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Poudel BH, Fletcher S, Wilton SD, Aung-Htut M. Limb Girdle Muscular Dystrophy Type 2B (LGMD2B): Diagnosis and Therapeutic Possibilities. Int J Mol Sci 2024; 25:5572. [PMID: 38891760 PMCID: PMC11171558 DOI: 10.3390/ijms25115572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Dysferlin is a large transmembrane protein involved in critical cellular processes including membrane repair and vesicle fusion. Mutations in the dysferlin gene (DYSF) can result in rare forms of muscular dystrophy; Miyoshi myopathy; limb girdle muscular dystrophy type 2B (LGMD2B); and distal myopathy. These conditions are collectively known as dysferlinopathies and are caused by more than 600 mutations that have been identified across the DYSF gene to date. In this review, we discuss the key molecular and clinical features of LGMD2B, the causative gene DYSF, and the associated dysferlin protein structure. We also provide an update on current approaches to LGMD2B diagnosis and advances in drug development, including splice switching antisense oligonucleotides. We give a brief update on clinical trials involving adeno-associated viral gene therapy and the current progress on CRISPR/Cas9 mediated therapy for LGMD2B, and then conclude by discussing the prospects of antisense oligomer-based intervention to treat selected mutations causing dysferlinopathies.
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Affiliation(s)
- Bal Hari Poudel
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; (B.H.P.); (S.F.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA 6009, Australia
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu 44618, Nepal
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; (B.H.P.); (S.F.); (S.D.W.)
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; (B.H.P.); (S.F.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA 6009, Australia
| | - May Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; (B.H.P.); (S.F.); (S.D.W.)
- Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA 6009, Australia
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2
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Boyle KB, Ellison CJ, Elliott PR, Schuschnig M, Grimes K, Dionne MS, Sasakawa C, Munro S, Martens S, Randow F. TECPR1 conjugates LC3 to damaged endomembranes upon detection of sphingomyelin exposure. EMBO J 2023; 42:e113012. [PMID: 37409490 PMCID: PMC10476172 DOI: 10.15252/embj.2022113012] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Invasive bacteria enter the cytosol of host cells through initial uptake into bacteria-containing vacuoles (BCVs) and subsequent rupture of the BCV membrane, thereby exposing to the cytosol intraluminal, otherwise shielded danger signals such as glycans and sphingomyelin. The detection of glycans by galectin-8 triggers anti-bacterial autophagy, but how cells sense and respond to cytosolically exposed sphingomyelin remains unknown. Here, we identify TECPR1 (tectonin beta-propeller repeat containing 1) as a receptor for cytosolically exposed sphingomyelin, which recruits ATG5 into an E3 ligase complex that mediates lipid conjugation of LC3 independently of ATG16L1. TECPR1 binds sphingomyelin through its N-terminal DysF domain (N'DysF), a feature not shared by other mammalian DysF domains. Solving the crystal structure of N'DysF, we identified key residues required for the interaction, including a solvent-exposed tryptophan (W154) essential for binding to sphingomyelin-positive membranes and the conjugation of LC3 to lipids. Specificity of the ATG5/ATG12-E3 ligase responsible for the conjugation of LC3 is therefore conferred by interchangeable receptor subunits, that is, the canonical ATG16L1 and the sphingomyelin-specific TECPR1, in an arrangement reminiscent of certain multi-subunit ubiquitin E3 ligases.
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Affiliation(s)
- Keith B Boyle
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
| | - Cara J Ellison
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Paul R Elliott
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Martina Schuschnig
- Max Perutz Labs, Vienna BioCenter (VBC)University of ViennaViennaAustria
| | - Krista Grimes
- MRC Centre for Molecular Bacteriology and InfectionImperial College LondonLondonUK
| | - Marc S Dionne
- MRC Centre for Molecular Bacteriology and InfectionImperial College LondonLondonUK
| | - Chihiro Sasakawa
- Medical Mycology Research CenterChiba UniversityChibaJapan
- Nippon Institute for Biological ScienceOmeJapan
| | - Sean Munro
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter (VBC)University of ViennaViennaAustria
- Center for Molecular Biology, Department of Biochemistry and Cell BiologyUniversity of ViennaViennaAustria
| | - Felix Randow
- Division of Protein and Nucleic Acid ChemistryMRC Laboratory of Molecular BiologyCambridgeUK
- Department of Medicine, Addenbrooke's HospitalUniversity of CambridgeCambridgeUK
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Leclère JC, Dulon D. Otoferlin as a multirole Ca 2+ signaling protein: from inner ear synapses to cancer pathways. Front Cell Neurosci 2023; 17:1197611. [PMID: 37538852 PMCID: PMC10394277 DOI: 10.3389/fncel.2023.1197611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023] Open
Abstract
Humans have six members of the ferlin protein family: dysferlin, myoferlin, otoferlin, fer1L4, fer1L5, and fer1L6. These proteins share common features such as multiple Ca2+-binding C2 domains, FerA domains, and membrane anchoring through their single C-terminal transmembrane domain, and are believed to play a key role in calcium-triggered membrane fusion and vesicle trafficking. Otoferlin plays a crucial role in hearing and vestibular function. In this review, we will discuss how we see otoferlin working as a Ca2+-dependent mechanical sensor regulating synaptic vesicle fusion at the hair cell ribbon synapses. Although otoferlin is also present in the central nervous system, particularly in the cortex and amygdala, its role in brain tissues remains unknown. Mutations in the OTOF gene cause one of the most frequent genetic forms of congenital deafness, DFNB9. These mutations produce severe to profound hearing loss due to a defect in synaptic excitatory glutamatergic transmission between the inner hair cells and the nerve fibers of the auditory nerve. Gene therapy protocols that allow normal rescue expression of otoferlin in hair cells have just started and are currently in pre-clinical phase. In parallel, studies have linked ferlins to cancer through their effect on cell signaling and development, allowing tumors to form and cancer cells to adapt to a hostile environment. Modulation by mechanical forces and Ca2+ signaling are key determinants of the metastatic process. Although ferlins importance in cancer has not been extensively studied, data show that otoferlin expression is significantly associated with survival in specific cancer types, including clear cell and papillary cell renal carcinoma, and urothelial bladder cancer. These findings indicate a role for otoferlin in the carcinogenesis of these tumors, which requires further investigation to confirm and understand its exact role, particularly as it varies by tumor site. Targeting this protein may lead to new cancer therapies.
