Cells use selective degradation of misfolded and intrinsically unstable proteins to maintain physiologically appropriate levels of functional proteins. Imbalances between intracellular protein folding and degradation cause severe human diseases, via excessive degradation of mutated proteins (e.g. cystic fibrosis, retinitis pigmentosa), or toxic accumulation of misfolded proteins that overwhelms cellular degradation capacity (e.g. Alzheimer's disease). A key gap in understanding of protein folding-degradation relationships and mechanisms is its current restriction to only water-soluble (cytosolic) proteins, whereas little is known about membrane proteins, despite their major physiological and pathogenic importance. This knowledge gap is mainly due to inherent difficulties of analyzing folding of membrane proteins within their native lipid bilayer environment. Based on our strong preliminary data and novel steric-trapping molecular tools, the long-term objective of this project is to elucidate molecular mechanisms and determinants of membrane protein degradation, by defining the molecular and quantitative relationships between intrinsic folding properties of membrane proteins, including global vs. local stability, unfolding rates, and hydrophobicity of transmembrane segments, and their degradation. We will use an innovative combined model consisting of the membrane- integrated ATP-dependent E. coli protease FtsH as model degradation machine, and the intramembrane protease GlpG from E. coli as model substrate, both of which are widely conserved in prokaryotic and eukaryotic cells.
The aims are: 1) To develop new methodologies for determining the stability of membrane proteins in their native bilayers, by adapting our prior steric trapping innovations, supported by preliminary findings. 2) Because substrate unfolding is a prerequisite to degradation mediated by ATP-dependent proteases, using these new methods, we will elucidate how the perturbation of GlpG structure caused by the force generated by FtsH-mediated ATP hydrolysis drives its unfolding, including cooperativity mechanisms, and identify the conformation of the resultant unfolded state that is targeted for degradation. 3) To define the quantitative relationship between folding and degradation rates of GlpG, including the influences of conformational stability and hydrophobicity, by analyzing degradation in a series of variants. Outcomes of this research will provide quantitative methods for analyzing membrane protein folding, will advance fundamental understanding and current concepts of cellular quality control systems for membrane proteins based on their folding properties, and will inform progress towards new therapies for diseases caused by aberrant protein- folding.

Public Health Relevance

Imbalances between intracellular protein folding and degradation cause debilitating and fatal human diseases, via excessive protein degradation (e.g. cystic fibrosis, retinitis pigmentosa), or toxic accumulation of misfolded proteins that overwhelm cellular degradation capacity (e.g. Alzheimer's disease). The key knowledge gap concerns the mechanisms and quantitative relationships of normal and aberrant folding and degradation of membrane proteins, which are physiologically essential but difficult to analyze in their native lipid environment. We will elucidate these principles using novel steric-trapping molecular tools we have developed, which will advance basic understanding of cellular protein quality-control, and may be translatable to new drug- screening methods to identify small-molecule agents to treat such diseases, by improving stability of disease-relevant membrane proteins.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Biochemistry and Biophysics of Membranes Study Section (BBM)
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Ainsztein, Alexandra M
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Michigan State University
Schools of Arts and Sciences
East Lansing
United States
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Yang, Yiqing; Guo, Ruiqiong; Gaffney, Kristen et al. (2018) Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-Dependent Protease FtsH. J Am Chem Soc 140:4656-4665
Shen, Xiaojing; Kou, Qiang; Guo, Ruiqiong et al. (2018) Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry. Anal Chem 90:10095-10099
Guo, Ruiqiong; Gaffney, Kristen; Yang, Zhongyu et al. (2016) Steric trapping reveals a cooperativity network in the intramembrane protease GlpG. Nat Chem Biol 12:353-360