Exploring Structural, Functional, and Kinetic Aspects of Nucleic Acid–Protein Complexes with Pressure: Nucleosomes and RNA Polymerase

Abstract

High pressure has provided us with new insights into two complex DNA-protein systems: nucleosomes and RNA polymerase. In spite of their complexity, we can derive new and useful information about them by coupling high pressure with a variety of other physical techniques and functional assays. These studies have shown clearly that multiple conformations of these large–molecular weight DNA-protein assemblies are present simultaneously in solution, although both molecular assemblies are generally considered to be single structures in most in vitro experiments. Considering the variety of different cellular situations encountered by nucleosomes and RNA polymerases, it is perhaps to be expected that evolution would select structures with flexible and multifarious conformations that possesses sufficient stability, rather than static, rigid, singular, and highly stable structures. The molecular organization in the nucleus of a biological cell is extensive and involves intricate protein-protein and protein–nucleic acid interactions that are changing continually during the cell cycle. These dynamic activities in the nucleus are tightly coordinated with many extranuclear events throughout the cell. Highly organized molecular complexes involving multisubunit proteins (and higher order protein assemblies) interacting with the nucleic acid components are the rule rather than the exception in the nucleus (Alberts et al., 1983; Darnell et al., 1990; Lewin, 1994). For instance, chromosomes are organized in a structural hierarchy culminating in the metaphase state in which they are packed tightly together with proteins in a highly specific and economical manner that still largely eludes our understanding; the DNA of a eukaryotic cell is replicated with the help of a complex assembly of proteins; and information coded within the DNA sequence is transcribed with the assistance of multisubunit DNA-binding proteins, some acting as enzymes and others serving mainly as organizational and structural assistants to the catalytic process. Many important features of protein-nucleic acid (DNA and RNA) interactions have been elucidated in the last decade (Pabo & Sauer, 1992; Steitz, 1990), and exciting results have been obtained for singleprotein molecules and dimers binding to DNA. Although we are a long way from understanding these interactions completely, enough aspects are known so that structural predictions are sometimes possible simply from the amino acid sequence.