ABSTRACT (Project Title: Folding and Degradation of Membrane Proteins) The goal of my research program is to elucidate the chemical and physical principles underlying the folding and degradation of membrane proteins. Cells should maintain physiologically optimal levels of functional proteins. This is achieved by the balanced actions of molecular chaperones to facilitate folding, proteases to degrade misfolded and superfluous proteins, and stress-response signaling pathways to regulate levels of chaperones and proteases. This protein quality control machinery uses multiple layers of mechanisms to monitor the folding status of a proteome. Thus, the fate of a given protein, whether it will fold or be degraded, strongly depends on the intrinsic folding properties of the protein. While a majority of folding and degradation studies have focused on water-soluble proteins, it is not well understood how the intrinsic folding properties of membrane proteins affect their degradation. The knowledge gap mainly stems from inherent difficulties in studying membrane protein folding in their native lipid bilayer environment as well as an insufficient understanding of folding and sequence determinants for degradation. We use a combined model employing the membrane-integrated ATP-dependent protease FtsH of E. coli as a model degradation machine, and the intramembrane protease GlpG of E. coli as a model substrate, both of which are widely conserved in prokaryotic and eukaryotic cells. We developed an array of methods to study membrane protein folding in the bilayers based on the novel steric-trapping principle. We also developed an in vitro bilayer system to study FtsH-mediated degradation of a membrane protein. Using these methodological innovations, my vision for future research is to learn the generalizable lessons of folding, protein-protein interactions and quality control of membrane proteins in the cell membranes. We will delve into three unanswered problems: 1) What is the detailed molecular mechanisms of FtsH-mediated membrane protein degradation? 2) Is the lipid bilayer a good solvent for the denatured states of membrane protein or a poor solvent that promotes their nonspecific collapse? 3) How do membrane proteins from thermophilic organisms achieve their unusual thermostability and activity? If successful, the outcome of this study will advance our fundamental understanding of mechanisms and energetics of membrane protein degradation, identify new physical properties of the lipid bilayer that control folding and interactions of membrane proteins, and discover new stabilizing motifs for membrane proteins that will provide a useful design and engineering principle.