Metal binding and conformation-encoded signaling and pathogenesis in the prion protein and low resolution structure determination using electron paramagnetic resonance and computer modeling

Abstract

The transmission of information is fundamental to both the dynamics and enduring stability of life. The genome of an organism was once solely believed to be capable of encoding biological data, by storing "bits" in the primary sequence of nucleic acid. At the same time, proteins and other macromolecules were understood to govern quotidian cellular processes. Recent scientific advances have removed these distinctions and forced the modern scientist to work in a less discrete realm in which the canonical boundaries of information storage no longer exist. This work therefore expands upon methods of protein structure determination and focuses on a group of polypeptides in which pathogenic information is encoded in the proteins tertiary conformation. The mechanism and structure of the cooperative binding of five coppers to the prion protein, and the influences of binding upon holoprotein structure is described herein, with the concomitant introduction of methodological applications for the study of metal binding to amyloidogenic proteins in general. Finally, a methodology for determining and or validating low-resolution protein structures using site-directed spin labeling electron spin resonance in conjunction with computer modeling is described in general and is specifically applied to the p85 inhibitory subunit of phosphoinositide 3-kinase and the E. coli T4-lysozyme.