Protein-Protein and Protein-DNA Interfaces of the Nucleosome

Johns Hopkins University, Baltimore MD

Investigators

Abstract

Moudrianakis 0091736 The goal of the this research is to elucidate the properties that govern the relations between the structure of the nucleosome and the functional remodeling (transitions between assembly and disassembly) that occurs during the cell cycle. The approach is based on integrated applications of classical biochemistry and biophysical chemistry with those of molecular genetics. This approach addresses the basic properties of both nucleosomal DNA and the octameric histone core within a dynamic structure. New evidence from the PI's laboratory (based on molecular dynamics calculations) suggests that the nucleosome is very dynamic, exhibiting large "breathing" motions in the nanosecond time scale and that the contact interfaces between the protein subunits show time-dependent fluctuations. The protein core is an "articulated endoskeleton" around which the DNA wraps in a "generic, non base-specific way" for most of its length, with relatively few site-specific contacts. Such a "fragile" arrangement serves the needs of regulation well; it is mediated to a large extent by the subunit contacts within the core histone octamer. These studies are examining a range of conditions that affect the intrinsic (molecular types) and extrinsic (microenvironment) parameters of native heterodimers and their assembly potential. This is important because a thorough understanding of the functional transitions of the nucleosome/chromatin entailed during chromatin remodeling, replication and transcription depends on the exact knowledge of the energetics and specificities of these interfacial contacts. Techniques to be employed are: analytical ultracentrifugation, high-resolution multi-angle light scattering and microcalorimetry as well as contemporary methods of analytical chemistry.