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Affiliation(s)
- Jean-Christophe Leclère
- Department of Head and Neck Surgery, Brest University Hospital, Brest, France
- Laboratory of Neurophysiologie de la Synapse Auditive, Université de Bordeaux, Bordeaux, France
| | - Didier Dulon
- Laboratory of Neurophysiologie de la Synapse Auditive, Université de Bordeaux, Bordeaux, France
- Institut de l’Audition, Institut Pasteur & INSERM UA06, Paris, France
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4
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Role of calcium-sensor proteins in cell membrane repair. Biosci Rep 2023; 43:232522. [PMID: 36728029 PMCID: PMC9970828 DOI: 10.1042/bsr20220765] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/03/2023] Open
Abstract
Cell membrane repair is a critical process used to maintain cell integrity and survival from potentially lethal chemical, and mechanical membrane injury. Rapid increases in local calcium levels due to a membrane rupture have been widely accepted as a trigger for multiple membrane-resealing models that utilize exocytosis, endocytosis, patching, and shedding mechanisms. Calcium-sensor proteins, such as synaptotagmins (Syt), dysferlin, S100 proteins, and annexins, have all been identified to regulate, or participate in, multiple modes of membrane repair. Dysfunction of membrane repair from inefficiencies or genetic alterations in these proteins contributes to diseases such as muscular dystrophy (MD) and heart disease. The present review covers the role of some of the key calcium-sensor proteins and their involvement in membrane repair.
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5
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Park J, Moon YJ, Kim DS. Miyoshi Muscular Dystrophy Type 1 with Mutated DYSF Gene Misdiagnosed as Becker Muscular Dystrophy: A Case Report and Literature Review. Genes (Basel) 2023; 14:200. [PMID: 36672942 PMCID: PMC9859596 DOI: 10.3390/genes14010200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/28/2022] [Accepted: 01/11/2023] [Indexed: 01/13/2023] Open
Abstract
Dysferlinopathy covers a spectrum of muscle disorder categorized by two major phenotypes, namely Miyoshi muscular dystrophy type 1 (MMD1, OMIM #254130) and limb-girdle muscular dystrophy autosomal recessive 2 (LGMDR2, OMIM #253601), and two minor symptoms, including asymptomatic hyperCKemia and distal myopathy with anterior tibial onset (DMAT, OMIM #606768). We report the first Korean MMD1 misdiagnosed as Becker muscular dystrophy (BMD), which was caused by a combination of compound heterozygous c.663 + 1G > C and p.Trp992Arg of the DYSF gene. A 70-year-old male previously diagnosed with BMD was admitted for genetic counseling. Since he was clinically suspected to have dysferlinopathy but not BMD, targeted panel sequencing was performed to discover the potential hereditary cause of the suspected muscular dystrophy in the proband. Consequently, two pathogenic single nucleotide variants of the DYSF gene, c.663 + 1G > C (rs398123800) and p.Trp992Arg (rs750028300), associated with dysferlinopathy were identified. These variants were previously reported with variant allele frequencies of 0.000455 (c.663 + 1G > C) and 0.000455 (c.2974T > C; p.Trp992Arg) in the Korean population. This report emphasizes the need for common variant screening in the diagnostic algorithms of certain muscle disorders or gene panels with potential pathogenic effects and high rates of recurrent variants.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
| | - Young Jae Moon
- Department of Orthopedic Surgery, Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
- Department of Biochemistry and Molecular Biology, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea
| | - Dal Sik Kim
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
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6
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Dominguez MJ, McCord JJ, Sutton RB. Redefining the architecture of ferlin proteins: Insights into multi-domain protein structure and function. PLoS One 2022; 17:e0270188. [PMID: 35901179 PMCID: PMC9333456 DOI: 10.1371/journal.pone.0270188] [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: 01/31/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Ferlins are complex, multi-domain proteins, involved in membrane trafficking, membrane repair, and exocytosis. The large size of ferlin proteins and the lack of consensus regarding domain boundaries have slowed progress in understanding molecular-level details of ferlin protein structure and function. However, in silico protein folding techniques have significantly enhanced our understanding of the complex ferlin family domain structure. We used RoseTTAFold to assemble full-length models for the six human ferlin proteins (dysferlin, myoferlin, otoferlin, Fer1L4, Fer1L5, and Fer1L6). Our full-length ferlin models were used to obtain objective domain boundaries, and these boundaries were supported by AlphaFold2 predictions. Despite the differences in amino acid sequence between the ferlin proteins, the domain ranges and distinct subdomains in the ferlin domains are remarkably consistent. Further, the RoseTTAFold/AlphaFold2 in silico boundary predictions allowed us to describe and characterize a previously unknown C2 domain, ubiquitous in all human ferlins, which we refer to as C2-FerA. At present, the ferlin domain-domain interactions implied by the full-length in silico models are predicted to have a low accuracy; however, the use of RoseTTAFold and AlphaFold2 as a domain finder has proven to be a powerful research tool for understanding ferlin structure.
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Affiliation(s)
- Matthew J. Dominguez
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
| | - Jon J. McCord
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
| | - R. Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
- Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
- * E-mail:
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7
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Schneiter R, Choudhary V. Seipin collaborates with the ER membrane to control the sites of lipid droplet formation. Curr Opin Cell Biol 2022; 75:102070. [PMID: 35306312 PMCID: PMC7615794 DOI: 10.1016/j.ceb.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 12/24/2022]
Abstract
Most cells store metabolic energy in lipid droplets (LDs). LDs are composed of a hydrophobic core, covered by a phospholipid monolayer, and functionalized by a specific set of proteins. Formation of LDs takes place in the endoplasmic reticulum (ER), where neutral lipid biosynthetic enzymes are located. Recent evidence indicate that this process is confined to specific ER subdomains, where proteins meet to initiate LD assembly. The lipodystrophy protein Seipin, is emerging as a major coordinator of LD biogenesis. Seipin forms a large oligomeric toroidal structure, which traps neutral lipids to promote LD nucleation. Here, we discuss the role of LD biogenesis factors that associate with Seipin to assemble functional LDs.
