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Chen S, Basiashvili T, Hutchings J, Sanz Murillo M, Villagran Suarez A, Alegrio Louro J, Leschziner AE, Villa E. Cryo-electron tomography reveals the microtubule-bound form of inactive LRRK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599606. [PMID: 38948781 PMCID: PMC11212993 DOI: 10.1101/2024.06.18.599606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Parkinson's Disease (PD) is the second most common neurodegenerative disorder. Mutations in leucine-rich repeat kinase 2 (LRRK2), a multi-domain protein containing both a kinase and a GTPase, are a leading cause of the familial form of PD. Pathogenic LRRK2 mutations increase LRRK2 kinase activity. While the bulk of LRRK2 is found in the cytosol, the protein associates with membranes where its Rab GTPase substrates are found, and under certain conditions, with microtubules. Integrative structural studies using single-particle cryo-electron microscopy (cryo-EM) and in situ cryo-electron tomography (cryo-ET) have revealed the architecture of microtubule-associated LRRK2 filaments, and that formation of these filaments requires LRRK2's kinase to be in the active-like conformation. However, whether LRRK2 can interact with and form filaments on microtubules in its autoinhibited state, where the kinase domain is in the inactive conformation and the N-terminal LRR domain covers the kinase active site, was not known. Using cryo-ET, we show that full-length LRRK2 can oligomerize on microtubules in its autoinhibited state. Both WT-LRRK2 and PD-linked LRRK2 mutants formed filaments on microtubules. While these filaments are stabilized by the same interfaces seen in the active-LRRK2 filaments, we observed a new interface involving the N-terminal repeats that were disordered in the active-LRRK2 filaments. The helical parameters of the autoinhibited-LRRK2 filaments are different from those reported for the active-LRRK2 filaments. Finally, the autoinhibited-LRRK2 filaments are shorter and less regular, suggesting they are less stable.
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2
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Keeney MT, Hoffman EK, Weir J, Wagner WG, Rocha EM, Castro S, Farmer K, Fazzari M, Di Maio R, Konradi A, Hastings TG, Pintchovski SA, Shrader WD, Greenamyre JT. 15-Lipoxygenase-Mediated Lipid Peroxidation Regulates LRRK2 Kinase Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598654. [PMID: 38915558 PMCID: PMC11195290 DOI: 10.1101/2024.06.12.598654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) that increase its kinase activity are strongly linked to genetic forms of Parkinson's disease (PD). However, the regulation of endogenous wild-type (WT) LRRK2 kinase activity remains poorly understood, despite its frequent elevation in idiopathic PD (iPD) patients. Various stressors such as mitochondrial dysfunction, lysosomal dyshomeostasis, or vesicle trafficking deficits can activate WT LRRK2 kinase, but the specific molecular mechanisms are not fully understood. We found that the production of 4-hydroxynonenal (4-HNE), a lipid hydroperoxidation end-product, is a common biochemical response to these diverse stimuli. 4-HNE forms post-translational adducts with Cys2024 and Cys2025 in the kinase activation loop of WT LRRK2, significantly increasing its kinase activity. Additionally, we discovered that the 4-HNE responsible for regulating LRRK2 is generated by the action of 15-lipoxygenase (15-LO), making 15-LO an upstream regulator of the pathogenic hyperactivation of LRRK2 kinase activity. Pharmacological inhibition or genetic ablation of 15-LO prevents 4-HNE post-translational modification of LRRK2 kinase and its subsequent pathogenic hyperactivation. Therefore, 15-LO inhibitors, or methods to lower 4-HNE levels, or the targeting of Cys2024/2025 could provide new therapeutic strategies to modulate LRRK2 kinase activity and treat PD.
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Trilling CR, Weng JH, Sharma PK, Nolte V, Wu J, Ma W, Boassa D, Taylor SS, Herberg FW. RedOx regulation of LRRK2 kinase activity by active site cysteines. NPJ Parkinsons Dis 2024; 10:75. [PMID: 38570484 PMCID: PMC10991482 DOI: 10.1038/s41531-024-00683-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Mutations of the human leucine-rich repeat kinase 2 (LRRK2) have been associated with both, idiopathic and familial Parkinson's disease (PD). Most of these pathogenic mutations are located in the kinase domain (KD) or GTPase domain of LRRK2. In this study we describe a mechanism in which protein kinase activity can be modulated by reversible oxidation or reduction, involving a unique pair of adjacent cysteines, the "CC" motif. Among all human protein kinases, only LRRK2 contains this "CC" motif (C2024 and C2025) in the Activation Segment (AS) of the kinase domain. In an approach combining site-directed mutagenesis, biochemical analyses, cell-based assays, and Gaussian accelerated Molecular Dynamics (GaMD) simulations we could attribute a role for each of those cysteines. We employed reducing and oxidizing agents with potential clinical relevance to investigate effects on kinase activity and microtubule docking. We find that each cysteine gives a distinct contribution: the first cysteine, C2024, is essential for LRRK2 protein kinase activity, while the adjacent cysteine, C2025, contributes significantly to redox sensitivity. Implementing thiolates (R-S-) in GaMD simulations allowed us to analyse how each of the cysteines in the "CC" motif interacts with its surrounding residues depending on its oxidation state. From our studies we conclude that oxidizing agents can downregulate kinase activity of hyperactive LRRK2 PD mutations and may provide promising tools for therapeutic strategies.
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Affiliation(s)
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, CA, USA
| | | | - Viktoria Nolte
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Wen Ma
- Department of Physics, University of Vermont, Burlington, VT, USA
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA, USA
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
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4
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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] [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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Zhu H, Tonelli F, Turk M, Prescott A, Alessi DR, Sun J. Rab29-dependent asymmetrical activation of leucine-rich repeat kinase 2. Science 2023; 382:1404-1411. [PMID: 38127736 PMCID: PMC10786121 DOI: 10.1126/science.adi9926] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Gain-of-function mutations in LRRK2, which encodes the leucine-rich repeat kinase 2 (LRRK2), are the most common genetic cause of late-onset Parkinson's disease. LRRK2 is recruited to membrane organelles and activated by Rab29, a Rab guanosine triphosphatase encoded in the PARK16 locus. We present cryo-electron microscopy structures of Rab29-LRRK2 complexes in three oligomeric states, providing key snapshots during LRRK2 recruitment and activation. Rab29 induces an unexpected tetrameric assembly of LRRK2, formed by two kinase-active central protomers and two kinase-inactive peripheral protomers. The central protomers resemble the active-like state trapped by the type I kinase inhibitor DNL201, a compound that underwent a phase 1 clinical trial. Our work reveals the structural mechanism of LRRK2 spatial regulation and provides insights into LRRK2 inhibitor design for Parkinson's disease treatment.
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Affiliation(s)
- Hanwen Zhu
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Martin Turk
- Cryo-EM and Tomography Center, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alan Prescott
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ji Sun
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Cao R, Chen C, Wen J, Zhao W, Zhang C, Sun L, Yuan L, Wu C, Shan L, Xi M, Sun H. Recent advances in targeting leucine-rich repeat kinase 2 as a potential strategy for the treatment of Parkinson's disease. Bioorg Chem 2023; 141:106906. [PMID: 37837728 DOI: 10.1016/j.bioorg.2023.106906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/24/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. Several single gene mutations involved in PD have been identified such as leucine-rich repeat kinase 2 (LRRK2), the most common cause of sporadic and familial PD. Its mutations have attracted much attention to therapeutically targeting this kinase. To date, many compounds including small chemical molecules with diverse scaffolds and RNA agents have been developed with significant amelioration in preclinical PD models. Currently, five candidates, DNL201, DNL151, WXWH0226, NEU-723 and BIIB094, have advanced to clinical trials for PD treatment. In this review, we describe the structure, pathogenic mutations and the mechanism of LRRK2, and summarize the development of LRRK2 inhibitors in preclinical and clinical studies, trying to provide an insight into targeting LRRK2 for PD intervention in future.
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Affiliation(s)
- Ruiwei Cao
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China; Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Caiping Chen
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China; Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Jing Wen
- Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Weihe Zhao
- Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | | | - Longhui Sun
- Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Liyan Yuan
- Zhejiang Medicine Co. Ltd., Shaoxing 312500, China
| | - Chunlei Wu
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, China
| | - Lei Shan
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China
| | - Meiyang Xi
- Zhejiang Engineering Research Center of Fat-soluble Vitamin, Shaoxing University, Shaoxing 312000, China; College of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, China.
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
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Pajarillo E, Kim S, Digman A, Dutton M, Son DS, Aschner M, Lee E. The role of microglial LRRK2 kinase in manganese-induced inflammatory neurotoxicity via NLRP3 inflammasome and RAB10-mediated autophagy dysfunction. J Biol Chem 2023; 299:104879. [PMID: 37269951 PMCID: PMC10331485 DOI: 10.1016/j.jbc.2023.104879] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/12/2023] [Accepted: 05/20/2023] [Indexed: 06/05/2023] Open
Abstract
Chronic manganese (Mn) exposure can lead to manganism, a neurological disorder sharing common symptoms with Parkinson's disease (PD). Studies have shown that Mn can increase the expression and activity of leucine-rich repeat kinase 2 (LRRK2), leading to inflammation and toxicity in microglia. LRRK2 G2019S mutation also elevates LRRK2 kinase activity. Thus, we tested if Mn-increased microglial LRRK2 kinase is responsible for Mn-induced toxicity, and exacerbated by G2019S mutation, using WT and LRRK2 G2019S knock-in mice and BV2 microglia. Mn (30 mg/kg, nostril instillation, daily for 3 weeks) caused motor deficits, cognitive impairments, and dopaminergic dysfunction in WT mice, which were exacerbated in G2019S mice. Mn induced proapoptotic Bax, NLRP3 inflammasome, IL-1β, and TNF-α in the striatum and midbrain of WT mice, and these effects were more pronounced in G2019S mice. BV2 microglia were transfected with human LRRK2 WT or G2019S, followed by Mn (250 μM) exposure to better characterize its mechanistic action. Mn increased TNF-α, IL-1β, and NLRP3 inflammasome activation in BV2 cells expressing WT LRRK2, which was elevated further in G2019S-expressing cells, while pharmacological inhibition of LRRK2 mitigated these effects in both genotypes. Moreover, the media from Mn-treated G2019S-expressing BV2 microglia caused greater toxicity to the cath.a-differentiated (CAD) neuronal cells compared to media from microglia expressing WT. Mn-LRRK2 activated RAB10 which was exacerbated in G2019S. RAB10 played a critical role in LRRK2-mediated Mn toxicity by dysregulating the autophagy-lysosome pathway and NLRP3 inflammasome in microglia. Our novel findings suggest that microglial LRRK2 via RAB10 plays a critical role in Mn-induced neuroinflammation.
