CHAPTER 3 Opposites Attract: Shape and Electrostatic Complementarity in Protein-DNA Complexes ROBERT C. HARRIS, a,b,w TRAVIS MACKOY, b,w ANA CAROLINA DANTAS MACHADO, c,w DARUI XU, b,d REMO ROHS* c AND MARCIA OLIVEIRA FENLEY* b a Department of Physics and b Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; c Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA; d Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA *Email: rohs@usc.edu; mfenley@sb.fsu.edu 3.1 Introduction Protein-DNA binding plays a key role in both gene regulation – through highly specific transcription factor-DNA interactions – and in chromatin organization, through the largely non-specific interactions of histones and other architectural proteins with DNA. 1 This biological importance has inspired the rapid expansion in structural knowledge of protein-DNA binding, derived from X-ray crystallographic and NMR spectroscopic data, 2 ever since RSC Biomolecular Sciences No. 24 Innovations in Biomolecular Modeling and Simulations: Volume 2 Edited by Tamar Schlick r Royal Society of Chemistry 2012 Published by the Royal Society of Chemistry, www.rsc.org w These authors contributed equally. 53