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Affiliation(s)
- Roger Schneiter
- University of Fribourg, Department of Biology, 1700, Fribourg, Switzerland.
| | - Vineet Choudhary
- All India Institute of Medical Sciences (AIIMS), Department of Biotechnology, New Delhi, 110029, India.
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8
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Deori NM, Infant T, Sundaravadivelu PK, Thummer RP, Nagotu S. Pex30 undergoes phosphorylation and regulates peroxisome number in Saccharomyces cerevisiae. Mol Genet Genomics 2022; 297:573-590. [PMID: 35218395 DOI: 10.1007/s00438-022-01872-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
Abstract
Pex30 is a dysferlin domain-containing protein whose role in peroxisome biogenesis has been studied by several research groups. Notably, recent studies have linked this protein to peroxisomes, endoplasmic reticulum and lipid bodies in Saccharomyces cerevisiae. Phosphoproteome studies of S. cerevisiae have identified several phosphorylation sites in Pex30. In this study we expressed and purified Pex30 from its native host. Analysis of the purified protein by circular dichroism spectroscopy showed that it retained its secondary structure and revealed primarily a helical structure. Further phosphorylation of Pex30 at three residues, Threonine 60, Serine 61 and Serine 511 was identified by mass spectrometry in this study. To understand the importance of this post-translational modification in peroxisome biogenesis, the identified residues were mutated to both non-phosphorylatable (alanine) and phosphomimetic (aspartic acid) variants. Upon analysis of the mutant variants by fluorescence microscopy, no alteration in the localization of the protein to ER and peroxisomes was observed. Interestingly, reduced number of peroxisomes were observed in cells expressing phosphomimetic mutations when cultured in peroxisome-inducing conditions. Our data suggest that phosphorylation and dephosphorylation of Pex30 may promote distinct interactions essential in regulating peroxisome number in a cell.
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Affiliation(s)
- Nayan Moni Deori
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Terence Infant
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Pradeep Kumar Sundaravadivelu
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India.
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9
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Ferreira JV, Carvalho P. Pex30-like proteins function as adaptors at distinct ER membrane contact sites. J Cell Biol 2021; 220:212563. [PMID: 34402813 PMCID: PMC8374871 DOI: 10.1083/jcb.202103176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/19/2021] [Accepted: 07/20/2021] [Indexed: 12/20/2022] Open
Abstract
Membrane lipids and proteins synthesized in the ER are used for de novo assembly of organelles, such as lipid droplets and peroxisomes. After assembly, the growth of these organelles is supported by ER-derived lipids transferred at membrane contact sites (MCSs). How ER sites for organelle biogenesis and lipid transfer are established and regulated is unclear. Here, we investigate how the ER membrane protein Pex30 and its family members Pex28, Pex29, Pex31, and Pex32 target and function at multiple MCSs. We show that different Pex30 complexes function at distinct ER domains and MCSs. Pex30 targets ER–peroxisome MCSs when bound to Pex28 and Pex32, organizes the nuclear–vacuolar junction when bound to Pex29, and promotes the biogenesis of lipid droplets independently of other family members. Importantly, the reticulon homology domain (RHD) mediates the assembly of the various Pex30 complexes. Given the role of RHD in membrane shaping, our findings offer a mechanistic link between MCS and regulation of membrane curvature.
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Affiliation(s)
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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10
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Mapping the interaction surface of scorpion β-toxins with an insect sodium channel. Biochem J 2021; 478:2843-2869. [PMID: 34195804 PMCID: PMC10081811 DOI: 10.1042/bcj20210336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023]
Abstract
The interaction of insect-selective scorpion depressant β-toxins (LqhIT2 and Lqh-dprIT3 from Leiurus quinquestriatus hebraeus) with the Blattella germanica sodium channel, BgNav1-1a, was investigated using site-directed mutagenesis, electrophysiological analyses, and structural modeling. Focusing on the pharmacologically defined binding site-4 of scorpion β-toxins at the voltage-sensing domain II (VSD-II), we found that charge neutralization of D802 in VSD-II greatly enhanced the channel sensitivity to Lqh-dprIT3. This was consistent with the high sensitivity of the splice variant BgNav2-1, bearing G802, to Lqh-dprIT3, and low sensitivity of BgNav2-1 mutant, G802D, to the toxin. Further mutational and electrophysiological analyses revealed that the sensitivity of the WT = D802E < D802G < D802A < D802K channel mutants to Lqh-dprIT3 correlated with the depolarizing shifts of activation in toxin-free channels. However, the sensitivity of single mutants involving IIS4 basic residues (K4E = WT << R1E < R2E < R3E) or double mutants (D802K = K4E/D802K = R3E/D802K > R2E/D802K > R1E/D802K > WT) did not correlate with the activation shifts. Using the cryo-EM structure of the Periplaneta americana channel, NavPaS, as a template and the crystal structure of LqhIT2, we constructed structural models of LqhIT2 and Lqh-dprIT3-c in complex with BgNav1-1a. These models along with the mutational analysis suggest that depressant toxins approach the salt-bridge between R1 and D802 at VSD-II to form contacts with linkers IIS1-S2, IIS3-S4, IIIP5-P1 and IIIP2-S6. Elimination of this salt-bridge enables deeper penetration of the toxin into a VSD-II gorge to form new contacts with the channel, leading to increased channel sensitivity to Lqh-dprIT3.