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Affiliation(s)
- Edward Pajarillo
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA
| | - Sanghoon Kim
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA
| | - Alexis Digman
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA
| | - Matthew Dutton
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA
| | - Deok-Soo Son
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Eunsook Lee
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, Florida, USA.
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Martinez-Banaclocha MA. Targeting the Cysteine Redox Proteome in Parkinson's Disease: The Role of Glutathione Precursors and Beyond. Antioxidants (Basel) 2023; 12:1373. [PMID: 37507913 PMCID: PMC10376658 DOI: 10.3390/antiox12071373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Encouraging recent data on the molecular pathways underlying aging have identified variants and expansions of genes associated with DNA replication and repair, telomere and stem cell maintenance, regulation of the redox microenvironment, and intercellular communication. In addition, cell rejuvenation requires silencing some transcription factors and the activation of pluripotency, indicating that hidden molecular networks must integrate and synchronize all these cellular mechanisms. Therefore, in addition to gene sequence expansions and variations associated with senescence, the optimization of transcriptional regulation and protein crosstalk is essential. The protein cysteinome is crucial in cellular regulation and plays unexpected roles in the aging of complex organisms, which show cumulative somatic mutations, telomere attrition, epigenetic modifications, and oxidative dysregulation, culminating in cellular senescence. The cysteine thiol groups are highly redox-active, allowing high functional versatility as structural disulfides, redox-active disulfides, active-site nucleophiles, proton donors, and metal ligands to participate in multiple regulatory sites in proteins. Also, antioxidant systems control diverse cellular functions, including the transcription machinery, which partially depends on the catalytically active cysteines that can reduce disulfide bonds in numerous target proteins, driving their biological integration. Since we have previously proposed a fundamental role of cysteine-mediated redox deregulation in neurodegeneration, we suggest that cellular rejuvenation of the cysteine redox proteome using GSH precursors, like N-acetyl-cysteine, is an underestimated multitarget therapeutic approach that would be particularly beneficial in Parkinson's disease.
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9
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Weng JH, Trilling CR, Kaila Sharma P, Störmer E, Wu J, Herberg FW, Taylor SS. Novel LRR-ROC Motif That Links the N- and C-terminal Domains in LRRK2 Undergoes an Order-Disorder Transition Upon Activation. J Mol Biol 2023; 435:167999. [PMID: 36764356 DOI: 10.1016/j.jmb.2023.167999] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Mutations in LRRK2, a large multi-domain protein kinase, create risk factors for Parkinson's Disease (PD). LRRK2 has seven well-folded domains that include three N-terminal scaffold domains (NtDs) and four C-terminal domains (CtDs). In full-length inactive LRRK2 there is an additional well-folded motif, the LRR-ROC Linker, that lies between the NtDs and the CtDs. This motif, which is stabilized by hydrophobic residues in the LRR and ROC/COR-A domains, is anchored to the C-Lobe of the kinase domain. The LRR-ROC Linker becomes disordered when the NtDs are unleashed from the CtDs following activation by Rab29 or by various PD mutations. A key residue within the LRR-ROC Linker, W1295, sterically blocks access of substrate proteins. The W1295A mutant blocks cis-autophosphorylation of S1292 and reduces phosphorylation of heterologous Rab substrates. GaMD simulations show that the LRR-Linker motif, P + 1 loop and the inhibitory helix in the DYGψ motif are very stable. Finally, in full-length inactive LRRK2 ATP is bound to the kinase domain and GDP:Mg to the GTPase/ROC domain. The fundamentally different mechanisms for binding nucleotide (G-Loop vs P-Loop) are captured by these GaMD simulations. In this model, where ATP binds with low affinity (μM range) to N-Lobe capping residues, the known auto-phosphorylation sites are located in the space that is sampled by the flexible phosphates thus providing a potential mechanism for cis-autophosphorylation.
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Affiliation(s)
- Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, USA
| | | | | | - Eliza Störmer
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, USA
| | | | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, USA; Department of Chemistry and Biochemistry, University of California, San Diego, USA
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Weng JH, Ma W, Wu J, Sharma PK, Silletti S, McCammon JA, Taylor S. Capturing Differences in the Regulation of LRRK2 Dynamics and Conformational States by Small Molecule Kinase Inhibitors. ACS Chem Biol 2023; 18:810-821. [PMID: 37043829 PMCID: PMC10127209 DOI: 10.1021/acschembio.2c00868] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023]
Abstract
Mutations in the human leucine rich repeat protein kinase-2 (LRRK2) create risk factors for Parkinson's disease, and pathological functions of LRRK2 are often correlated with aberrant kinase activity. Past research has focused on developing selective LRRK2 kinase inhibitors. In this study, we combined enhanced sampling simulations with HDX-MS to characterize the inhibitor-induced dynamic changes and the allosteric communications within the C-terminal domains of LRRK2, LRRK2RCKW. We find that the binding of MLi-2 (a type I kinase inhibitor) stabilizes a closed kinase conformation and reduces the global dynamics of LRRK2RCKW, leading to a more compact LRRK2RCKW structure. In contrast, the binding of Rebastinib (a type II kinase inhibitor) stabilizes an open kinase conformation, which promotes a more extended LRRK2RCKW structure. By probing the distinct effects of the type I and type II inhibitors, key interdomain interactions are found to regulate the communication between the kinase domain and the GTPase domain. The intermediate states revealed in our simulations facilitate the efforts toward in silico design of allosteric modulators that control LRRK2 conformations and potentially mediate the oligomeric states of LRRK2 and its interactions with other proteins.
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Affiliation(s)
- Jui-Hung Weng
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Wen Ma
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - Jian Wu
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Pallavi Kaila Sharma
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Steve Silletti
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - J. Andrew McCammon
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - Susan Taylor
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
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11
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Di Maio R, Keeney MT, Cechova V, Mortimer A, Sekandari A, Rowart P, Greenamyre JT, Freeman BA, Fazzari M. Neuroprotective actions of a fatty acid nitroalkene in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:55. [PMID: 37029127 PMCID: PMC10082007 DOI: 10.1038/s41531-023-00502-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
To date there are no therapeutic strategies that limit the progression of Parkinson's disease (PD). The mechanisms underlying PD-related nigrostriatal neurodegeneration remain incompletely understood, with multiple factors modulating the course of PD pathogenesis. This includes Nrf2-dependent gene expression, oxidative stress, α-synuclein pathology, mitochondrial dysfunction, and neuroinflammation. In vitro and sub-acute in vivo rotenone rat models of PD were used to evaluate the neuroprotective potential of a clinically-safe, multi-target metabolic and inflammatory modulator, the electrophilic fatty acid nitroalkene 10-nitro-oleic acid (10-NO2-OA). In N27-A dopaminergic cells and in the substantia nigra pars compacta of rats, 10-NO2-OA activated Nrf2-regulated gene expression and inhibited NOX2 and LRRK2 hyperactivation, oxidative stress, microglial activation, α-synuclein modification, and downstream mitochondrial import impairment. These data reveal broad neuroprotective actions of 10-NO2-OA in a sub-acute model of PD and motivate more chronic studies in rodents and primates.
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Affiliation(s)
- Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases, Pittsburgh, PA, 15213, USA.
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
| | - Matthew T Keeney
- Pittsburgh Institute for Neurodegenerative Diseases, Pittsburgh, PA, 15213, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA, 15261, USA
| | - Veronika Cechova
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA, 15261, USA
| | - Amanda Mortimer
- Pittsburgh Institute for Neurodegenerative Diseases, Pittsburgh, PA, 15213, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ahssan Sekandari
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA, 15261, USA
| | - Pascal Rowart
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA, 15261, USA
| | - J Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases, Pittsburgh, PA, 15213, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Bruce A Freeman
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA, 15261, USA
| | - Marco Fazzari
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA, 15261, USA.
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12
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Pajarillo E, Kim SH, Digman A, Dutton M, Son DS, Aschner M, Lee E. The role of microglial LRRK2 in manganese-induced inflammatory neurotoxicity via NLRP3 inflammasome and RAB10-mediated autophagy dysfunction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535418. [PMID: 37066140 PMCID: PMC10103982 DOI: 10.1101/2023.04.03.535418] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Chronic exposure to manganese (Mn) can lead to manganism, a neurological disorder sharing common symptoms with Parkinson's disease (PD). Studies have shown that Mn can increase the expression and activity of leucine-rich repeat kinase 2 (LRRK2), leading to inflammation and toxicity in microglia. LRRK2 G2019S mutation also elevates LRRK2 kinase activity. Thus, we tested if Mn-increased microglial LRRK2 kinase is responsible for Mn-induced toxicity, and exacerbated by G2019S mutation, using WT and LRRK2 G2019S knock-in mice, and BV2 microglia. Mn (30 mg/kg, nostril instillation, daily for 3 weeks) caused motor deficits, cognitive impairments, and dopaminergic dysfunction in WT mice, which were exacerbated in G2019S mice. Mn induced proapoptotic Bax, NLRP3 inflammasome, IL-1β and TNF-α in the striatum and midbrain of WT mice, and these effects were exacerbated in G2019S mice. BV2 microglia were transfected with human LRRK2 WT or G2019S, followed by Mn (250 μM) exposure to better characterize its mechanistic action. Mn increased TNF-α, IL-1β, and NLRP3 inflammasome activation in BV2 cells expressing WT LRRK2, which was exacerbated in G2019S-expressing cells, while pharmacological inhibition of LRRK2 mitigated these effects in both genotypes. Moreover, the media from Mn-treated BV2 microglia expressing G2019S caused greater toxicity to cath.a-differentiated (CAD) neuronal cells compared to media from microglia expressing WT. Mn-LRRK2 activated RAB10, which was exacerbated in G2019S. RAB10 played a critical role in LRRK2-mediated Mn toxicity by dysregulating the autophagy-lysosome pathway, and NLRP3 inflammasome in microglia. Our novel findings suggest that microglial LRRK2 via RAB10 plays a critical role in Mn-induced neuroinflammation.
