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Nadel CM, Wucherer K, Oehler A, Thwin AC, Basu K, Callahan MD, Southworth DR, Mordes DA, Craik CS, Gestwicki JE. Phosphorylation of a Cleaved Tau Proteoform at a Single Residue Inhibits Binding to the E3 Ubiquitin Ligase, CHIP. bioRxiv 2023:2023.08.16.553575. [PMID: 37645969 PMCID: PMC10462110 DOI: 10.1101/2023.08.16.553575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Microtubule-associated protein tau (MAPT/tau) accumulates in a family of neurodegenerative diseases, including Alzheimer's disease (AD). In disease, tau is aberrantly modified by post-translational modifications (PTMs), including hyper-phosphorylation. However, it is often unclear which of these PTMs contribute to tau's accumulation or what mechanisms might be involved. To explore these questions, we focused on a cleaved proteoform of tau (tauC3), which selectively accumulates in AD and was recently shown to be degraded by its direct binding to the E3 ubiquitin ligase, CHIP. Here, we find that phosphorylation of tauC3 at a single residue, pS416, is sufficient to block its interaction with CHIP. A co-crystal structure of CHIP bound to the C-terminus of tauC3 revealed the mechanism of this clash and allowed design of a mutation (CHIPD134A) that partially restores binding and turnover of pS416 tauC3. We find that pS416 is produced by the known AD-associated kinase, MARK2/Par-1b, providing a potential link to disease. In further support of this idea, an antibody against pS416 co-localizes with tauC3 in degenerative neurons within the hippocampus of AD patients. Together, these studies suggest a discrete molecular mechanism for how phosphorylation at a specific site contributes to accumulation of an important tau proteoform.
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Affiliation(s)
- Cory M Nadel
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Kristin Wucherer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | - Abby Oehler
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Aye C Thwin
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Koli Basu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | - Matthew D Callahan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Daniel R Southworth
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Daniel A Mordes
- Department of Pathology, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158
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Nadel CM, Thwin AC, Callahan M, Lee K, Connelly E, Craik CS, Southworth DR, Gestwicki JE. The E3 Ubiquitin Ligase, CHIP/STUB1, Inhibits Aggregation of Phosphorylated Proteoforms of Microtubule-associated Protein Tau (MAPT). J Mol Biol 2023; 435:168026. [PMID: 37330289 PMCID: PMC10491737 DOI: 10.1016/j.jmb.2023.168026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Hyper-phosphorylated tau accumulates as insoluble fibrils in Alzheimer's disease (AD) and related dementias. The strong correlation between phosphorylated tau and disease has led to an interest in understanding how cellular factors discriminate it from normal tau. Here, we screen a panel of chaperones containing tetratricopeptide repeat (TPR) domains to identify those that might selectively interact with phosphorylated tau. We find that the E3 ubiquitin ligase, CHIP/STUB1, binds 10-fold more strongly to phosphorylated tau than unmodified tau. The presence of even sub-stoichiometric concentrations of CHIP strongly suppresses aggregation and seeding of phosphorylated tau. We also find that CHIP promotes rapid ubiquitination of phosphorylated tau, but not unmodified tau, in vitro. Binding to phosphorylated tau requires CHIP's TPR domain, but the binding mode is partially distinct from the canonical one. In cells, CHIP restricts seeding by phosphorylated tau, suggesting that it could be an important barrier in cell-to-cell spreading. Together, these findings show that CHIP recognizes a phosphorylation-dependent degron on tau, establishing a pathway for regulating the solubility and turnover of this pathological proteoform.