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11
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Retrospective analysis and reclassification of DYSF variants in a large French series of dysferlinopathy patients. Genet Med 2021; 23:1574-1577. [PMID: 33927379 DOI: 10.1038/s41436-021-01164-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/07/2021] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Recent evolution of sequencing technologies and the development of international standards in variant interpretation have profoundly changed the diagnostic approaches in clinical genetics. As a consequence, many variants that were initially claimed to be disease-causing can be now reclassified as benign or uncertain in light of the new data available. Unfortunately, the misclassified variants are still present in the scientific literature and variant databases, greatly interfering with interpretation of diagnostic sequencing results. Despite the urgent need, large-scale efforts to update the classifications of these variants are still not sufficient. METHODS We retrospectively analyzed 176 DYSF gene variants that were identified in dysferlinopathy patients referred to the Marseille Medical Genetics Department for diagnostic sequencing since 2001. RESULTS We reclassified all variants into five-tier American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) pathogenicity classes, revealing changed pathogenicity for 17 variants. We then updated the information for the variants that have been previously published in the variant database and submitted 46 additional DYSF variants. CONCLUSION Besides direct benefit for dysferlinopathy diagnostics, our study contributes to the much needed effort to reanalyze variants from previously published cohorts and to work with curators of variant databases to update the entries for erroneously classified variants.
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12
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Xia Q, Huang X, Huang J, Zheng Y, March ME, Li J, Wei Y. The Role of Autophagy in Skeletal Muscle Diseases. Front Physiol 2021; 12:638983. [PMID: 33841177 PMCID: PMC8027491 DOI: 10.3389/fphys.2021.638983] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle is the most abundant type of tissue in human body, being involved in diverse activities and maintaining a finely tuned metabolic balance. Autophagy, characterized by the autophagosome–lysosome system with the involvement of evolutionarily conserved autophagy-related genes, is an important catabolic process and plays an essential role in energy generation and consumption, as well as substance turnover processes in skeletal muscles. Autophagy in skeletal muscles is finely tuned under the tight regulation of diverse signaling pathways, and the autophagy pathway has cross-talk with other pathways to form feedback loops under physiological conditions and metabolic stress. Altered autophagy activity characterized by either increased formation of autophagosomes or inhibition of lysosome-autophagosome fusion can lead to pathological cascades, and mutations in autophagy genes and deregulation of autophagy pathways have been identified as one of the major causes for a variety of skeleton muscle disorders. The advancement of multi-omics techniques enables further understanding of the molecular and biochemical mechanisms underlying the role of autophagy in skeletal muscle disorders, which may yield novel therapeutic targets for these disorders.
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Affiliation(s)
- Qianghua Xia
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xubo Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jieru Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yongfeng Zheng
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Michael E March
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jin Li
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Yongjie Wei
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
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13
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Diercks BP, Jensen HH, Chalmers SB, Coode E, Vaughan MB, Tadayon R, Sáez PJ, Davis FM, Brohus M. The first junior European Calcium Society meeting: calcium research across scales, Kingdoms and countries. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:118999. [PMID: 33711364 DOI: 10.1016/j.bbamcr.2021.118999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/20/2021] [Indexed: 01/09/2023]
Abstract
The first junior European Calcium Society online meeting, held October 20-21, 2020, aimed to promote junior researchers in the Ca2+ community. The meeting included four scientific sessions, covering Ca2+ research from molecular detail to whole organisms. Each session featured one invited speaker and three speakers selected based on submitted abstracts, with the overall aim of actively involving early-career researchers. Consequently, the meeting underlined the diversity of Ca2+ physiology, by showcasing research across scales and Kingdoms, as presented by a correspondingly diverse speaker panel across career stages and countries. In this meeting report, we introduce the visions of the junior European Calcium Society board and summarize the meeting content.
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Affiliation(s)
- Björn-Philipp Diercks
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg - Eppendorf, Hamburg, Germany.
| | - Helene H Jensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Silke B Chalmers
- School of Pharmacy, The University of Queensland, Brisbane, Queensland, Australia
| | - Emily Coode
- School of Life, Health and Chemical Sciences, The Open University, Walton Hall, Milton Keynes, UK
| | - Michael B Vaughan
- Department of Physiology, School of Medicine, University College Cork, Cork, Ireland
| | - Roya Tadayon
- Department of Biochemistry, School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Pablo J Sáez
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg - Eppendorf, Hamburg, Germany
| | - Felicity M Davis
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Malene Brohus
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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14
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Izumi R, Takahashi T, Suzuki N, Niihori T, Ono H, Nakamura N, Katada S, Kato M, Warita H, Tateyama M, Aoki Y, Aoki M. The genetic profile of dysferlinopathy in a cohort of 209 cases: Genotype-phenotype relationship and a hotspot on the inner DysF domain. Hum Mutat 2020; 41:1540-1554. [PMID: 32400077 DOI: 10.1002/humu.24036] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/27/2022]
Abstract
Dysferlinopathy is a group of autosomal recessive muscular dystrophies caused by variants in the dysferlin gene (DYSF), with variable proximal and distal muscle involvement. We performed DYSF gene analyses of 200 cases suspected of having dysferlinopathy (Cohort 1), and identified diagnostic variants in 129/200 cases, including 19 novel variants. To achieve a comprehensive genetic profile of dysferlinopathy, we analyzed the variant data from 209 affected cases from unrelated 209 families, including 80 previously diagnosed and 129 newly diagnosed cases (Cohort 2). Among the 90 types of variants identified in 209 cases, the NM_003494.3: c.2997G>T; p.Trp999Cys, was the most frequent (96/420; 22.9%), followed by c.1566C>G; p.Tyr522* (45/420; 10.7%) on an allele base. p.Trp999Cys was found in 70/209 cases (33.5%), including 20/104 cases (19.2%) with the Miyoshi muscular phenotype and 43/82 cases (52.4%) with the limb-girdle phenotype. In the analysis of missense variants, p.Trp992Arg, p.Trp999Arg, p.Trp999Cys, p.Ser1000Phe, p.Arg1040Trp, and p.Arg1046His were located in the inner DysF domain, representing in 113/160 missense variants (70.6%). This large cohort highlighted the frequent missense variants located in the inner DysF domain as a hotspot for missense variants among our cohort of 209 cases (>95%, Japanese) and hinted at their potential as targets for future therapeutic strategies.