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13
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Sarkar A, Rasheed MSU, Singh MP. Redox Modulation of Mitochondrial Proteins in the Neurotoxicant Models of Parkinson's Disease. Antioxid Redox Signal 2023; 38:824-852. [PMID: 36401516 DOI: 10.1089/ars.2022.0106] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Significance: Mitochondrial proteins regulate the oxidative phosphorylation, cellular metabolism, and free radical generation. Redox modulation alters the mitochondrial proteins and instigates the damage to dopaminergic neurons. Toxicants contribute to Parkinson's disease (PD) pathogenesis in conjunction with aging and genetic factors. While oxidative modulation of a number of mitochondrial proteins is linked to xenobiotic exposure, little is known about its role in the toxicant-induced PD. Understanding the role of redox modulation of mitochondrial proteins in complex cellular events leading to neurodegeneration is highly relevant. Recent Advances: Many toxicants are shown to inhibit complex I or III and elicit free radical production that alters the redox status of mitochondrial proteins. Implication of redox modulation of the mitochondrial proteins makes them a target to comprehend the underlying mechanism of toxicant-induced PD. Critical Issues: Owing to multifactorial etiology, exploration of onset and progression and treatment outcomes needs a comprehensive approach. The article explains about a few mitochondrial proteins that undergo redox changes along with the promising strategies, which help to alleviate the toxicant-induced redox imbalance leading to neurodegeneration. Future Directions: Although mitochondrial proteins are linked to PD, their role in toxicant-induced parkinsonism is not yet completely known. Preservation of antioxidant defense machinery could alleviate the redox modulation of mitochondrial proteins. Targeted antioxidant delivery, use of metal chelators, and activation of nuclear factor erythroid 2-related factor 2, and combinational therapy that encounters multiple free radicals, could ameliorate the redox modulation of mitochondrial proteins and thereby PD progression.
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Affiliation(s)
- Alika Sarkar
- Toxicogenomics and Predictive Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohd Sami Ur Rasheed
- Toxicogenomics and Predictive Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mahendra Pratap Singh
- Toxicogenomics and Predictive Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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14
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Tang X, Xing S, Ma M, Xu Z, Guan Q, Chen Y, Feng F, Liu W, Chen T, Chen Y, Sun H. The Development and Design Strategy of Leucine-Rich Repeat Kinase 2 Inhibitors: Promising Therapeutic Agents for Parkinson's Disease. J Med Chem 2023; 66:2282-2307. [PMID: 36758171 DOI: 10.1021/acs.jmedchem.2c01552] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder affecting millions of people worldwide. Mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) are the most common genetic risk factor for PD. Elevated LRRK2 kinase activity is found in idiopathic and familial PD cases. LRRK2 mutations are involved in multiple PD pathogeneses, including dysregulation of mitochondrial homeostasis, ciliogenesis, etc. Here, we provide a comprehensive overview of the biological function, structure, and mutations of LRRK2. We also examine recent advances and challenges in developing LRRK2 inhibitors and address prospective protein-based targeting strategies. The binding mechanisms, structure-activity relationships, and pharmacokinetic features of inhibitors are emphasized to provide a comprehensive compendium on the rational design of LRRK2 inhibitors. We hope that this publication can serve as a guide for designing novel LRRK2 inhibitors based on the summarized facts and perspectives.
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Affiliation(s)
- Xu Tang
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Shuaishuai Xing
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Mingkang Ma
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Ziwei Xu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Qianwen Guan
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Yuting Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Feng Feng
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, People's Republic of China
- Jiangsu Food and Pharmaceuticals Science College, Institute of Food and Pharmaceuticals Research, Huai'an 223005, People's Republic of China
| | - Wenyuan Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Tingkai Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People's Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People's Republic of China
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15
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Boecker CA. The Role of LRRK2 in Intracellular Organelle Dynamics. J Mol Biol 2023:167998. [PMID: 36764357 DOI: 10.1016/j.jmb.2023.167998] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Pathogenic mutations in the leucine-rich repeat kinase 2 (LRRK2) gene hyperactivate LRRK2 kinase activity and lead to the development of Parkinson's disease (PD). Membrane recruitment of LRRK2 and the identification of RAB GTPases as bona fide LRRK2 substrates strongly indicate that LRRK2 regulates intracellular trafficking. This review highlights the current literature on the role of LRRK2 in intracellular organelle dynamics. With a focus on the effects of LRRK2 on microtubule function, mitochondrial dynamics, the autophagy-lysosomal pathway, and synaptic vesicle trafficking, it summarizes our current understanding of how intracellular dynamics are altered upon pathogenic LRRK2 hyperactivation.
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Affiliation(s)
- C Alexander Boecker
- Department of Neurology, University Medical Center Goettingen, Robert-Koch-Strasse 40, 37075 Goettingen, Germany.
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16
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Regulators of proteostasis are translationally repressed in fibroblasts from patients with sporadic and LRRK2-G2019S Parkinson's disease. NPJ Parkinsons Dis 2023; 9:20. [PMID: 36746972 PMCID: PMC9902458 DOI: 10.1038/s41531-023-00460-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
Deficits in protein synthesis are associated with Parkinson's disease (PD). However, it is not known which proteins are affected or if there are synthesis differences between patients with sporadic and Leucine-Rich Repeat Kinase 2 (LRRK2) G2019S PD, the most common monogenic form. Here we used bio-orthogonal non-canonical amino acid tagging for global analysis of newly translated proteins in fibroblasts from sporadic and LRKK2-G2019S patients. Quantitative proteomic analysis revealed that several nascent proteins were reduced in PD samples compared to healthy without any significant change in mRNA levels. Using targeted proteomics, we validated which of these proteins remained dysregulated at the static proteome level and found that regulators of endo-lysosomal sorting, mRNA processing and components of the translation machinery remained low. These proteins included autophagy-related protein 9A (ATG9A) and translational stability regulator YTH N6-ethyladenosine RNA binding protein 3 (YTHDF3). Notably, 77% of the affected proteins in sporadic patients were also repressed in LRRK2-G2019S patients (False discovery rate (FDR) < 0.05) in both sporadic and LRRK2-G2019S samples. This analysis of nascent proteomes from PD patient skin cells reveals that regulators of proteostasis are repressed in both sporadic and LRRK2-G2019S PD.
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17
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Snead DM, Matyszewski M, Dickey AM, Lin YX, Leschziner AE, Reck-Peterson SL. Structural basis for Parkinson's disease-linked LRRK2's binding to microtubules. Nat Struct Mol Biol 2022; 29:1196-1207. [PMID: 36510024 PMCID: PMC9758056 DOI: 10.1038/s41594-022-00863-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/10/2022] [Indexed: 12/14/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is one of the most commonly mutated genes in familial Parkinson's disease (PD). Under some circumstances, LRRK2 co-localizes with microtubules in cells, an association enhanced by PD mutations. We report a cryo-EM structure of the catalytic half of LRRK2, containing its kinase, in a closed conformation, and GTPase domains, bound to microtubules. We also report a structure of the catalytic half of LRRK1, which is closely related to LRRK2 but is not linked to PD. Although LRRK1's structure is similar to that of LRRK2, we find that LRRK1 does not interact with microtubules. Guided by these structures, we identify amino acids in LRRK2's GTPase that mediate microtubule binding; mutating them disrupts microtubule binding in vitro and in cells, without affecting LRRK2's kinase activity. Our results have implications for the design of therapeutic LRRK2 kinase inhibitors.
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Affiliation(s)
- David M Snead
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, MD, USA
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mariusz Matyszewski
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, MD, USA
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Andrea M Dickey
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, MD, USA
| | - Yu Xuan Lin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, MD, USA
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, MD, USA.
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, MD, USA.
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, Maryland, MD, USA.
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18
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Sterling KG, Dodd GK, Alhamdi S, Asimenios PG, Dagda RK, De Meirleir KL, Hudig D, Lombardi VC. Mucosal Immunity and the Gut-Microbiota-Brain-Axis in Neuroimmune Disease. Int J Mol Sci 2022; 23:13328. [PMID: 36362150 PMCID: PMC9655506 DOI: 10.3390/ijms232113328] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 07/30/2023] Open
Abstract
Recent advances in next-generation sequencing (NGS) technologies have opened the door to a wellspring of information regarding the composition of the gut microbiota. Leveraging NGS technology, early metagenomic studies revealed that several diseases, such as Alzheimer's disease, Parkinson's disease, autism, and myalgic encephalomyelitis, are characterized by alterations in the diversity of gut-associated microbes. More recently, interest has shifted toward understanding how these microbes impact their host, with a special emphasis on their interactions with the brain. Such interactions typically occur either systemically, through the production of small molecules in the gut that are released into circulation, or through signaling via the vagus nerves which directly connect the enteric nervous system to the central nervous system. Collectively, this system of communication is now commonly referred to as the gut-microbiota-brain axis. While equally important, little attention has focused on the causes of the alterations in the composition of gut microbiota. Although several factors can contribute, mucosal immunity plays a significant role in shaping the microbiota in both healthy individuals and in association with several diseases. The purpose of this review is to provide a brief overview of the components of mucosal immunity that impact the gut microbiota and then discuss how altered immunological conditions may shape the gut microbiota and consequently affect neuroimmune diseases, using a select group of common neuroimmune diseases as examples.
