Showing papers by "Madeline A. Shea published in 1992"

Analysis of site-specific interaction parameters in protein-DNA complexes.

Abstract: Publisher Summary 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 λ c I 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, X i and Y i . 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 (O R ).