The integrity of the cellular proteome is critically dependent on an elaborate network of protein quality control machines that both aid in the folding of newly made proteins and allow for the recognition and disposal of terminally misfolded forms. Many diverse human diseases, including familial protein folding diseases, neurodegenerative diseases, diabetes, and cancer, as well as normal aging have been linked to the failure to maintain proper protein homeostasis. Thus defining the mechanism of action of the protein quality control machinery is a major goal in the quest for understanding of health and pathology in all living cells. A common theme to this machinery is the ability to recognize portions of unfolded polypeptide chains, either to facilitate their subsequent folding/refolding or degradation, or to signal in adaptive responses aimed at restoring the balance between supply and demand of the protein folding capacity. Most molecular events in protein quality control work on many diverse substrates and hence possess considerable plasticity in substrate binding. While much progress has been made in structural and functional analysis of individual components of these machines, there are few examples where substrate-bound structures have been determined or where a substrate """"""""recognition code"""""""" has been defined and validated. As such, we are lacking in our understanding of core principles that govern workings of these protein machines. We propose to bridge this gap by focusing on a core set of physiologically critical systems that cover a range of molecular features but share the common requirement of having to balance specificity and plasticity in molecular recognition events. In particular, we wil focus on cytosolic chaperone substrate recognition (using examples of the hsp70, hsp90, and TRIC families of chaperones) and the recognition of unfolded proteins in the lumen of the endoplasmic reticulum (ER) for degradation via the ER-associated degradation pathway (ERAD) and for signaling via the unfolded protein response (UPR).

Public Health Relevance

The proper folding of newly made proteins is very important for every cell. Numerous human diseases, including neurodegenerative diseases, diabetes, and cancer, as well as normal aging are linked to the failure to fold proteins properly. We will determine the structure of cellular machines that recognize misfolded proteins to help them fold or target them for degration. A detailed structural understanding will contribute to the development of new therapies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project--Cooperative Agreements (U01)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-CBB-0 (BP))
Program Officer
Gindhart, Joseph G
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Francisco
Schools of Medicine
San Francisco
United States
Zip Code
Elnatan, Daniel; Agard, David A (2018) Calcium binding to a remote site can replace magnesium as cofactor for mitochondrial Hsp90 (TRAP1) ATPase activity. J Biol Chem 293:13717-13724
Verba, Kliment A; Agard, David A (2017) Protein Expression and Purification of the Hsp90-Cdc37-Cdk4 Kinase Complex from Saccharomyces cerevisiae. Bio Protoc 7:
Elnatan, Daniel; Betegon, Miguel; Liu, Yanxin et al. (2017) Symmetry broken and rebroken during the ATP hydrolysis cycle of the mitochondrial Hsp90 TRAP1. Elife 6:
Liu, Yi-Chang; Fujimori, Danica Galoni?; Weissman, Jonathan S (2016) Htm1p-Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation. Proc Natl Acad Sci U S A 113:E4015-24
Rao, Meera; Okreglak, Voytek; Chio, Un Seng et al. (2016) Multiple selection filters ensure accurate tail-anchored membrane protein targeting. Elife 5:
Verba, Kliment A; Wang, Ray Yu-Ruei; Arakawa, Akihiko et al. (2016) Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase. Science 352:1542-7
Pimentel-Elardo, Sheila M; Sørensen, Dan; Ho, Louis et al. (2015) Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference. ACS Chem Biol 10:2616-23
Shen, Peter S; Park, Joseph; Qin, Yidan et al. (2015) Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. Science 347:75-8
Partridge, James R; Lavery, Laura A; Elnatan, Daniel et al. (2014) A novel N-terminal extension in mitochondrial TRAP1 serves as a thermal regulator of chaperone activity. Elife 3:
Joachimiak, Lukasz A; Walzthoeni, Thomas; Liu, Corey W et al. (2014) The structural basis of substrate recognition by the eukaryotic chaperonin TRiC/CCT. Cell 159:1042-1055

Showing the most recent 10 out of 15 publications