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Affiliation(s)
| | - Griffin Kutler Dodd
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Shatha Alhamdi
- Clinical Immunology and Allergy Division, Department of Pediatrics, King Abdullah Specialist Children’s Hospital, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | | | - Ruben K. Dagda
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
| | | | - Dorothy Hudig
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Vincent C. Lombardi
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
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19
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Kalogeropulou AF, Purlyte E, Tonelli F, Lange SM, Wightman M, Prescott AR, Padmanabhan S, Sammler E, Alessi DR. Impact of 100 LRRK2 variants linked to Parkinson's disease on kinase activity and microtubule binding. Biochem J 2022; 479:1759-1783. [PMID: 35950872 PMCID: PMC9472821 DOI: 10.1042/bcj20220161] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/01/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
Mutations enhancing the kinase activity of leucine-rich repeat kinase-2 (LRRK2) cause Parkinson's disease (PD) and therapies that reduce LRRK2 kinase activity are being tested in clinical trials. Numerous rare variants of unknown clinical significance have been reported, but how the vast majority impact on LRRK2 function is unknown. Here, we investigate 100 LRRK2 variants linked to PD, including previously described pathogenic mutations. We identify 23 LRRK2 variants that robustly stimulate kinase activity, including variants within the N-terminal non-catalytic regions (ARM (E334K, A419V), ANK (R767H), LRR (R1067Q, R1325Q)), as well as variants predicted to destabilize the ROC:CORB interface (ROC (A1442P, V1447M), CORA (R1628P) CORB (S1761R, L1795F)) and COR:COR dimer interface (CORB (R1728H/L)). Most activating variants decrease LRRK2 biomarker site phosphorylation (pSer935/pSer955/pSer973), consistent with the notion that the active kinase conformation blocks their phosphorylation. We conclude that the impact of variants on kinase activity is best evaluated by deploying a cellular assay of LRRK2-dependent Rab10 substrate phosphorylation, compared with a biochemical kinase assay, as only a minority of activating variants (CORB (Y1699C, R1728H/L, S1761R) and kinase (G2019S, I2020T, T2031S)), enhance in vitro kinase activity of immunoprecipitated LRRK2. Twelve variants including several that activate LRRK2 and have been linked to PD, suppress microtubule association in the presence of a Type I kinase inhibitor (ARM (M712V), LRR (R1320S), ROC (A1442P, K1468E, S1508R), CORA (A1589S), CORB (Y1699C, R1728H/L) and WD40 (R2143M, S2350I, G2385R)). Our findings will stimulate work to better understand the mechanisms by which variants impact biology and provide rationale for variant carrier inclusion or exclusion in ongoing and future LRRK2 inhibitor clinical trials.
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Affiliation(s)
- Alexia F. Kalogeropulou
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
| | - Elena Purlyte
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
| | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
| | - Sven M. Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
| | - Melanie Wightman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
| | - Alan R. Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | | | - Esther Sammler
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
- Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, U.K
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
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20
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LRRK2 and Proteostasis in Parkinson's Disease. Int J Mol Sci 2022; 23:ijms23126808. [PMID: 35743250 PMCID: PMC9224256 DOI: 10.3390/ijms23126808] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 02/01/2023] Open
Abstract
Parkinson’s disease is a neurodegenerative condition initially characterized by the presence of tremor, muscle stiffness and impaired balance, with the deposition of insoluble protein aggregates in Lewy’s Bodies the histopathological hallmark of the disease. Although different gene variants are linked to Parkinson disease, mutations in the Leucine-Rich Repeat Kinase 2 (LRRK2) gene are one of the most frequent causes of Parkinson’s disease related to genetic mutations. LRRK2 toxicity has been mainly explained by an increase in kinase activity, but alternative mechanisms have emerged as underlying causes for Parkinson’s disease, such as the imbalance in LRRK2 homeostasis and the involvement of LRRK2 in aggregation and spreading of α-synuclein toxicity. In this review, we recapitulate the main LRRK2 pathological mutations that contribute to Parkinson’s disease and the different cellular and therapeutic strategies devised to correct LRRK2 homeostasis. In this review, we describe the main cellular control mechanisms that regulate LRRK2 folding and aggregation, such as the chaperone network and the protein-clearing pathways such as the ubiquitin–proteasome system and the autophagic-lysosomal pathway. We will also address the more relevant strategies to modulate neurodegeneration in Parkinson’s disease through the regulation of LRRK2, using small molecules or LRRK2 silencing.
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21
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Stormo AE, Shavarebi F, FitzGibbon M, Earley EM, Ahrendt H, Lum LS, Verschueren E, Swaney DL, Skibinski G, Ravisankar A, van Haren J, Davis EJ, Johnson JR, Von Dollen J, Balen C, Porath J, Crosio C, Mirescu C, Iaccarino C, Dauer WT, Nichols RJ, Wittmann T, Cox TC, Finkbeiner S, Krogan NJ, Oakes SA, Hiniker A. The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity. J Cell Biol 2022; 221:e202010065. [PMID: 35266954 PMCID: PMC8919618 DOI: 10.1083/jcb.202010065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/26/2021] [Accepted: 01/04/2022] [Indexed: 11/22/2022] Open
Abstract
Missense mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease (PD); however, pathways regulating LRRK2 subcellular localization, function, and turnover are not fully defined. We performed quantitative mass spectrometry-based interactome studies to identify 48 novel LRRK2 interactors, including the microtubule-associated E3 ubiquitin ligase TRIM1 (tripartite motif family 1). TRIM1 recruits LRRK2 to the microtubule cytoskeleton for ubiquitination and proteasomal degradation by binding LRRK2911-919, a nine amino acid segment within a flexible interdomain region (LRRK2853-981), which we designate the "regulatory loop" (RL). Phosphorylation of LRRK2 Ser910/Ser935 within LRRK2 RL influences LRRK2's association with cytoplasmic 14-3-3 versus microtubule-bound TRIM1. Association with TRIM1 modulates LRRK2's interaction with Rab29 and prevents upregulation of LRRK2 kinase activity by Rab29 in an E3-ligase-dependent manner. Finally, TRIM1 rescues neurite outgrowth deficits caused by PD-driving mutant LRRK2 G2019S. Our data suggest that TRIM1 is a critical regulator of LRRK2, controlling its degradation, localization, binding partners, kinase activity, and cytotoxicity.
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Affiliation(s)
- Adrienne E.D. Stormo
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Farbod Shavarebi
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Molly FitzGibbon
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Elizabeth M. Earley
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Hannah Ahrendt
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Lotus S. Lum
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Erik Verschueren
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - Danielle L. Swaney
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - Gaia Skibinski
- Taube/Koret Center for Neurodegenerative Disease Research, J. David Gladstone Institutes, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Abinaya Ravisankar
- Taube/Koret Center for Neurodegenerative Disease Research, J. David Gladstone Institutes, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Jeffrey van Haren
- Departments of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Emily J. Davis
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Jeffrey R. Johnson
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - John Von Dollen
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - Carson Balen
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Jacob Porath
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - William T. Dauer
- Departments of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
- Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Torsten Wittmann
- Departments of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA
| | - Timothy C. Cox
- Department of Oral and Craniofacial Sciences, School of Medicine, University of Missouri Kansas City, Kansas City, MO
- School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Steve Finkbeiner
- Departments of Neurology, University of California San Francisco, San Francisco, CA
- Departments of Physiology, University of California San Francisco, San Francisco, CA
- Taube/Koret Center for Neurodegenerative Disease Research, J. David Gladstone Institutes, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Nevan J. Krogan
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Scott A. Oakes
- Departments of Pathology, University of California San Francisco, San Francisco, CA
- Department of Pathology, University of Chicago, Chicago, IL
| | - Annie Hiniker
- Department of Pathology, University of California San Diego, San Diego, CA
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22
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Nanobodies as allosteric modulators of Parkinson's disease-associated LRRK2. Proc Natl Acad Sci U S A 2022; 119:2112712119. [PMID: 35217606 PMCID: PMC8892280 DOI: 10.1073/pnas.2112712119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 02/07/2023] Open
Abstract
Parkinson’s disease (PD) is the second-most common neurodegenerative disorder. Mutations leading to overactivation of LRRK2 are a leading cause of familial PD, and this protein is therefore considered as an appealing target for drug design. Here, we describe the discovery and characterization of a diverse set of LRRK2-targeting nanobodies. A subset of these nanobodies inhibit LRRK2 via a mechanism that differs from the commonly used LRRK2 kinase inhibitors. Importantly, some of these nanobodies selectively inhibit certain LRRK2 activities (Rab phosphorylation) while leaving other activities (autophosphorylation) unaffected. We anticipate that these nanobodies will find multiple applications as research tools and will open up opportunities for the development of new PD diagnostics and therapeutics in parallel to other currently pursued strategies. Mutations in the gene coding for leucine-rich repeat kinase 2 (LRRK2) are a leading cause of the inherited form of Parkinson’s disease (PD), while LRRK2 overactivation is also associated with the more common idiopathic form of PD. LRRK2 is a large multidomain protein, including a GTPase as well as a Ser/Thr protein kinase domain. Common, disease-causing mutations increase LRRK2 kinase activity, presenting LRRK2 as an attractive target for drug discovery. Currently, drug development has mainly focused on ATP-competitive kinase inhibitors. Here, we report the identification and characterization of a variety of nanobodies that bind to different LRRK2 domains and inhibit or activate LRRK2 in cells and in in vitro. Importantly, nanobodies were identified that inhibit LRRK2 kinase activity while binding to a site that is topographically distinct from the active site and thus act through an allosteric inhibitory mechanism that does not involve binding to the ATP pocket or even to the kinase domain. Moreover, while certain nanobodies completely inhibit the LRRK2 kinase activity, we also identified nanobodies that specifically inhibit the phosphorylation of Rab protein substrates. Finally, in contrast to current type I kinase inhibitors, the studied kinase-inhibitory nanobodies did not induce LRRK2 microtubule association. These comprehensively characterized nanobodies represent versatile tools to study the LRRK2 function and mechanism and can pave the way toward novel diagnostic and therapeutic strategies for PD.
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23
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LRRK2 and idiopathic Parkinson's disease. Trends Neurosci 2022; 45:224-236. [PMID: 34991886 PMCID: PMC8854345 DOI: 10.1016/j.tins.2021.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/30/2021] [Accepted: 12/09/2021] [Indexed: 12/22/2022]
Abstract
The etiology of idiopathic Parkinson's disease (iPD) is multifactorial, and both genetics and environmental exposures are risk factors. While mutations in leucine-rich repeat kinase-2 (LRRK2) that are associated with increased kinase activity are the most common cause of autosomal dominant PD, the role of LRRK2 in iPD, independent of mutations, remains uncertain. In this review, we discuss how the architecture of LRRK2 influences kinase activation and how enhanced LRRK2 substrate phosphorylation might contribute to pathogenesis. We describe how oxidative stress and endolysosomal dysfunction, both of which occur in iPD, can activate non-mutated LRRK2 to a similar degree as pathogenic mutations. Similarly, environmental toxicants that are linked epidemiologically to iPD risk can also activate LRRK2. In aggregate, current evidence suggests an important role for LRRK2 in iPD.