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Affiliation(s)
- Rumiko Izumi
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toshiaki Takahashi
- Department of Neurology, National Hospital Organization Sendai-Nishitaga Hospital, Sendai, Japan
| | - Naoki Suzuki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroya Ono
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Neurology, National Hospital Organization Iwate Hospital, Ichinoseki, Japan
| | - Naoko Nakamura
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shinichi Katada
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masaaki Kato
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hitoshi Warita
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Maki Tateyama
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Neurology, National Hospital Organization Iwate Hospital, Ichinoseki, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
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15
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Abstract
Ferlins are multiple-C2-domain proteins involved in Ca2+-triggered membrane dynamics within the secretory, endocytic and lysosomal pathways. In bony vertebrates there are six ferlin genes encoding, in humans, dysferlin, otoferlin, myoferlin, Fer1L5 and 6 and the long noncoding RNA Fer1L4. Mutations in DYSF (dysferlin) can cause a range of muscle diseases with various clinical manifestations collectively known as dysferlinopathies, including limb-girdle muscular dystrophy type 2B (LGMD2B) and Miyoshi myopathy. A mutation in MYOF (myoferlin) was linked to a muscular dystrophy accompanied by cardiomyopathy. Mutations in OTOF (otoferlin) can be the cause of nonsyndromic deafness DFNB9. Dysregulated expression of any human ferlin may be associated with development of cancer. This review provides a detailed description of functions of the vertebrate ferlins with a focus on muscle ferlins and discusses the mechanisms leading to disease development.
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16
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Zhu W, Zhou B, Zhao C, Ba Z, Xu H, Yan X, Liu W, Zhu B, Wang L, Ren C. Myoferlin, a multifunctional protein in normal cells, has novel and key roles in various cancers. J Cell Mol Med 2019; 23:7180-7189. [PMID: 31475450 PMCID: PMC6815776 DOI: 10.1111/jcmm.14648] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/30/2019] [Accepted: 07/29/2019] [Indexed: 12/24/2022] Open
Abstract
Myoferlin, a protein of the ferlin family, has seven C2 domains and exhibits activity in some cells, including myoblasts and endothelial cells. Recently, myoferlin was identified as a promising target and biomarker in non-small-cell lung cancer, breast cancer, pancreatic adenocarcinoma, hepatocellular carcinoma, colon cancer, melanoma, oropharyngeal squamous cell carcinoma, head and neck squamous cell carcinoma, clear cell renal cell carcinoma and endometrioid carcinoma. This evidence indicated that myoferlin was involved in the proliferation, invasion and migration of tumour cells, the mechanism of which mainly included promoting angiogenesis, vasculogenic mimicry, energy metabolism reprogramming, epithelial-mesenchymal transition and modulating exosomes. The roles of myoferlin in both normal cells and cancer cells are of great significance to provide novel and efficient methods of tumour treatment. In this review, we summarize recent studies and findings of myoferlin and suggest that myoferlin is a novel potential candidate for clinical diagnosis and targeted cancer therapy.
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Affiliation(s)
- Wei Zhu
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Bolun Zhou
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Chenxuan Zhao
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zhengqing Ba
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Hongjuan Xu
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xuejun Yan
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Weidong Liu
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Bin Zhu
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Lei Wang
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Caiping Ren
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Cancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, Hunan, China
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17
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Harsini FM, Bui AA, Rice AM, Chebrolu S, Fuson KL, Turtoi A, Bradberry M, Chapman ER, Sutton RB. Structural Basis for the Distinct Membrane Binding Activity of the Homologous C2A Domains of Myoferlin and Dysferlin. J Mol Biol 2019; 431:2112-2126. [PMID: 31004665 DOI: 10.1016/j.jmb.2019.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 02/03/2023]
Abstract
Dysferlin has been implicated in acute membrane repair processes, whereas myoferlin's activity is maximal during the myoblast fusion stage of early skeletal muscle cell development. Both proteins are similar in size and domain structure; however, despite the overall similarity, myoferlin's known physiological functions do not overlap with those of dysferlin. Here we present for the first time the X-ray crystal structure of human myoferlin C2A to 1.9 Å resolution bound to two divalent cations, and compare its three-dimensional structure and membrane binding activities to that of dysferlin C2A. We find that while dysferlin C2A binds membranes in a Ca2+-dependent manner, Ca2+ binding was the rate-limiting kinetic step for this interaction. Myoferlin C2A, on the other hand, binds two calcium ions with an affinity 3-fold lower than that of dysferlin C2A; and, surprisingly, myoferlin C2A binds only marginally to phospholipid mixtures with a high fraction of phosphatidylserine.