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Affiliation(s)
- Cory M Nadel
- Departments of Pharmaceutical Chemistry and University of California San Francisco, San Francisco, CA 94508, USA; Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94508, USA
| | - Aye C Thwin
- Biochemistry & Biophysics and the University of California San Francisco, San Francisco, CA 94508, USA; Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94508, USA
| | - Matthew Callahan
- Departments of Pharmaceutical Chemistry and University of California San Francisco, San Francisco, CA 94508, USA; Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94508, USA
| | - Kanghyun Lee
- Biochemistry & Biophysics and the University of California San Francisco, San Francisco, CA 94508, USA; Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94508, USA
| | - Emily Connelly
- Departments of Pharmaceutical Chemistry and University of California San Francisco, San Francisco, CA 94508, USA
| | - Charles S Craik
- Departments of Pharmaceutical Chemistry and University of California San Francisco, San Francisco, CA 94508, USA
| | - Daniel R Southworth
- Biochemistry & Biophysics and the University of California San Francisco, San Francisco, CA 94508, USA; Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94508, USA.
| | - Jason E Gestwicki
- Departments of Pharmaceutical Chemistry and University of California San Francisco, San Francisco, CA 94508, USA; Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94508, USA.
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Nadel CM, Gestwicki JE. Intersecting PTMS regulate clearance of pathogenic tau by the CHIP ubiquitin ligase. Alzheimers Dement 2022. [DOI: 10.1002/alz.062036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Cory M Nadel
- University of California, San Francisco SAN FRANCISCO CA USA
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Johnson OT, Nadel CM, Carroll EC, Arhar T, Gestwicki JE. Two distinct classes of cochaperones compete for the EEVD motif in heat shock protein 70 to tune its chaperone activities. J Biol Chem 2022; 298:101697. [PMID: 35148989 PMCID: PMC8913300 DOI: 10.1016/j.jbc.2022.101697] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/30/2022] Open
Abstract
Chaperones of the heat shock protein 70 (Hsp70) family engage in protein-protein interactions with many cochaperones. One "hotspot" for cochaperone binding is the EEVD motif, found at the extreme C terminus of cytoplasmic Hsp70s. This motif is known to bind tetratricopeptide repeat domain cochaperones, such as the E3 ubiquitin ligase CHIP. In addition, the EEVD motif also interacts with a structurally distinct domain that is present in class B J-domain proteins, such as DnaJB4. These observations suggest that CHIP and DnaJB4 might compete for binding to Hsp70's EEVD motif; however, the molecular determinants of such competition are not clear. Using a collection of EEVD-derived peptides, including mutations and truncations, we explored which residues are critical for binding to both CHIP and DnaJB4. These results revealed that some features, such as the C-terminal carboxylate, are important for both interactions. However, CHIP and DnaJB4 also had unique preferences, especially at the isoleucine position immediately adjacent to the EEVD. Finally, we show that competition between these cochaperones is important in vitro, as DnaJB4 limits the ubiquitination activity of the Hsp70-CHIP complex, whereas CHIP suppresses the client refolding activity of the Hsp70-DnaJB4 complex. Together, these data suggest that the EEVD motif has evolved to support diverse protein-protein interactions, such that competition between cochaperones may help guide whether Hsp70-bound proteins are folded or degraded.
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Affiliation(s)
- Oleta T Johnson
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA
| | - Cory M Nadel
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA
| | - Emma C Carroll
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA
| | - Taylor Arhar
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA; Department of Chemistry, Beloit College, Beloit, Wisconsin, USA.
| | - Jason E Gestwicki
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.
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Arhar T, Shkedi A, Nadel CM, Gestwicki JE. The interactions of molecular chaperones with client proteins: why are they so weak? J Biol Chem 2021; 297:101282. [PMID: 34624315 PMCID: PMC8567204 DOI: 10.1016/j.jbc.2021.101282] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/30/2022] Open
Abstract
The major classes of molecular chaperones have highly variable sequences, sizes, and shapes, yet they all bind to unfolded proteins, limit their aggregation, and assist in their folding. Despite the central importance of this process to protein homeostasis, it has not been clear exactly how chaperones guide this process or whether the diverse families of chaperones use similar mechanisms. For the first time, recent advances in NMR spectroscopy have enabled detailed studies of how unfolded, "client" proteins interact with both ATP-dependent and ATP-independent classes of chaperones. Here, we review examples from four distinct chaperones, Spy, Trigger Factor, DnaK, and HscA-HscB, highlighting the similarities and differences between their mechanisms. One striking similarity is that the chaperones all bind weakly to their clients, such that the chaperone-client interactions are readily outcompeted by stronger, intra- and intermolecular contacts in the folded state. Thus, the relatively weak affinity of these interactions seems to provide directionality to the folding process. However, there are also key differences, especially in the details of how the chaperones release clients and how ATP cycling impacts that process. For example, Spy releases clients in a largely folded state, while clients seem to be unfolded upon release from Trigger Factor or DnaK. Together, these studies are beginning to uncover the similarities and differences in how chaperones use weak interactions to guide protein folding.