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24
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Martinez-Banaclocha M. N-Acetyl-Cysteine: Modulating the Cysteine Redox Proteome in Neurodegenerative Diseases. Antioxidants (Basel) 2022; 11:antiox11020416. [PMID: 35204298 PMCID: PMC8869501 DOI: 10.3390/antiox11020416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 12/14/2022] Open
Abstract
In the last twenty years, significant progress in understanding the pathophysiology of age-associated neurodegenerative diseases has been made. However, the prevention and treatment of these diseases remain without clinically significant therapeutic advancement. While we still hope for some potential genetic therapeutic approaches, the current reality is far from substantial progress. With this state of the issue, emphasis should be placed on early diagnosis and prompt intervention in patients with increased risk of neurodegenerative diseases to slow down their progression, poor prognosis, and decreasing quality of life. Accordingly, it is urgent to implement interventions addressing the psychosocial and biochemical disturbances we know are central in managing the evolution of these disorders. Genomic and proteomic studies have shown the high molecular intricacy in neurodegenerative diseases, involving a broad spectrum of cellular pathways underlying disease progression. Recent investigations indicate that the dysregulation of the sensitive-cysteine proteome may be a concurrent pathogenic mechanism contributing to the pathophysiology of major neurodegenerative diseases, opening new therapeutic opportunities. Considering the incidence and prevalence of these disorders and their already significant burden in Western societies, they will become a real pandemic in the following decades. Therefore, we propose large-scale investigations, in selected groups of people over 40 years of age with decreased blood glutathione levels, comorbidities, and/or mild cognitive impairment, to evaluate supplementation of the diet with low doses of N-acetyl-cysteine, a promising and well-tolerated therapeutic agent suitable for long-term use.
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25
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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] [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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26
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The Roc domain of LRRK2 as a hub for protein-protein interactions: a focus on PAK6 and its impact on RAB phosphorylation. Brain Res 2022; 1778:147781. [DOI: 10.1016/j.brainres.2022.147781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 12/17/2022]
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27
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Helton LG, Rideout HJ, Herberg FW, Kennedy EJ. Leucine rich repeat kinase 2 (
LRRK2
) peptide modulators: Recent advances and future directions. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Leah G. Helton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
| | - Hardy J. Rideout
- Center for Clinical, Experimental Surgery, and Translational Research Biomedical Research Foundation of the Academy of Athens Athens Greece
| | - Friedrich W. Herberg
- Department of Biochemistry Institute for Biology, University of Kassel Kassel Germany
| | - Eileen J. Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
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28
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Tasegian A, Singh F, Ganley IG, Reith AD, Alessi DR. Impact of Type II LRRK2 inhibitors on signaling and mitophagy. Biochem J 2021; 478:3555-3573. [PMID: 34515301 PMCID: PMC8589421 DOI: 10.1042/bcj20210375] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/21/2023]
Abstract
Much effort has been devoted to the development of selective inhibitors of the LRRK2 as a potential treatment for LRRK2 driven Parkinson's disease. In this study, we first compare the properties of Type I (GSK3357679A and MLi-2) and Type II (GZD-824, Rebastinib and Ponatinib) kinase inhibitors that bind to the closed or open conformations of the LRRK2 kinase domain, respectively. We show that Type I and Type II inhibitors suppress phosphorylation of Rab10 and Rab12, key physiological substrates of LRRK2 and also promote mitophagy, a process suppressed by LRRK2. Type II inhibitors also display higher potency towards wild-type LRRK2 compared with pathogenic mutants. Unexpectedly, we find that Type II inhibitors, in contrast with Type I compounds, fail to induce dephosphorylation of a set of well-studied LRRK2 biomarker phosphorylation sites at the N-terminal region of LRRK2, including Ser935. These findings emphasize that the biomarker phosphorylation sites on LRRK2 are likely reporting on the open vs closed conformation of LRRK2 kinase and that only inhibitors which stabilize the closed conformation induce dephosphorylation of these biomarker sites. Finally, we demonstrate that the LRRK2[A2016T] mutant which is resistant to MLi-2 Type 1 inhibitor, also induces resistance to GZD-824 and Rebastinib suggesting this mutation could be exploited to distinguish off target effects of Type II inhibitors. Our observations provide a framework of knowledge to aid with the development of more selective Type II LRRK2 inhibitors.
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Affiliation(s)
- Anna Tasegian
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Francois Singh
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Ian G. Ganley
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Alastair D. Reith
- GlaxoSmithKline Pharmaceuticals R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Dario R. Alessi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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29
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Li D, Liu Y, Yi P, Zhu Z, Li W, Zhang QC, Li JB, Ou G. RNA editing restricts hyperactive ciliary kinases. Science 2021; 373:984-991. [PMID: 34446600 DOI: 10.1126/science.abd8971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/01/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Protein kinase activity must be precisely regulated, but how a cell governs hyperactive kinases remains unclear. In this study, we generated a constitutively active mitogen-activated protein kinase DYF-5 (DYF-5CA) in Caenorhabditis elegans that disrupted sensory cilia. Genetic suppressor screens identified that mutations of ADR-2, an RNA adenosine deaminase, rescued ciliary phenotypes of dyf-5CA We found that dyf-5CA animals abnormally transcribed antisense RNAs that pair with dyf-5CA messenger RNA (mRNA) to form double-stranded RNA, recruiting ADR-2 to edit the region ectopically. RNA editing impaired dyf-5CA mRNA splicing, and the resultant intron retentions blocked DYF-5CA protein translation and activated nonsense-mediated dyf-5CA mRNA decay. The kinase RNA editing requires kinase hyperactivity. The similar RNA editing-dependent feedback regulation restricted the other ciliary kinases NEKL-4/NEK10 and DYF-18/CCRK, which suggests a widespread mechanism that underlies kinase regulation.
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Affiliation(s)
- Dongdong Li
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Yufan Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Peishan Yi
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Zhiwen Zhu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Wei Li
- School of Medicine, Tsinghua University, Beijing, China
| | - Qiangfeng Cliff Zhang
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China. .,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
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30
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Leschziner AE, Reck-Peterson SL. Structural Biology of LRRK2 and its Interaction with Microtubules. Mov Disord 2021; 36:2494-2504. [PMID: 34423856 PMCID: PMC9290818 DOI: 10.1002/mds.28755] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/02/2022] Open
Abstract
Mutations in leucine rich repeat kinase 2 (LRRK2) are a major cause of familial Parkinson's disease (PD) and a risk factor for its sporadic form. LRRK2 hyperactivity has also been reported in sporadic PD, making LRRK2 an appealing target for PD small‐molecule therapeutics. At a cellular level, increasing evidence suggests that LRRK2 regulates membrane trafficking. Under some conditions LRRK2 also associates with microtubules, the cellular tracks used by dynein and kinesin motors to move membranes. At a structural level, however, relatively little was known about LRRK2. An important step toward bridging this gap took place last year with the publication of structures of LRRK2's cytosolic and microtubule‐bound forms. Here, we review the main findings from these studies and discuss what we see as the major challenges going forward with a focus on areas that will require structural information. We also introduce the structural techniques—cryo‐electron microscopy and cryo‐electron tomography—that were instrumental to solving the structures of LRRK2. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society
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Affiliation(s)
- Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, California, USA
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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31
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Li D, Ma C, Xiang J, Zhang K, Yang L, Gan Q. A Disulfide Switch Providing Absolute Handedness Control in Double Helices via Conversion from the Antiparallel to Parallel Helical Pattern. Chemistry 2021; 27:11663-11669. [PMID: 34014575 DOI: 10.1002/chem.202101221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 11/09/2022]
Abstract
A strategy to reversibly switch the parallel/antiparallel helical conformation of aromatic double helices through the formation/breakage of a disulfide bond is presented. Single-crystal X-ray structures, NMR, and circular dichroism spectroscopy demonstrate that the double helices with terminal thiol groups favor an antiparallel helical arrangement both in the solid state and in solution, while the P/M bias of helicity induced by chiral segments from another extremity of the sequence is weak in this structural motif. The antiparallel helices can be rearranged to parallel helices through the disulfide connection of the sequences. This change enhances the bias of helical handedness and results in absolute chirality control of the double helices. The handedness-mediated process can be governed by the oxidation-reduction cycle, thereby switching the structural arrangement and the enhancement of chiral bias. In addition, we find that the sequences can dimerize into an intermolecular double helix with the disulfide connection. And the helical handedness is also fully controlled due to the head-to-head structural motif.
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Affiliation(s)
- Dongyao Li
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Chunmiao Ma
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Junfeng Xiang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Kai Zhang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Ling Yang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Quan Gan
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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32
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Allosteric inhibition of LRRK2, where are we now. Biochem Soc Trans 2021; 48:2185-2194. [PMID: 33079169 PMCID: PMC7609032 DOI: 10.1042/bst20200424] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. In recent years, it has been shown that leucine-rich repeat kinase 2 (LRRK2) has a crucial function in both familial and sporadic forms of PD. LRRK2 pathogenic mutations are thought to result in an increase in LRRK2 kinase activity. Thus, inhibiting LRRK2 kinase activity has become a main therapeutic target. Many compounds capable of inhibiting LRRK2 kinase activity with high selectivity and brain availability have been described. However, the safety of long-term use of these ATP-competitive LRRK2 kinase inhibitors has been challenged by several studies. Therefore, alternative ways of targeting LRRK2 activity will have a great benefit. In this review, we discuss the recent progress in the development of allosteric inhibitors of LRRK2, mainly via interfering with GTPase activity, and propose potential new intra and interprotein interactions targets that can lead to open doors toward new therapeutics.
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33
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Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proc Natl Acad Sci U S A 2021; 118:2100844118. [PMID: 34088839 PMCID: PMC8201809 DOI: 10.1073/pnas.2100844118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To explore how pathogenic mutations of the multidomain leucine-rich repeat kinase 2 (LRRK2) hijack its finely tuned activation process and drive Parkinson's disease (PD), we used a multitiered approach. Most mutations mimic Rab-mediated activation by "unleashing" kinase activity, and many, like the kinase inhibitor MLi-2, trap LRRK2 onto microtubules. Here we mimic activation by simply deleting the inhibitory N-terminal domains and then characterize conformational changes induced by MLi-2 and PD mutations. After confirming that LRRK2RCKW retains full kinase activity, we used hydrogen-deuterium exchange mass spectrometry to capture breathing dynamics in the presence and absence of MLi-2. Solvent-accessible regions throughout the entire protein are reduced by MLi-2 binding. With molecular dynamics simulations, we created a dynamic portrait of LRRK2RCKW and demonstrate the consequences of kinase domain mutations. Although all domains contribute to regulating kinase activity, the kinase domain, driven by the DYGψ motif, is the allosteric hub that drives LRRK2 regulation.
