The mitochondrial inner membrane is the site of essential cellular functions such as oxidative phosphorylation, phospholipid metabolism, and the regulation of apoptosis. The inner membrane is under constant assault from reactive oxygen species, inevitable by-products of respiration. To limit the effects of this damage and to maintain proteostasis throughout mitochondria, AAA+ proteases harness the energy of ATP to recognize, unfold and degrade protein substrates both from within and surrounding the inner membrane. AAA+ proteases assemble as hexamers to form an internal proteolytic chamber into which substrates are forcibly translocated by an ATPase module. The ATPase active site is created by interactions from adjacent subunits such that oligomerization is a requirement for activity. The mitochondrial AAA+ proteases YME1L and AFG3L2 are largely soluble enzymes that are anchored in the inner membrane and represent a significantly understudied class of proteolytic system that operate at the membrane interface. In humans, dysfunction of these proteases has been linked to the development of severe neurodegenerative disorders such as spinocerebellar ataxia. Understanding the molecular mechanisms of these important enzymes has been hampered by the difficulty in studying membrane-anchored enzymes in vitro. I have developed a novel approach to assemble previously membrane-constrained hexameric proteases in a soluble, active form. This breakthrough allows for the application of established solution biochemical and biophysical techniques to the study of proteostasis at the mitochondrial inner membrane for the first time.
The first aim of the proposal is to define how substrate proteins are selected for degradation among the myriad proteins housed in the inner membrane. Both model proteins and known physiological substrates will be used to determine what features are necessary and sufficient to drive degradation.
The second aim i s analyze the coordination of ATP hydrolysis and the production of pulling forces to understand how these molecular machines are capable of extracting substrates from within the inner membrane. Finally, the ability to produce large quantities of soluble active protease will be leveraged to determine crystal structures of the proteases in their active state, and in complex with nucleotide and protein substrates. Together, these experiments will form the first rigorous mechanistic analysis of the mitochondrial AAA+ proteases and provide foundational knowledge to aid the development of small molecule modulators as future therapeutics.

Public Health Relevance

Mitochondria are the major energy producing organelles in eukaryotic cells and their dysfunction is implicated in many human diseases. AAA+ proteases help maintain mitochondrial function by removing damaged and/or unneeded protein components in a timely fashion. This grant seeks to understand the molecular details of AAA+ protease activity in mitochondria and lay the foundation for the development of new therapeutics.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM115898-03
Application #
9300980
Study Section
Membrane Biology and Protein Processing Study Section (MBPP)
Program Officer
Barski, Oleg
Project Start
2015-07-15
Project End
2020-06-30
Budget Start
2017-07-01
Budget End
2018-06-30
Support Year
3
Fiscal Year
2017
Total Cost
Indirect Cost
Name
State University New York Stony Brook
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
804878247
City
Stony Brook
State
NY
Country
United States
Zip Code
11794
Puchades, Cristina; Rampello, Anthony J; Shin, Mia et al. (2017) Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing. Science 358:
Rampello, Anthony J; Glynn, Steven E (2017) Identification of a Degradation Signal Sequence within Substrates of the Mitochondrial i-AAA Protease. J Mol Biol 429:873-885
Glynn, Steven E (2017) Multifunctional Mitochondrial AAA Proteases. Front Mol Biosci 4:34
Glynn, Steven E; Chien, Peter (2016) Sending protein aggregates into a downward spiral. Nat Struct Mol Biol 23:769-70
Shi, Hui; Rampello, Anthony J; Glynn, Steven E (2016) Engineered AAA+ proteases reveal principles of proteolysis at the mitochondrial inner membrane. Nat Commun 7:13301