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Affiliation(s)
- Taylor Arhar
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Arielle Shkedi
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Cory M Nadel
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA.
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Nadel CM, Ran X, Gestwicki JE. Luminescence complementation assay for measurement of binding to protein C-termini in live cells. Anal Biochem 2020; 611:113947. [PMID: 32918866 DOI: 10.1016/j.ab.2020.113947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions (PPIs) involving the extreme C-terminus serve important scaffolding and regulatory functions. Here, we leveraged NanoBiT technology to build a luminescent complementation assay for use in studying this subcategory of PPI. As a model system, we fused one component of NanoBiT to the disordered C-terminus of heat shock protein (Hsp70) and the other to its binding partner, the tetratricopeptide repeat (TPR) domain of CHIP/STUB1. We found that HEK293 cells that stably express these chimeras under a doxycycline promoter produced a robust luminescence signal. This signal was sensitive to mutations and it was further tuned by the expression of competitive C-termini. Using this system, we identified a promising, membrane permeable inhibitor of the Hsp70-CHIP interaction. More broadly, we anticipate that NanoBiT is well-suited for studying PPIs that involve C-termini.
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Affiliation(s)
- Cory M Nadel
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Xu Ran
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA, 94158, USA.
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Groves B, Khakhar A, Nadel CM, Gardner RG, Seelig G. Rewiring MAP kinases in Saccharomyces cerevisiae to regulate novel targets through ubiquitination. eLife 2016; 5. [PMID: 27525484 PMCID: PMC5019841 DOI: 10.7554/elife.15200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/14/2016] [Indexed: 12/18/2022] Open
Abstract
Evolution has often copied and repurposed the mitogen-activated protein kinase (MAPK) signaling module. Understanding how connections form during evolution, in disease and across individuals requires knowledge of the basic tenets that govern kinase-substrate interactions. We identify criteria sufficient for establishing regulatory links between a MAPK and a non-native substrate. The yeast MAPK Fus3 and human MAPK ERK2 can be functionally redirected if only two conditions are met: the kinase and substrate contain matching interaction domains and the substrate includes a phospho-motif that can be phosphorylated by the kinase and recruit a downstream effector. We used a panel of interaction domains and phosphorylation-activated degradation motifs to demonstrate modular and scalable retargeting. We applied our approach to reshape the signaling behavior of an existing kinase pathway. Together, our results demonstrate that a MAPK can be largely defined by its interaction domains and compatible phospho-motifs and provide insight into how MAPK-substrate connections form. DOI:http://dx.doi.org/10.7554/eLife.15200.001 Nature has evolved a number of ways to link signals from a cell’s environment, like the concentration of a hormone, to the behavior of that cell. These new connections often form by reusing certain common signaling components, such as mitogen-activated protein kinases. These enzymes – referred to as MAPKs for short – are activated by specific signals and alter the activity of target proteins in the cell by adding a phosphate group to them: a process called phosphorylation. These connections thus dictate how cells respond to their environments – and consequently, disruptions to the connections are a common source of disease. Groves, Khakhar et al. set out to understand how connections can be made between a MAPK and a new target protein to gain insights into how these links emerge through evolution and how they might break in disease. Their approach focused on one of the ways that phosphorylation can alter the activity of a target protein: marking it for degradation. Experiments with budding yeast showed that a MAPK could only achieve this if two conditions are met. First, the target protein and kinase need to bind to each other. Second, the target needs to contain a site that when phosphorylated is subsequently recognized by the cell’s protein degradation machinery. By engineering proteins so that they fulfilled these two criteria, Groves, Khakhar et al. created new connections between a yeast MAPK called Fus3 or a human MAPK called ERK2 and a variety of targets. The results showed that the parts of the proteins involved in the interaction step could be completely separate from the parts that are involved in the phosphorylation step. This suggests that connections between kinases and their targets can be rewired simple by mixing together parts of other existing proteins. Finally, Groves, Khakhar et al. confirmed that engineered connections between kinases and targets could predictably change how yeast cells responded to a hormone that normally controls the yeast’s reproductive cycle. Together these results bring us one step closer to understanding how cells assemble the signaling pathways that they use to process information. However further work is needed to see if these findings can be generalized to other signaling components, and if so, to explore if new connections can be built to yield more complicated cellular behaviors. DOI:http://dx.doi.org/10.7554/eLife.15200.002