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34
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Myasnikov A, Zhu H, Hixson P, Xie B, Yu K, Pitre A, Peng J, Sun J. Structural analysis of the full-length human LRRK2. Cell 2021; 184:3519-3527.e10. [PMID: 34107286 DOI: 10.1016/j.cell.2021.05.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/23/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are commonly implicated in the pathogenesis of both familial and sporadic Parkinson's disease (PD). LRRK2 regulates critical cellular processes at membranous organelles and forms microtubule-based pathogenic filaments, yet the molecular basis underlying these biological roles of LRRK2 remains largely enigmatic. Here, we determined high-resolution structures of full-length human LRRK2, revealing its architecture and key interdomain scaffolding elements for rationalizing disease-causing mutations. The kinase domain of LRRK2 is captured in an inactive state, a conformation also adopted by the most common PD-associated mutation, LRRK2G2019S. This conformation serves as a framework for structure-guided design of conformational specific inhibitors. We further determined the structure of COR-mediated LRRK2 dimers and found that single-point mutations at the dimer interface abolished pathogenic filamentation in cells. Overall, our study provides mechanistic insights into physiological and pathological roles of LRRK2 and establishes a structural template for future therapeutic intervention in PD.
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Affiliation(s)
- Alexander Myasnikov
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Cryo-EM and Tomography Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hanwen Zhu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Patricia Hixson
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Boer Xie
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kaiwen Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Aaron Pitre
- Cell & Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ji Sun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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35
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Azeggagh S, Berwick DC. The development of inhibitors of leucine-rich repeat kinase 2 (LRRK2) as a therapeutic strategy for Parkinson's disease: the current state of play. Br J Pharmacol 2021; 179:1478-1495. [PMID: 34050929 DOI: 10.1111/bph.15575] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 12/29/2022] Open
Abstract
Current therapeutic approaches for Parkinson's disease (PD) are based around treatments that alleviate symptoms but do not slow or prevent disease progression. As such, alternative strategies are needed. A promising approach is the use of molecules that reduce the function of leucine-rich repeat kinase (LRRK2). Gain-of-function mutations in LRRK2 account for a notable proportion of familial Parkinson's disease cases, and significantly, elevated LRRK2 kinase activity is reported in idiopathic Parkinson's disease. Here, we describe progress in finding therapeutically effective LRRK2 inhibitors, summarising studies that range from in vitro experiments to clinical trials. LRRK2 is a complex protein with two enzymatic activities and a myriad of functions. This creates opportunities for a rich variety of strategies and also increases the risk of unintended consequences. We comment on the strength and limitations of the different approaches and conclude that with two molecules under clinical trial and a diversity of alternative options in the pipeline, there is cause for optimism.
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Affiliation(s)
- Sonia Azeggagh
- School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Daniel C Berwick
- Institute of Medical and Biomedical Education, St George's, University of London, London, UK
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36
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Salman MM, Al-Obaidi Z, Kitchen P, Loreto A, Bill RM, Wade-Martins R. Advances in Applying Computer-Aided Drug Design for Neurodegenerative Diseases. Int J Mol Sci 2021; 22:4688. [PMID: 33925236 PMCID: PMC8124449 DOI: 10.3390/ijms22094688] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative diseases (NDs) including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease are incurable and affect millions of people worldwide. The development of treatments for this unmet clinical need is a major global research challenge. Computer-aided drug design (CADD) methods minimize the huge number of ligands that could be screened in biological assays, reducing the cost, time, and effort required to develop new drugs. In this review, we provide an introduction to CADD and examine the progress in applying CADD and other molecular docking studies to NDs. We provide an updated overview of potential therapeutic targets for various NDs and discuss some of the advantages and disadvantages of these tools.
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Affiliation(s)
- Mootaz M. Salman
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3QX, UK;
- Oxford Parkinson’s Disease Centre, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Zaid Al-Obaidi
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Alkafeel, Najaf 54001, Iraq;
- Department of Chemistry and Biochemistry, College of Medicine, University of Kerbala, Karbala 56001, Iraq
| | - Philip Kitchen
- School of Biosciences, College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK; (P.K.); (R.M.B.)
| | - Andrea Loreto
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3QX, UK;
- John Van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Roslyn M. Bill
- School of Biosciences, College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK; (P.K.); (R.M.B.)
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3QX, UK;
- Oxford Parkinson’s Disease Centre, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
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37
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Abstract
Point mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease (PD) and are implicated in a significant proportion of apparently sporadic PD cases. Clinically, LRRK2-driven PD is indistinguishable from sporadic PD, making it an attractive genetic model for the much more common sporadic PD. In this review, we highlight recent advances in understanding LRRK2's subcellular functions using LRRK2-driven PD models, while also considering some of the limitations of these model systems. Recent developments of particular importance include new evidence of key LRRK2 functions in the endolysosomal system and LRRK2's regulation of and by Rab GTPases. Additionally, LRRK2's interaction with the cytoskeleton allowed elucidation of the LRRK2 structure and appears relevant to LRRK2 protein degradation and LRRK2 inhibitor therapies. We further discuss how LRRK2's interactions with other PD-driving genes, such as the VPS35, GBA1, and SNCA genes, may highlight cellular pathways more broadly disrupted in PD.
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Affiliation(s)
- Ahsan Usmani
- Department of Pathology, University of California, San Diego, San Diego, California, USA
| | - Farbod Shavarebi
- Department of Pathology, University of California, San Diego, San Diego, California, USA
| | - Annie Hiniker
- Department of Pathology, University of California, San Diego, San Diego, California, USA
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Follett J, Farrer MJ. LRRK2; a dynamic regulator of cellular trafficking. Brain Res 2021; 1761:147394. [PMID: 33662339 DOI: 10.1016/j.brainres.2021.147394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/11/2021] [Accepted: 02/20/2021] [Indexed: 12/26/2022]
Abstract
Parkinson's disease (PD) represents the second most common neurodegenerative disorder, characterized clinically by bradykinesia, resting tremor, rigidity and postural instability, and a variety of non-motor features. The etiology of PD is unknown, however genetic, environmental and inflammatory factors may influence disease onset and progression. Genetic variability in leucine-rich repeat kinase 2 confers significant genotypic and population-attributable risk for LRRK2-parkinsonism that is clinically indistinguishable from idiopathic PD. Nevertheless, the age-associated midbrain pathology observed post-mortem in LRRK2-parkinsonism may involve the abnormal accumulation of either α-synuclein or tau, or just the loss of dopaminergic neurons and gliosis. While diverse biological functions have been described for this multi-domain protein in many cell types, evidence suggests LRRK2 may sense endosomal trafficking to orchestrate dynamic changes in vesicular flux and cytoskeletal architecture. This review posits the long-held belief that synaptic-axonal dysfunction and terminal degeneration may precede dopaminergic cell loss, and provocatively questions how facets of LRRK2 biology may influence this molecular pathogenesis.
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Affiliation(s)
- Jordan Follett
- Laboratory of Neurogenetics and Neuroscience, Department of Neurology, University of Florida, Gainesville, FL, USA.
| | - Matthew J Farrer
- Laboratory of Neurogenetics and Neuroscience, Department of Neurology, University of Florida, Gainesville, FL, USA
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39
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Malik AU, Karapetsas A, Nirujogi RS, Mathea S, Chatterjee D, Pal P, Lis P, Taylor M, Purlyte E, Gourlay R, Dorward M, Weidlich S, Toth R, Polinski NK, Knapp S, Tonelli F, Alessi DR. Deciphering the LRRK code: LRRK1 and LRRK2 phosphorylate distinct Rab proteins and are regulated by diverse mechanisms. Biochem J 2021; 478:553-578. [PMID: 33459343 PMCID: PMC7886321 DOI: 10.1042/bcj20200937] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 01/05/2023]
Abstract
Autosomal dominant mutations in LRRK2 that enhance kinase activity cause Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases including Rab8A and Rab10 within its effector binding motif. Here, we explore whether LRRK1, a less studied homolog of LRRK2 that regulates growth factor receptor trafficking and osteoclast biology might also phosphorylate Rab proteins. Using mass spectrometry, we found that in LRRK1 knock-out cells, phosphorylation of Rab7A at Ser72 was most impacted. This residue lies at the equivalent site targeted by LRRK2 on Rab8A and Rab10. Accordingly, recombinant LRRK1 efficiently phosphorylated Rab7A at Ser72, but not Rab8A or Rab10. Employing a novel phospho-specific antibody, we found that phorbol ester stimulation of mouse embryonic fibroblasts markedly enhanced phosphorylation of Rab7A at Ser72 via LRRK1. We identify two LRRK1 mutations (K746G and I1412T), equivalent to the LRRK2 R1441G and I2020T Parkinson's mutations, that enhance LRRK1 mediated phosphorylation of Rab7A. We demonstrate that two regulators of LRRK2 namely Rab29 and VPS35[D620N], do not influence LRRK1. Widely used LRRK2 inhibitors do not inhibit LRRK1, but we identify a promiscuous inhibitor termed GZD-824 that inhibits both LRRK1 and LRRK2. The PPM1H Rab phosphatase when overexpressed dephosphorylates Rab7A. Finally, the interaction of Rab7A with its effector RILP is not affected by LRRK1 phosphorylation and we observe that maximal stimulation of the TBK1 or PINK1 pathway does not elevate Rab7A phosphorylation. Altogether, these findings reinforce the idea that the LRRK enzymes have evolved as major regulators of Rab biology with distinct substrate specificity.