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Affiliation(s)
- Faraz M Harsini
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Anthony A Bui
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Anne M Rice
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Sukanya Chebrolu
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Kerry L Fuson
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Andrei Turtoi
- Tumor Microenvironment and Resistance to Treatment Lab, Institut de Recherche en Cancrologie de Montpellier, 34090 Montpellier, France; Institut du Cancer Montpellier, 34090 Montpellier, France; Universit Montpellier, 34298 Montpellier, France
| | - Mazdak Bradberry
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Edwin R Chapman
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, 53705, USA; Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - R Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
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18
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Lee JJA, Maruyama R, Duddy W, Sakurai H, Yokota T. Identification of Novel Antisense-Mediated Exon Skipping Targets in DYSF for Therapeutic Treatment of Dysferlinopathy. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:596-604. [PMID: 30439648 PMCID: PMC6234522 DOI: 10.1016/j.omtn.2018.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 12/20/2022]
Abstract
Dysferlinopathy is a progressive myopathy caused by mutations in the dysferlin (DYSF) gene. Dysferlin protein plays a major role in plasma-membrane resealing. Some patients with DYSF deletion mutations exhibit mild symptoms, suggesting some regions of DYSF can be removed without significantly impacting protein function. Antisense-mediated exon-skipping therapy uses synthetic molecules called antisense oligonucleotides to modulate splicing, allowing exons harboring or near genetic mutations to be removed and the open reading frame corrected. Previous studies have focused on DYSF exon 32 skipping as a potential therapeutic approach, based on the association of a mild phenotype with the in-frame deletion of exon 32. To date, no other DYSF exon-skipping targets have been identified, and the relationship between DYSF exon deletion pattern and protein function remains largely uncharacterized. In this study, we utilized a membrane-wounding assay to evaluate the ability of plasmid constructs carrying mutant DYSF, as well as antisense oligonucleotides, to rescue membrane resealing in patient cells. We report that multi-exon skipping of DYSF exons 26–27 and 28–29 rescues plasma-membrane resealing. Successful translation of these findings into the development of clinical antisense drugs would establish new therapeutic approaches that would be applicable to ∼5%–7% (exons 26–27 skipping) and ∼8% (exons 28–29 skipping) of dysferlinopathy patients worldwide.
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Affiliation(s)
- Joshua J A Lee
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Rika Maruyama
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - William Duddy
- Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry, United Kingdom
| | - Hidetoshi Sakurai
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada; The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB T6G 2H7, Canada.
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19
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Harsini FM, Chebrolu S, Fuson KL, White MA, Rice AM, Sutton RB. FerA is a Membrane-Associating Four-Helix Bundle Domain in the Ferlin Family of Membrane-Fusion Proteins. Sci Rep 2018; 8:10949. [PMID: 30026467 PMCID: PMC6053371 DOI: 10.1038/s41598-018-29184-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 07/04/2018] [Indexed: 12/15/2022] Open
Abstract
Ferlin proteins participate in such diverse biological events as vesicle fusion in C. elegans, fusion of myoblast membranes to form myotubes, Ca2+-sensing during exocytosis in the hair cells of the inner ear, and Ca2+-dependent membrane repair in skeletal muscle cells. Ferlins are Ca2+-dependent, phospholipid-binding, multi-C2 domain-containing proteins with a single transmembrane helix that spans a vesicle membrane. The overall domain composition of the ferlins resembles the proteins involved in exocytosis; therefore, it is thought that they participate in membrane fusion at some level. But if ferlins do fuse membranes, then they are distinct from other known fusion proteins. Here we show that the central FerA domain from dysferlin, myoferlin, and otoferlin is a novel four-helix bundle fold with its own Ca2+-dependent phospholipid-binding activity. Small-angle X-ray scattering (SAXS), spectroscopic, and thermodynamic analysis of the dysferlin, myoferlin, and otoferlin FerA domains, in addition to clinically-defined dysferlin FerA mutations, suggests that the FerA domain interacts with the membrane and that this interaction is enhanced by the presence of Ca2+.
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Affiliation(s)
- Faraz M Harsini
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430-6551, USA
| | - Sukanya Chebrolu
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430-6551, USA
| | - Kerry L Fuson
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430-6551, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anne M Rice
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - R Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX, 79430-6551, USA. .,Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430-6551, USA.
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20
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Woolger N, Bournazos A, Sophocleous RA, Evesson FJ, Lek A, Driemer B, Sutton RB, Cooper ST. Limited proteolysis as a tool to probe the tertiary conformation of dysferlin and structural consequences of patient missense variant L344P. J Biol Chem 2017; 292:18577-18591. [PMID: 28904177 DOI: 10.1074/jbc.m117.790014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/13/2017] [Indexed: 12/19/2022] Open
Abstract
Dysferlin is a large transmembrane protein that plays a key role in cell membrane repair and underlies a recessive form of inherited muscular dystrophy. Dysferlinopathy is characterized by absence or marked reduction of dysferlin protein with 43% of reported pathogenic variants being missense variants that span the length of the dysferlin protein. The unique structure of dysferlin, with seven tandem C2 domains separated by linkers, suggests dysferlin may dynamically associate with phospholipid membranes in response to Ca2+ signaling. However, the overall conformation of the dysferlin protein is uncharacterized. To dissect the structural architecture of dysferlin, we have applied the method of limited proteolysis, which allows nonspecific digestion of unfolded peptides by trypsin. Using five antibodies spanning the dysferlin protein, we identified a highly reproducible jigsaw map of dysferlin fragments protected from digestion. Our data infer a modular architecture of four tertiary domains: 1) C2A, which is readily removed as a solo domain; 2) midregion C2B-C2C-Fer-DysF, commonly excised as an intact module, with subdigestion to different fragments suggesting several dynamic folding options; 3) C-terminal four-C2 domain module; and 4) calpain-cleaved mini-dysferlinC72, which is particularly resistant to proteolysis. Importantly, we reveal a patient missense variant, L344P, that largely escapes proteasomal surveillance and shows subtle but clear changes in tertiary conformation. Accompanying evidence from immunohistochemistry and flow cytometry using antibodies with conformationally sensitive epitopes supports proteolysis data. Collectively, we provide insight into the structural topology of dysferlin and show how a single missense mutation within dysferlin can exert local changes in tertiary conformation.
