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Sharma PK, Weng JH, Manschwetus JT, Wu J, Ma W, Herberg FW, Taylor SS. Role of the leucine-rich repeat protein kinase 2 C-terminal tail in domain cross-talk. Biochem J 2024; 481:313-327. [PMID: 38305364 PMCID: PMC10903466 DOI: 10.1042/bcj20230477] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/03/2024]
Abstract
Leucine-rich repeat protein kinase 2 (LRRK2) is a multi-domain protein encompassing two of biology's most critical molecular switches, a kinase and a GTPase, and mutations in LRRK2 are key players in the pathogenesis of Parkinson's disease (PD). The availability of multiple structures (full-length and truncated) has opened doors to explore intra-domain cross-talk in LRRK2. A helix extending from the WD40 domain and stably docking onto the kinase domain is common in all available structures. This C-terminal (Ct) helix is a hub of phosphorylation and organelle-localization motifs and thus serves as a multi-functional protein : protein interaction module. To examine its intra-domain interactions, we have recombinantly expressed a stable Ct motif (residues 2480-2527) and used peptide arrays to identify specific binding sites. We have identified a potential interaction site between the Ct helix and a loop in the CORB domain (CORB loop) using a combination of Gaussian accelerated molecular dynamics simulations and peptide arrays. This Ct-Motif contains two auto-phosphorylation sites (T2483 and T2524), and T2524 is a 14-3-3 binding site. The Ct helix, CORB loop, and the CORB-kinase linker together form a part of a dynamic 'CAP' that regulates the N-lobe of the kinase domain. We hypothesize that in inactive, full-length LRRK2, the Ct-helix will also mediate interactions with the N-terminal armadillo, ankyrin, and LRR domains (NTDs) and that binding of Rab substrates, PD mutations, or kinase inhibitors will unleash the NTDs.
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Affiliation(s)
- Pallavi Kaila Sharma
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
| | - Jascha T. Manschwetus
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Hessen, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
| | - Wen Ma
- Department of Physics, University of Vermont, Burlington, Vermont
| | - Friedrich W. Herberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Hessen, Germany
| | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
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Weng JH, Aoto PC, Lorenz R, Wu J, Schmidt SH, Manschwetus JT, Kaila-Sharma P, Silletti S, Mathea S, Chatterjee D, Knapp S, Herberg FW, Taylor SS. LRRK2 dynamics analysis identifies allosteric control of the crosstalk between its catalytic domains. PLoS Biol 2022; 20:e3001427. [PMID: 35192607 PMCID: PMC8863276 DOI: 10.1371/journal.pbio.3001427] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 09/11/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
The 2 major molecular switches in biology, kinases and GTPases, are both contained in the Parkinson disease-related leucine-rich repeat kinase 2 (LRRK2). Using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations, we generated a comprehensive dynamic allosteric portrait of the C-terminal domains of LRRK2 (LRRK2RCKW). We identified 2 helices that shield the kinase domain and regulate LRRK2 conformation and function. One helix in COR-B (COR-B Helix) tethers the COR-B domain to the αC helix of the kinase domain and faces its activation loop, while the C-terminal helix (Ct-Helix) extends from the WD40 domain and interacts with both kinase lobes. The Ct-Helix and the N-terminus of the COR-B Helix create a "cap" that regulates the N-lobe of the kinase domain. Our analyses reveal allosteric sites for pharmacological intervention and confirm the kinase domain as the central hub for conformational control.
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Affiliation(s)
- Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Phillip C. Aoto
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Robin Lorenz
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Sven H. Schmidt
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | | | - Pallavi Kaila-Sharma
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Steve Silletti
- Department of Chemistry and Biochemistry, University of California, San Diego, California, United States of America
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Deep Chatterjee
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, California, United States of America
- * E-mail:
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Helton LG, Soliman A, von Zweydorf F, Kentros M, Manschwetus JT, Hall S, Gilsbach B, Ho FY, Athanasopoulos PS, Singh RK, LeClair TJ, Versées W, Raimondi F, Herberg FW, Gloeckner CJ, Rideout H, Kortholt A, Kennedy EJ. Allosteric Inhibition of Parkinson's-Linked LRRK2 by Constrained Peptides. ACS Chem Biol 2021; 16:2326-2338. [PMID: 34496561 DOI: 10.1021/acschembio.1c00487] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Leucine-Rich Repeat Kinase 2 (LRRK2) is a large, multidomain protein with dual kinase and GTPase function that is commonly mutated in both familial and idiopathic Parkinson's Disease (PD). While dimerization of LRRK2 is commonly detected in PD models, it remains unclear whether inhibition of dimerization can regulate catalytic activity and pathogenesis. Here, we show constrained peptides that are cell-penetrant, bind LRRK2, and inhibit LRRK2 activation by downregulating dimerization. We further show that inhibited dimerization decreases kinase activity and inhibits ROS production and PD-linked apoptosis in primary cortical neurons. While many ATP-competitive LRRK2 inhibitors induce toxicity and mislocalization of the protein in cells, these constrained peptides were found to not affect LRRK2 localization. The ability of these peptides to inhibit pathogenic LRRK2 kinase activity suggests that disruption of dimerization may serve as a new allosteric strategy to downregulate PD-related signaling pathways.