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Affiliation(s)
- Asad U. Malik
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Athanasios Karapetsas
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Raja S. Nirujogi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Sebastian Mathea
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Deep Chatterjee
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Prosenjit Pal
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Pawel Lis
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Matthew Taylor
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Elena Purlyte
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Robert Gourlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Mark Dorward
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Simone Weidlich
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Rachel Toth
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Nicole K. Polinski
- Michael J Fox Foundation for Parkinson's Research, Grand Central Station, PO Box 4777, New York, NY 10163, U.S.A
| | - Stefan Knapp
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Francesca Tonelli
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Dario R. Alessi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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40
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Pischedda F, Piccoli G. LRRK2 at the pre-synaptic site: A 16-years perspective. J Neurochem 2021; 157:297-311. [PMID: 33206398 DOI: 10.1111/jnc.15240] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022]
Abstract
Parkinson's disease is a common neurodegenerative disorder and is clinically characterized by bradykinesia, rigidity, and resting tremor. Missense mutations in the leucine-rich repeat protein kinase-2 gene (LRRK2) are a recognized cause of inherited Parkinson's disease. The physiological and pathological impact of LRRK2 is still obscure, but accumulating evidence indicates that LRRK2 orchestrates diverse aspects of membrane trafficking, such as membrane fusion and vesicle formation and transport along actin and tubulin tracks. In the present review, we focus on the special relation between LRRK2 and synaptic vesicles. LRRK2 binds and phosphorylates key actors within the synaptic vesicle cycle. Accordingly, alterations in dopamine and glutamate transmission have been described upon LRRK2 manipulations. However, the different modeling strategies and phenotypes observed require a critical approach to decipher the outcome of LRRK2 at the pre-synaptic site.
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Affiliation(s)
- Francesca Pischedda
- CIBIO, Università degli Studi di Trento, Italy & Dulbecco Telethon Institute, Trento, Italy
| | - Giovanni Piccoli
- CIBIO, Università degli Studi di Trento, Italy & Dulbecco Telethon Institute, Trento, Italy
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41
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Chittoor-Vinod VG, Nichols RJ, Schüle B. Genetic and Environmental Factors Influence the Pleomorphy of LRRK2 Parkinsonism. Int J Mol Sci 2021; 22:1045. [PMID: 33494262 PMCID: PMC7864502 DOI: 10.3390/ijms22031045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/16/2021] [Accepted: 01/17/2021] [Indexed: 12/25/2022] Open
Abstract
Missense mutations in the LRRK2 gene were first identified as a pathogenic cause of Parkinson's disease (PD) in 2004. Soon thereafter, a founder mutation in LRRK2, p.G2019S (rs34637584), was described, and it is now estimated that there are approximately 100,000 people worldwide carrying this risk variant. While the clinical presentation of LRRK2 parkinsonism has been largely indistinguishable from sporadic PD, disease penetrance and age at onset can be quite variable. In addition, its neuropathological features span a wide range from nigrostriatal loss with Lewy body pathology, lack thereof, or atypical neuropathology, including a large proportion of cases with concomitant Alzheimer's pathology, hailing LRRK2 parkinsonism as the "Rosetta stone" of parkinsonian disorders, which provides clues to an understanding of the different neuropathological trajectories. These differences may result from interactions between the LRRK2 mutant protein and other proteins or environmental factors that modify LRRK2 function and, thereby, influence pathobiology. This review explores how potential genetic and biochemical modifiers of LRRK2 function may contribute to the onset and clinical presentation of LRRK2 parkinsonism. We review which genetic modifiers of LRRK2 influence clinical symptoms, age at onset, and penetrance, what LRRK2 mutations are associated with pleomorphic LRRK2 neuropathology, and which environmental modifiers can augment LRRK2 mutant pathophysiology. Understanding how LRRK2 function is influenced and modulated by other interactors and environmental factors-either increasing toxicity or providing resilience-will inform targeted therapeutic development in the years to come. This will allow the development of disease-modifying therapies for PD- and LRRK2-related neurodegeneration.
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Affiliation(s)
| | - R. Jeremy Nichols
- Department Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Birgitt Schüle
- Department Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
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42
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Deniston CK, Salogiannis J, Mathea S, Snead DM, Lahiri I, Matyszewski M, Donosa O, Watanabe R, Böhning J, Shiau AK, Knapp S, Villa E, Reck-Peterson SL, Leschziner AE. Structure of LRRK2 in Parkinson's disease and model for microtubule interaction. Nature 2020; 588:344-349. [PMID: 32814344 PMCID: PMC7726071 DOI: 10.1038/s41586-020-2673-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 08/12/2020] [Indexed: 12/22/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is the most commonly mutated gene in familial Parkinson's disease1 and is also linked to its idiopathic form2. LRRK2 has been proposed to function in membrane trafficking3 and colocalizes with microtubules4. Despite the fundamental importance of LRRK2 for understanding and treating Parkinson's disease, structural information on the enzyme is limited. Here we report the structure of the catalytic half of LRRK2, and an atomic model of microtubule-associated LRRK2 built using a reported cryo-electron tomography in situ structure5. We propose that the conformation of the LRRK2 kinase domain regulates its interactions with microtubules, with a closed conformation favouring oligomerization on microtubules. We show that the catalytic half of LRRK2 is sufficient for filament formation and blocks the motility of the microtubule-based motors kinesin 1 and cytoplasmic dynein 1 in vitro. Kinase inhibitors that stabilize an open conformation relieve this interference and reduce the formation of LRRK2 filaments in cells, whereas inhibitors that stabilize a closed conformation do not. Our findings suggest that LRRK2 can act as a roadblock for microtubule-based motors and have implications for the design of therapeutic LRRK2 kinase inhibitors.
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Affiliation(s)
- C K Deniston
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - J Salogiannis
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - S Mathea
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - D M Snead
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - I Lahiri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, India
| | - M Matyszewski
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - O Donosa
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - R Watanabe
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - J Böhning
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
- Sir William Dunn School of Pathology, Oxford University, Oxford, UK
| | - A K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S Knapp
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
| | - E Villa
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA
| | - S L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, USA.
| | - A E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, Molecular Biology Section, University of California San Diego, La Jolla, CA, USA.
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43
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Kalogeropulou AF, Freemantle JB, Lis P, Vides EG, Polinski NK, Alessi DR. Endogenous Rab29 does not impact basal or stimulated LRRK2 pathway activity. Biochem J 2020; 477:4397-4423. [PMID: 33135724 PMCID: PMC7702304 DOI: 10.1042/bcj20200458] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Mutations that enhance LRRK2 protein kinase activity cause inherited Parkinson's disease. LRRK2 phosphorylates a group of Rab GTPase proteins, including Rab10 and Rab12, within the effector-binding switch-II motif. Previous work has indicated that the PARK16 locus, which harbors the gene encoding for Rab29, is involved in Parkinson's, and that Rab29 operates in a common pathway with LRRK2. Co-expression of Rab29 and LRRK2 stimulates LRRK2 activity by recruiting LRRK2 to the surface of the trans Golgi network. Here, we report that knock-out of Rab29 does not influence endogenous LRRK2 activity, based on the assessment of Rab10 and Rab12 phosphorylation, in wild-type LRRK2, LRRK2[R1441C] or VPS35[D620N] knock-in mouse tissues and primary cell lines, including brain extracts and embryonic fibroblasts. We find that in brain extracts, Rab12 phosphorylation is more robustly impacted by LRRK2 inhibitors and pathogenic mutations than Rab10 phosphorylation. Transgenic overexpression of Rab29 in a mouse model was also insufficient to stimulate basal LRRK2 activity. We observed that stimulation of Rab10 and Rab12 phosphorylation induced by agents that stress the endolysosomal system (nigericin, monensin, chloroquine and LLOMe) is suppressed by LRRK2 inhibitors but not blocked in Rab29 deficient cells. From the agents tested, nigericin induced the greatest increase in Rab10 and Rab12 phosphorylation (5 to 9-fold). Our findings indicate that basal, pathogenic, as well as nigericin and monensin stimulated LRRK2 pathway activity is not controlled by Rab29. Further work is required to establish how LRRK2 activity is regulated, and whether other Rab proteins can control LRRK2 by targeting it to diverse membranes.
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Affiliation(s)
- Alexia F. Kalogeropulou
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Jordana B. Freemantle
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Pawel Lis
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Edmundo G. Vides
- Department of Biochemistry, Stanford University School of Medicine, Stanford 94305-5307, U.S.A
| | - Nicole K. Polinski
- Michael J Fox Foundation for Parkinson's Research, Grand Central Station, PO Box 4777, New York, NY 10163, U.S.A
| | - Dario R. Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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44
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Martinez-Banaclocha M. Proteomic Complexity in Parkinson's Disease: A Redox Signaling Perspective of the Pathophysiology and Progression. Neuroscience 2020; 453:287-300. [PMID: 33212217 DOI: 10.1016/j.neuroscience.2020.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/19/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
Parkinson's disease (PD) is a prevalent age-related neurodegenerative disorder that results in the progressive impairment of motor and cognitive functions. The majority of PD cases are sporadic, and only 5% of patients are associated with mutations in a few genes, which cause the early onset or familial PD. Environmental toxic substances and the individual genetic susceptibility play a role in sporadic cases, but despite significant efforts to treat and prevent the disease, the pathophysiological mechanisms leading to its onset and progress are not fully understood. In the last decade, genomic and proteomic studies have shown an increasing molecular complexity of sporadic PD, suggesting that a broad spectrum of biochemical pathways underlie its progression. Recent investigations and the literature review suggest the potential role of deregulation of the sensitive-cysteine proteome as a convergent pathogenic mechanism that may contribute to this complexity, opening new therapeutic opportunities.
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45
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Ditsiou A, Cilibrasi C, Simigdala N, Papakyriakou A, Milton-Harris L, Vella V, Nettleship JE, Lo JH, Soni S, Smbatyan G, Ntavelou P, Gagliano T, Iachini MC, Khurshid S, Simon T, Zhou L, Hassell-Hart S, Carter P, Pearl LH, Owen RL, Owens RJ, Roe SM, Chayen NE, Lenz HJ, Spencer J, Prodromou C, Klinakis A, Stebbing J, Giamas G. The structure-function relationship of oncogenic LMTK3. SCIENCE ADVANCES 2020; 6:6/46/eabc3099. [PMID: 33188023 PMCID: PMC7673765 DOI: 10.1126/sciadv.abc3099] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/30/2020] [Indexed: 05/10/2023]
Abstract
Elucidating signaling driven by lemur tyrosine kinase 3 (LMTK3) could help drug development. Here, we solve the crystal structure of LMTK3 kinase domain to 2.1Å resolution, determine its consensus motif and phosphoproteome, unveiling in vitro and in vivo LMTK3 substrates. Via high-throughput homogeneous time-resolved fluorescence screen coupled with biochemical, cellular, and biophysical assays, we identify a potent LMTK3 small-molecule inhibitor (C28). Functional and mechanistic studies reveal LMTK3 is a heat shock protein 90 (HSP90) client protein, requiring HSP90 for folding and stability, while C28 promotes proteasome-mediated degradation of LMTK3. Pharmacologic inhibition of LMTK3 decreases proliferation of cancer cell lines in the NCI-60 panel, with a concomitant increase in apoptosis in breast cancer cells, recapitulating effects of LMTK3 gene silencing. Furthermore, LMTK3 inhibition reduces growth of xenograft and transgenic breast cancer mouse models without displaying systemic toxicity at effective doses. Our data reinforce LMTK3 as a druggable target for cancer therapy.