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Affiliation(s)
- Natalie Woolger
- From the Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead 2145, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine, University of Sydney, Sydney 2006, Australia, and
| | - Adam Bournazos
- From the Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead 2145, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine, University of Sydney, Sydney 2006, Australia, and
| | - Reece A Sophocleous
- From the Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead 2145, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine, University of Sydney, Sydney 2006, Australia, and
| | - Frances J Evesson
- From the Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead 2145, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine, University of Sydney, Sydney 2006, Australia, and
| | - Angela Lek
- From the Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead 2145, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine, University of Sydney, Sydney 2006, Australia, and
| | - Birgit Driemer
- From the Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead 2145, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine, University of Sydney, Sydney 2006, Australia, and
| | - R Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
| | - Sandra T Cooper
- From the Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead 2145, Australia, .,Discipline of Child and Adolescent Health, Faculty of Medicine, University of Sydney, Sydney 2006, Australia, and
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21
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Jin SQ, Yu M, Zhang W, Lyu H, Yuan Y, Wang ZX. Dysferlin Gene Mutation Spectrum in a Large Cohort of Chinese Patients with Dysferlinopathy. Chin Med J (Engl) 2017; 129:2287-93. [PMID: 27647186 PMCID: PMC5040013 DOI: 10.4103/0366-6999.190671] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Dysferlinopathy is caused by mutations in the dysferlin (DYSF) gene. Here, we described the genetic features of a large cohort of Chinese patients with this disease. METHODS Eighty-nine index patients were included in the study. DYSF gene analysis was performed by Sanger sequencing in 41 patients and targeted next generation sequencing (NGS) in 48 patients. Multiplex ligation-dependent probe amplification (MLPA) was performed to detect exon duplication/deletion in patients with only one pathogenic mutation. RESULTS Among the 89 index patients, 79 patients were demonstrated to carry two disease-causing (73 cases) or possibly disease-causing mutations (6 cases), including 26 patients with homozygous mutations. We identified 105 different mutations, including 59 novel ones. Notably, in 13 patients in whom only one pathogenic mutation was initially found by Sanger sequencing or NGS, 3 were further identified to carry exon deletions by MLPA. The mutations identified in this study appeared to cluster in the N-terminal region. Mutation types included missense mutations (30.06%), nonsense mutations (17.18%), frameshift mutations (30.67%), in-frame deletions (2.45%), intronic mutations (17.79%), and exonic rearrangement (1.84%). No genotype-phenotype correlation was identified. CONCLUSIONS DYSF mutations in Chinese patients clustered in the N-terminal region of the gene. Exonic rearrangements were found in 23% of patients with only one pathogenic mutation identified by Sanger sequencing or NGS. The novel mutations found in this study greatly expanded the mutational spectrum of dysferlinopathy.
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Affiliation(s)
- Su-Qin Jin
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - He Lyu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Zhao-Xia Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
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22
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Redpath GMI, Sophocleous RA, Turnbull L, Whitchurch CB, Cooper ST. Ferlins Show Tissue-Specific Expression and Segregate as Plasma Membrane/Late Endosomal or Trans-Golgi/Recycling Ferlins. Traffic 2016; 17:245-66. [PMID: 26707827 DOI: 10.1111/tra.12370] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 01/10/2023]
Abstract
Ferlins are a family of transmembrane-anchored vesicle fusion proteins uniquely characterized by 5-7 tandem cytoplasmic C2 domains, Ca(2+)-regulated phospholipid-binding domains that regulate vesicle fusion in the synaptotagmin family. In humans, dysferlin mutations cause limb-girdle muscular dystrophy type 2B (LGMD2B) due to defective Ca(2+)-dependent, vesicle-mediated membrane repair and otoferlin mutations cause non-syndromic deafness due to defective Ca(2+)-triggered auditory neurotransmission. In this study, we describe the tissue-specific expression, subcellular localization and endocytic trafficking of the ferlin family. Studies of endosomal transit together with 3D-structured illumination microscopy reveals dysferlin and myoferlin are abundantly expressed at the PM and cycle to Rab7-positive late endosomes, supporting potential roles in the late-endosomal pathway. In contrast, Fer1L6 shows concentrated localization to a specific compartment of the trans-Golgi/recycling endosome, cycling rapidly between this compartment and the PM via Rab11 recycling endosomes. Otoferlin also shows trans-Golgi to PM cycling, with very low levels of PM otoferlin suggesting either brief PM residence, or rare incorporation of otoferlin molecules into the PM. Thus, type-I and type-II ferlins segregate as PM/late-endosomal or trans-Golgi/recycling ferlins, consistent with different ferlins mediating vesicle fusion events in specific subcellular locations.
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Affiliation(s)
- Gregory M I Redpath
- Institute for Neuroscience and Muscle Research, Kid's Research Institute, Children's Hospital at Westmead, Sydney, Australia.,Discipline of Paediatrics and Child Health, Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Reece A Sophocleous
- Institute for Neuroscience and Muscle Research, Kid's Research Institute, Children's Hospital at Westmead, Sydney, Australia
| | - Lynne Turnbull
- Microbial Imaging Facility, The iThree Institute, University of Technology Sydney, Ultimo, Australia
| | - Cynthia B Whitchurch
- Microbial Imaging Facility, The iThree Institute, University of Technology Sydney, Ultimo, Australia
| | - Sandra T Cooper
- Institute for Neuroscience and Muscle Research, Kid's Research Institute, Children's Hospital at Westmead, Sydney, Australia.,Discipline of Paediatrics and Child Health, Faculty of Medicine, University of Sydney, Sydney, Australia
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23
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Espinoza-Fonseca LM. Pathogenic mutation R959W alters recognition dynamics of dysferlin inner DysF domain. MOLECULAR BIOSYSTEMS 2016; 12:973-81. [PMID: 26806107 DOI: 10.1039/c5mb00772k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dysferlin, a 220 kD protein, plays a major role in regulating plasma membrane repair in muscle cells. Mutations in the dysferlin inner DysF domain are known to cause different types of muscular dystrophy, including limb-girdle muscular dystrophy type 2B (LGMD2B) and Miyoshi myopathy (MM). Replacement of arginine in position 959 by tryptophan has been frequently associated with both LGMD2B and MM, but the molecular mechanisms by which this mutation alters dysferlin function remain unknown. In this study, we have used protein binding site predictions and microsecond molecular dynamics (MD) simulations to determine the effects pathogenic mutation R959W on the structural dynamics of dysferlin inner DysF domain. Analysis of 2 μs long MD trajectories revealed that mutation R959W does not induce local destabilization, unfolding or misfolding of the domain. We used a binding site predictor to discover a protein-binding site (residues T958-I966 and E1031-H1037) that resembles pincers in shape. Cartesian principal component analysis and interresidue distance distributions of the wild-type domain showed that the predicted protein-binding site undergoes a pincer motion, and populates two structural states, open and closed. We found that mutation R959W inhibits the pincer motion of the protein-binding site and completely shifts the equilibrium toward the open state. These differences in the structural dynamics of the predicted binding site suggest that mutation R959W alters recognition dynamics of the inner DysF domain. Based on these findings and on previous experimental studies, we propose a novel role for the inner DysF domain in muscle membrane repair through recruitment of dysferlin to plasma membrane. In conclusion, these findings have important implications for our understanding of the structural aspects of muscular dystrophies in atomic-level resolution.
