Protein-DNA Cooperativity

Table of Contents

  1. Introduction

  2. Global Nonlinear Analysis

  3. Math Models for Protein/DNA Binding

  4. The Example: DctD Binding to the dctA UAS

  5. The Software: Where to get it!

This article describes in detail how to perform a global nonlinear regression analysis of DNAse 1 footprint data. It is intended for students and researchers wanting to determine if cooperativity is involved in the systems that they are investigating. The executable software runs on PC computers, but the fortran source code defining the math model is also provided. This module can be recompiled for use with the statistical modules of NONLIN that can be obtained from Michael Johnson of the Pharmacology Department at the University of Virginia, Charlottesville, VA 22908.

This document was prepared by B. Tracy Nixon as a contribution to the Internet course on Principles of Protein Structure organized by Birbeck College in collaboration with the Virtual School of Natural Sciences [VSNS] of the Globewide Network Academy [GNA] for the Spring of 1995. Molecular biologists are free to download the associated software, but they are solely responsible for its legal and proper use.

This work was funded by Public Health Service Grant GM40404.

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