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Affiliation(s)
- Angeliki Ditsiou
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Chiara Cilibrasi
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Nikiana Simigdala
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos," 15341 Athens, Greece
| | - Leanne Milton-Harris
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Viviana Vella
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Joanne E Nettleship
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics Headington, Oxford OX3 7BN, UK
- Protein Production UK, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Jae Ho Lo
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Goar Smbatyan
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Panagiota Ntavelou
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Teresa Gagliano
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Maria Chiara Iachini
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Sahir Khurshid
- Faculty of Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, UK
| | - Thomas Simon
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Lihong Zhou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Storm Hassell-Hart
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Philip Carter
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London W12 0NN, UK
| | - Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Raymond J Owens
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics Headington, Oxford OX3 7BN, UK
- Protein Production UK, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- The Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, UK
| | - S Mark Roe
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN1 9RQ, UK
| | - Naomi E Chayen
- Faculty of Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ, UK
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Chrisostomos Prodromou
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Apostolos Klinakis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Justin Stebbing
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London W12 0NN, UK
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK.
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46
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Taylor SS, Kaila-Sharma P, Weng JH, Aoto P, Schmidt SH, Knapp S, Mathea S, Herberg FW. Kinase Domain Is a Dynamic Hub for Driving LRRK2 Allostery. Front Mol Neurosci 2020; 13:538219. [PMID: 33122997 PMCID: PMC7573214 DOI: 10.3389/fnmol.2020.538219] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
Protein kinases and GTPases are the two major molecular switches that regulate much of biology, and both of these domains are embedded within the large multi-domain Leucine-Rich Repeat Kinase 2 (LRRK2). Mutations in LRRK2 are the most common cause of familial Parkinson's disease (PD) and are also implicated in Crohn's disease. The recent Cryo-Electron Microscopy (Cryo-EM) structure of the four C-terminal domains [ROC COR KIN WD40 (RCKW)] of LRRK2 includes both of the catalytic domains. Although the important allosteric N-terminal domains are missing in the Cryo-EM structure this structure allows us to not only explore the conserved features of the kinase domain, which is trapped in an inactive and open conformation but also to observe the direct allosteric cross-talk between the two domains. To define the unique features of the kinase domain and to better understand the dynamic switch mechanism that allows LRRK2 to toggle between its inactive and active conformations, we have compared the LRRK2 kinase domain to Src, BRaf, and PKA. We also compare and contrast the two canonical glycine-rich loop motifs in LRRK2 that anchor the nucleotide: the G-Loop in protein kinases that anchors ATP and the P-Loop in GTPases that anchors GTP. The RCKW structure also provides a template for the cross-talk between the kinase and GTPase domains and brings new mechanistic insights into the physiological function of LRRK2 and how the kinase domain, along with key phosphorylation sites, can serve as an allosteric hub for mediating conformational changes.
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Affiliation(s)
- Susan S Taylor
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States
| | - Pallavi Kaila-Sharma
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Phillip Aoto
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Sven H Schmidt
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Frankfurt, Germany
| | - Sebastian Mathea
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Frankfurt, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
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47
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Xie T, Saleh T, Rossi P, Kalodimos CG. Conformational states dynamically populated by a kinase determine its function. Science 2020; 370:science.abc2754. [PMID: 33004676 DOI: 10.1126/science.abc2754] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022]
Abstract
Protein kinases intrinsically sample a number of conformational states with distinct catalytic and binding activities. We used nuclear magnetic resonance spectroscopy to describe in atomic-level detail how Abl kinase interconverts between an active and two discrete inactive structures. Extensive differences in key structural elements between the conformational states give rise to multiple intrinsic regulatory mechanisms. The findings explain how oncogenic mutants can counteract inhibitory mechanisms to constitutively activate the kinase. Energetic dissection revealed the contributions of the activation loop, the Asp-Phe-Gly (DFG) motif, the regulatory spine, and the gatekeeper residue to kinase regulation. Characterization of the transient conformation to which the drug imatinib binds enabled the elucidation of drug-resistance mechanisms. Structural insight into inactive states highlights how they can be leveraged for the design of selective inhibitors.
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Affiliation(s)
- Tao Xie
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tamjeed Saleh
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paolo Rossi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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48
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The In Situ Structure of Parkinson's Disease-Linked LRRK2. Cell 2020; 182:1508-1518.e16. [PMID: 32783917 DOI: 10.1016/j.cell.2020.08.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/28/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of familial Parkinson's disease. LRRK2 is a multi-domain protein containing a kinase and GTPase. Using correlative light and electron microscopy, in situ cryo-electron tomography, and subtomogram analysis, we reveal a 14-Å structure of LRRK2 bearing a pathogenic mutation that oligomerizes as a right-handed double helix around microtubules, which are left-handed. Using integrative modeling, we determine the architecture of LRRK2, showing that the GTPase and kinase are in close proximity, with the GTPase closer to the microtubule surface, whereas the kinase is exposed to the cytoplasm. We identify two oligomerization interfaces mediated by non-catalytic domains. Mutation of one of these abolishes LRRK2 microtubule-association. Our work demonstrates the power of cryo-electron tomography to generate models of previously unsolved structures in their cellular environment.
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49
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Padmanabhan S, Fiske BK, Baptista MA. The Michael J. Fox Foundation's Strategies for Accelerating Translation of LRRK2 into Therapies for Parkinson Disease. Cells 2020; 9:E1878. [PMID: 32796584 PMCID: PMC7466022 DOI: 10.3390/cells9081878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/01/2020] [Accepted: 08/07/2020] [Indexed: 12/16/2022] Open
Abstract
Since 2005, The Michael J. Fox Foundation for Parkinson's Research (MJFF) has invested significant funding and non-funding effort to accelerate research and drug development activity around the Parkinson disease (PD)-associated protein LRRK2. MJFF has spearheaded multiple public/private pre-competitive collaborations that have contributed to our understanding of LRRK2 function; de-risked potential safety questions around the therapeutic use of LRRK2 kinase inhibitors; and generated critical research tools, biosamples, and data for the field. Several LRRK2-targeted therapies are now in human testing due to the hard work of so many in the PD community. In this perspective, we present a holistic description and model of how our Foundation's support targeted important barriers to LRRK2 research and helped move the field into clinical trials.
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Affiliation(s)
- Shalini Padmanabhan
- The Michael J. Fox Foundation for Parkinson’s Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA
| | | | - Marco A.S. Baptista
- The Michael J. Fox Foundation for Parkinson’s Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA
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50
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Melachroinou K, Kang MS, Liong C, Narayan S, Levers N, Joshi N, Kopil K, Hutten SJ, Baptista MAS, Padmanabhan S, Kang UJ, Stefanis L, Alcalay RN, Rideout HJ. Elevated In Vitro Kinase Activity in Peripheral Blood Mononuclear Cells of Leucine-Rich Repeat Kinase 2 G2019S Carriers: A Novel Enzyme-Linked Immunosorbent Assay-Based Method. Mov Disord 2020; 35:2095-2100. [PMID: 32652692 PMCID: PMC7754308 DOI: 10.1002/mds.28175] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/17/2020] [Accepted: 05/11/2020] [Indexed: 01/20/2023] Open
Abstract
Background Leucine‐rich repeat kinase 2 kinase inhibitors are being vigorously pursued as potential therapeutic options; however, there is a critical need for sensitive and quantitative assays of leucine‐rich repeat kinase 2 function and target engagement. Objectives Our objective was to compare collection and storage protocols for peripheral blood mononuclear cells, and to determine the optimal conditions for downstream analyses of leucine‐rich repeat kinase 2 in PD cohorts. Methods Here, we describe enzyme‐linked immunosorbent assay–based assays capable of detecting multiple aspects of leucine‐rich repeat kinase 2 function at endogenous levels in human tissues. Results In peripheral blood mononuclear cells from both healthy and affected carriers of the G2019S mutation in leucine‐rich repeat kinase 2, we report, for the first time, significantly elevated in vitro kinase activity, while detecting a significant increase in pS935/leucine‐rich repeat kinase 2 in idiopathic PD patients. Conclusions Quantitative assays such as these described here could potentially uncover specific markers of leucine‐rich repeat kinase 2 function that are predictive of disease progression, aid in patient stratification, and be a critical component of upcoming clinical trials. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Katerina Melachroinou
- Division of Basic Neurosciences, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Min Suk Kang
- Department of Neurology, Columbia University, New York, New York, USA
| | - Christopher Liong
- Department of Neurology, Columbia University, New York, New York, USA
| | - Sushma Narayan
- Department of Neurology, Columbia University, New York, New York, USA
| | - Najah Levers
- Department of Neurology, Columbia University, New York, New York, USA
| | - Neal Joshi
- Department of Neurology, Columbia University, New York, New York, USA
| | - Katie Kopil
- The Michael J. Fox Foundation for Parkinson's Research, New York, New York, USA
| | - Samantha J Hutten
- The Michael J. Fox Foundation for Parkinson's Research, New York, New York, USA
| | - Marco A S Baptista
- The Michael J. Fox Foundation for Parkinson's Research, New York, New York, USA
| | - Shalini Padmanabhan
- The Michael J. Fox Foundation for Parkinson's Research, New York, New York, USA
| | - Un Jung Kang
- Department of Neurology, NYU Langone Health, New York, New York, USA
| | - Leonidas Stefanis
- Division of Basic Neurosciences, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Department of Neurology, University of Athens Medical School, Athens, Greece
| | - Roy N Alcalay
- Department of Neurology, Columbia University, New York, New York, USA
| | - Hardy J Rideout
- Division of Basic Neurosciences, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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