMID
- 1584044
- eISSN
- 1557-7988
- ISSN
- 0076-6879
- Language
- English
- Date published
- 1992
- Academic Unit
- Molecular Physiology and Biophysics; Iowa Neuroscience Institute; Biochemistry and Molecular Biology
- Record Identifier
- 9984025248302771
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