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Haspel N, Jang H, Nussinov R. Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics. Biophys J 2021; 120:306-318. [PMID: 33347888 PMCID: PMC7840443 DOI: 10.1016/j.bpj.2020.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/26/2022] Open
Abstract
Cell division control protein 42 homolog (Cdc42) protein, a Ras superfamily GTPase, regulates cellular activities, including cancer progression. Using all-atom molecular dynamics (MD) simulations and essential dynamic analysis, we investigated the structure and dynamics of the catalytic domains of GDP-bound (inactive) and GTP-bound (active) Cdc42 in solution. We discovered substantial differences in the dynamics of the inactive and active forms, particularly in the "insert region" (residues 122-135), which plays a role in Cdc42 activation and binding to effectors. The insert region has larger conformational flexibility in the GDP-bound Cdc42 than in the GTP-bound Cdc42. The G2 loop and switch I at the effector lobe of the catalytic domain exhibit large conformational changes in both the GDP- and the GTP-bound systems, but in the GTP-bound Cdc42, the switch I interactions with GTP are retained. Oncogenic mutations were identified in the Ras superfamily. In Cdc42, the G12V and Q61L mutations decrease the GTPase activity. We simulated these mutations in both GDP- and GTP-bound Cdc42. Although the overall structural organization is quite similar between the wild type and the mutants, there are small differences in the conformational dynamics, especially in the two switch regions. Taken together, the G12V and Q61L mutations may play a role similar to their K-Ras counterparts in nucleotide binding and activation. The conformational differences, which are mainly in the insert region and, to a lesser extent, in the switch regions flanking the nucleotide binding site, can shed light on binding and activation. We propose that the differences are due to a network of hydrogen bonds that gets disrupted when Cdc42 is bound to GDP, a disruption that does not exist in other Rho GTPases. The differences in the dynamics between the two Cdc42 states suggest that the inactive conformation has reduced ability to bind to effectors.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, University of Massachusetts Boston, Boston, Massachusetts
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Baur JD, Rösler R, Wiese S, Johnsson N, Gronemeyer T. Dissecting the nucleotide binding properties of the septins from S. cerevisiae. Cytoskeleton (Hoboken) 2018; 76:45-54. [PMID: 30091242 DOI: 10.1002/cm.21484] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/24/2018] [Accepted: 07/30/2018] [Indexed: 11/11/2022]
Abstract
Septins are a conserved family of guanosine triphosphate (GTP)-binding proteins that assemble into an ordered array of filaments at the mother bud neck in Saccharomyces cerevisiae cells. They are present in all higher eukaryotes except plants. Septins belong structurally to the P-Loop nucleoside triphosphatase (NTPases) like Rab and Ras. However, unlike other small guanosine triphosphatase (GTPases) septins are supposed to act as scaffolds rather than signalling mediators. This is why they are considered as the fourth class of cytoskeletal proteins. It is assumed that septins fulfil their functions independently of the bound nucleotide. The role of guanosine diphosphosphate (GDP) and GTP binding and subsequent hydrolysis was controversial debated in the last couple of years. Lack of crystal structures of yeast septin subunits or rods and difficulties to isolate single monomeric septin subunits often hindered the correlation of results obtained from in vivo studies with biochemical data. Recently, nucleotide binding and hydrolysis was connected to the formation of septin rods from its subunits. However, the evidence was only indirectly obtained through the use of septin mutants in the context of intact cells. We provide here mechanistic insight into the nucleotide binding of the yeast septins by in vitro assays using purified septin rods and building blocks, thereby adding further insights to the already available models on septin filament formation.
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Affiliation(s)
- Julian David Baur
- Institute of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany
| | - Reinhild Rösler
- Core Unit Mass Spectrometry and Proteomics, Ulm University, Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, Ulm, Germany
| | - Nils Johnsson
- Institute of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany
| | - Thomas Gronemeyer
- Institute of Molecular Genetics and Cell Biology, Ulm University, Ulm, Germany
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Hautbergue GM, Castelli LM, Ferraiuolo L, Sanchez-Martinez A, Cooper-Knock J, Higginbottom A, Lin YH, Bauer CS, Dodd JE, Myszczynska MA, Alam SM, Garneret P, Chandran JS, Karyka E, Stopford MJ, Smith EF, Kirby J, Meyer K, Kaspar BK, Isaacs AM, El-Khamisy SF, De Vos KJ, Ning K, Azzouz M, Whitworth AJ, Shaw PJ. SRSF1-dependent nuclear export inhibition of C9ORF72 repeat transcripts prevents neurodegeneration and associated motor deficits. Nat Commun 2017; 8:16063. [PMID: 28677678 PMCID: PMC5504286 DOI: 10.1038/ncomms16063] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 05/24/2017] [Indexed: 12/13/2022] Open
Abstract
Hexanucleotide repeat expansions in the C9ORF72 gene are the commonest known genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Expression of repeat transcripts and dipeptide repeat proteins trigger multiple mechanisms of neurotoxicity. How repeat transcripts get exported from the nucleus is unknown. Here, we show that depletion of the nuclear export adaptor SRSF1 prevents neurodegeneration and locomotor deficits in a Drosophila model of C9ORF72-related disease. This intervention suppresses cell death of patient-derived motor neuron and astrocytic-mediated neurotoxicity in co-culture assays. We further demonstrate that either depleting SRSF1 or preventing its interaction with NXF1 specifically inhibits the nuclear export of pathological C9ORF72 transcripts, the production of dipeptide-repeat proteins and alleviates neurotoxicity in Drosophila, patient-derived neurons and neuronal cell models. Taken together, we show that repeat RNA-sequestration of SRSF1 triggers the NXF1-dependent nuclear export of C9ORF72 transcripts retaining expanded hexanucleotide repeats and reveal a novel promising therapeutic target for neuroprotection.
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Affiliation(s)
- Guillaume M. Hautbergue
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Lydia M. Castelli
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Alvaro Sanchez-Martinez
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Adrian Higginbottom
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Claudia S. Bauer
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Jennifer E. Dodd
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Monika A. Myszczynska
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Sarah M. Alam
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Pierre Garneret
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Jayanth S. Chandran
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Evangelia Karyka
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Matthew J. Stopford
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Emma F. Smith
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Kathrin Meyer
- Nationwide Children’s Research Institute, Department of Pediatrics, The Ohio State University, 700 Children’s Drive, Rm. WA3022, Columbus, Ohio 43205, USA
| | - Brian K. Kaspar
- Nationwide Children’s Research Institute, Department of Pediatrics, The Ohio State University, 700 Children’s Drive, Rm. WA3022, Columbus, Ohio 43205, USA
| | - Adrian M. Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Sherif F. El-Khamisy
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Kurt J. De Vos
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Ke Ning
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Mimoun Azzouz
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
| | - Alexander J. Whitworth
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK
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