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Affiliation(s)
- Leah G. Helton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Ahmed Soliman
- Department of Cell Biochemistry, University of Groningen, 9747 Groningen, The Netherlands
| | - Felix von Zweydorf
- DZNE, German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany
| | - Michalis Kentros
- Center for Clinical, Experimental Surgery, and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Jascha T. Manschwetus
- Department of Biochemistry, Institute for Biology, University of Kassel, 34132, Kassel, Germany
| | - Scotty Hall
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Bernd Gilsbach
- DZNE, German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany
| | - Franz Y. Ho
- Department of Cell Biochemistry, University of Groningen, 9747 Groningen, The Netherlands
| | | | - Ranjan K. Singh
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Timothy J. LeClair
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Francesco Raimondi
- Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, 56126, Pisa, Italy
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, 34132, Kassel, Germany
| | - Christian Johannes Gloeckner
- DZNE, German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany
- Core Facility for Medical Bioanalytics, Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Hardy Rideout
- Center for Clinical, Experimental Surgery, and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, 9747 Groningen, The Netherlands
- Department of Pharmacology, Innovative Technologies Application and Research Center, Suleyman Demirel University, 32260 Isparta, Turkey
| | - Eileen J. Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
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Manschwetus JT, Wallbott M, Fachinger A, Obergruber C, Pautz S, Bertinetti D, Schmidt SH, Herberg FW. Binding of the Human 14-3-3 Isoforms to Distinct Sites in the Leucine-Rich Repeat Kinase 2. Front Neurosci 2020; 14:302. [PMID: 32317922 PMCID: PMC7155755 DOI: 10.3389/fnins.2020.00302] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 02/01/2020] [Accepted: 03/16/2020] [Indexed: 12/25/2022] Open
Abstract
Proteins of the 14-3-3 family are well known modulators of the leucine-rich repeat kinase 2 (LRRK2) regulating kinase activity, cellular localization, and ubiquitylation. Although binding between those proteins has been investigated, a comparative study of all human 14-3-3 isoforms interacting with LRRK2 is lacking so far. In a comprehensive approach, we quantitatively analyzed the interaction between the seven human 14-3-3 isoforms and LRRK2-derived peptides covering both, reported and putative 14-3-3 binding sites. We observed that phosphorylation is an absolute prerequisite for 14-3-3 binding and generated binding patterns of 14-3-3 isoforms to interact with peptides derived from the N-terminal phosphorylation cluster (S910 and S935), the Roc domain (S1444) and the C-terminus. The tested 14-3-3 binding sites in LRRK2 preferentially were recognized by the isoforms γ and η, whereas the isoforms ϵ and especially σ showed the weakest or no binding. Interestingly, the possible pathogenic mutation Q930R in LRRK2 drastically increases binding affinity to a peptide encompassing pS935. We then identified the autophosphorylation site T2524 as a so far not described 14-3-3 binding site at the very C-terminus of LRRK2. Binding affinities of all seven 14-3-3 isoforms were quantified for all three binding regions with pS1444 displaying the highest affinity of all measured singly phosphorylated peptides. The strongest binding was detected for the combined phosphosites S910 and S935, suggesting that avidity effects are important for high affinity interaction between 14-3-3 proteins and LRRK2.
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Affiliation(s)
| | | | | | | | | | | | | | - Friedrich W. Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
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Manschwetus JT, Bendzunas GN, Limaye AJ, Knape MJ, Herberg FW, Kennedy EJ. A Stapled Peptide Mimic of the Pseudosubstrate Inhibitor PKI Inhibits Protein Kinase A. Molecules 2019; 24:molecules24081567. [PMID: 31009996 PMCID: PMC6514771 DOI: 10.3390/molecules24081567] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 11/16/2022] Open
Abstract
Kinases regulate multiple and diverse signaling pathways and misregulation is implicated in a multitude of diseases. Although significant efforts have been put forth to develop kinase-specific inhibitors, specificity remains a challenge. As an alternative to catalytic inhibition, allosteric inhibitors can target areas on the surface of an enzyme, thereby providing additional target diversity. Using cAMP-dependent protein kinase A (PKA) as a model system, we sought to develop a hydrocarbon-stapled peptide targeting the pseudosubstrate domain of the kinase. A library of peptides was designed from a Protein Kinase Inhibitor (PKI), a naturally encoded protein that serves as a pseudosubstrate inhibitor for PKA. The binding properties of these peptide analogs were characterized by fluorescence polarization and surface plasmon resonance, and two compounds were identified with KD values in the 500-600 pM range. In kinase activity assays, both compounds demonstrated inhibition with 25-35 nM IC50 values. They were also found to permeate cells and localize within the cytoplasm and inhibited PKA activity within the cellular environment. To the best of our knowledge, these stapled peptide inhibitors represent some of the highest affinity binders reported to date for hydrocarbon stapled peptides.
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Affiliation(s)
- Jascha T Manschwetus
- Department of Biochemistry, Institute for Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany.
| | - George N Bendzunas
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 240 W. Green St, Athens, GA 30602, USA.
| | - Ameya J Limaye
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 240 W. Green St, Athens, GA 30602, USA.
| | - Matthias J Knape
- Department of Biochemistry, Institute for Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany.
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany.
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 240 W. Green St, Athens, GA 30602, USA.
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