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Affiliation(s)
- Benjamin Groves
- Department of Electrical Engineering, University of Washington, Seattle, United States
| | - Arjun Khakhar
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Cory M Nadel
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Richard G Gardner
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, United States.,Department of Computer Science and Engineering, University of Washington, Seattle, United States
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Oeser ML, Amen T, Nadel CM, Bradley AI, Reed BJ, Jones RD, Gopalan J, Kaganovich D, Gardner RG. Dynamic Sumoylation of a Conserved Transcription Corepressor Prevents Persistent Inclusion Formation during Hyperosmotic Stress. PLoS Genet 2016; 12:e1005809. [PMID: 26800527 PMCID: PMC4723248 DOI: 10.1371/journal.pgen.1005809] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 12/22/2015] [Indexed: 11/29/2022] Open
Abstract
Cells are often exposed to physical or chemical stresses that can damage the structures of essential biomolecules. Stress-induced cellular damage can become deleterious if not managed appropriately. Rapid and adaptive responses to stresses are therefore crucial for cell survival. In eukaryotic cells, different stresses trigger post-translational modification of proteins with the small ubiquitin-like modifier SUMO. However, the specific regulatory roles of sumoylation in each stress response are not well understood. Here, we examined the sumoylation events that occur in budding yeast after exposure to hyperosmotic stress. We discovered by proteomic and biochemical analyses that hyperosmotic stress incurs the rapid and transient sumoylation of Cyc8 and Tup1, which together form a conserved transcription corepressor complex that regulates hundreds of genes. Gene expression and cell biological analyses revealed that sumoylation of each protein directs distinct outcomes. In particular, we discovered that Cyc8 sumoylation prevents the persistence of hyperosmotic stress-induced Cyc8-Tup1 inclusions, which involves a glutamine-rich prion domain in Cyc8. We propose that sumoylation protects against persistent inclusion formation during hyperosmotic stress, allowing optimal transcriptional function of the Cyc8-Tup1 complex. Cells have evolved complex stress responses to cope with environmental challenges that could otherwise inflict severe damage on the molecules essential for life. Stress responses must ameliorate the immediate damage caused by stress exposure and also adjust metabolic capacity, gene expression output, and other cellular functions to protect against further damage that could be incurred by prolonged exposure to stress. Posttranslational protein modifications are a major means by which cells respond to changing environmental conditions. These modifications can alter the function, localization, and molecular interactions of their target proteins. In addition, evidence is emerging that some posttranslational modifications may also change the physical characteristics of target proteins. In this study, we present evidence that during hyperosmotic stress, a condition known to induce protein misfolding, cells rapidly but transiently use the small ubiquitin-modifier SUMO to protect against persistent inclusion formation of a conserved transcriptional repressor complex. We propose that this rapid protective action via posttranslational modification enables optimal gene regulation during the cellular response to hyperosmotic stress.
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Affiliation(s)
- Michelle L. Oeser
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Pharmacology, University of Washington, Seattle, Washington, United States of America
| | - Triana Amen
- Alexander Grass Center for Bioengineering, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Cory M. Nadel
- Department of Pharmacology, University of Washington, Seattle, Washington, United States of America
| | - Amanda I. Bradley
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Benjamin J. Reed
- Department of Pharmacology, University of Washington, Seattle, Washington, United States of America
| | - Ramon D. Jones
- Department of Pharmacology, University of Washington, Seattle, Washington, United States of America
| | - Janani Gopalan
- Department of Pharmacology, University of Washington, Seattle, Washington, United States of America
| | - Daniel Kaganovich
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Richard G. Gardner
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Pharmacology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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