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Affiliation(s)
- L Michel Espinoza-Fonseca
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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24
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The Dysferlin Domain-Only Protein, Spo73, Is Required for Prospore Membrane Extension in Saccharomyces cerevisiae. mSphere 2015; 1:mSphere00038-15. [PMID: 27303688 PMCID: PMC4863634 DOI: 10.1128/msphere.00038-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 11/18/2015] [Indexed: 01/11/2023] Open
Abstract
Sporulation of Saccharomyces cerevisiae is a developmental process in which an ascus containing four haploid spores forms from a diploid cell. During this process, newly formed membrane structures called prospore membranes extend along the nuclear envelope and engulf and package daughter nuclei along with cytosol and organelles to form precursors of spores. Proteins involved in prospore membrane extension, Vps13 and Spo71, have recently been reported; however, the overall mechanism of membrane extension remains unclear. Here, we identified Spo73 as an additional factor involved in prospore membrane extension. Analysis of a spo73∆ mutant revealed that it shows defects similar to those of a spo71∆ mutant during prospore membrane formation. Spo73 localizes to the prospore membrane, and this localization is independent of Spo71 and Vps13. In contrast, a Spo73 protein carrying mutations in a surface basic patch mislocalizes to the cytoplasm and overexpression of Spo71 can partially rescue localization to the prospore membrane. Similar to spo71∆ mutants, spo73∆ mutants display genetic interactions with the mutations in the SMA2 and SPO1 genes involved in prospore membrane bending. Further, our bioinformatic analysis revealed that Spo73 is a dysferlin domain-only protein. Thus, these results suggest that a dysferlin domain-only protein, Spo73, functions with a dual pleckstrin homology domain protein, Spo71, in prospore membrane extension. Analysis of Spo73 will provide insights into the conserved function of dysferlin domains, which is related to dysferlinopathy. IMPORTANCE Prospore membrane formation consists of de novo double-membrane formation, which occurs during the developmental process of sporulation in Saccharomyces cerevisiae. Membranes are formed into their proper size and shape, and thus, prospore membrane formation has been studied as a general model of membrane formation. We identified SPO73, previously shown to be required for spore wall formation, as an additional gene involved in prospore membrane extension. Genetic and cell biological analyses suggested that Spo73 functions on the prospore membrane with other factors in prospore membrane extension, counteracting the bending force of the prospore membrane. Spo73 is the first dysferlin domain-only protein ever analyzed. The dysferlin domain is conserved from yeast to mammals and is found in dysferlin proteins, which are involved in dysferlinopathy, although the precise function of the domain is unknown. Continued analysis of Spo73 will contribute to our understanding of the function of dysferlin domains and dysferlinopathy.
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25
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Mnatsakanyan N, Nishtala SN, Pandhare A, Fiori MC, Goyal R, Pauwels JE, Navetta AF, Ahrorov A, Jansen M. Functional Chimeras of GLIC Obtained by Adding the Intracellular Domain of Anion- and Cation-Conducting Cys-Loop Receptors. Biochemistry 2015; 54:2670-2682. [PMID: 25861708 DOI: 10.1021/acs.biochem.5b00203] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pentameric ligand-gated ion channels (pLGICs), also called Cys-loop receptors in eukaryotic superfamily members, play diverse roles in neurotransmission and serve as primary targets for many therapeutic drugs. Structural studies of full-length eukaryotic pLGICs have been challenging because of glycosylation, large size, pentameric assembly, and hydrophobicity. X-ray structures of prokaryotic pLGICs, including the Gloeobacter violaceus LGIC (GLIC) and the Erwinia chrysanthemi LGIC (ELIC), and truncated eukaryotic pLGICs have significantly improved and complemented the understanding of structural details previously obtained with acetylcholine-binding protein and Torpedo nicotinic acetylcholine receptors. Prokaryotic pLGICs share their overall structural features with eukaryotic pLGICs for the ligand-binding extracellular and channel-lining transmembrane domains. The large intracellular domain (ICD) is present only in eukaryotic members and is characterized by a low level of sequence conservation and significant variability in length (50-250 amino acids), making the ICD a potential target for the modulation of specific pLGIC subunits. None of the structures includes a complete ICD. Here, we created chimeras by adding the ICD of cation-conducting (nAChR-α7) and anion-conducting (GABAρ1, Glyα1) eukaryotic homopentamer-forming pLGICs to GLIC. GLIC-ICD chimeras assemble into pentamers to form proton-gated channels, as does the parent GLIC. Additionally, the sensitivity of the chimeras toward modulation of functional maturation by chaperone protein RIC-3 is preserved as in those of the parent eukaryotic channels. For a previously described GLIC-5HT3A-ICD chimera, we now provide evidence of its successful large-scale expression and purification to homogeneity. Overall, the chimeras provide valuable tools for functional and structural studies of eukaryotic pLGIC ICDs.
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Affiliation(s)
- Nelli Mnatsakanyan
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Sita Nirupama Nishtala
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Akash Pandhare
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Mariana C Fiori
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Raman Goyal
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Jonathan E Pauwels
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79430, United States
| | - Andrew F Navetta
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Medical Student Summer Research Program, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Afzal Ahrorov
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Undergraduate Science Education Program of the Howard Hughes Medical Institute, Texas Tech University, Lubbock, Texas 79430, United States
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States.,Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
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