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Veit S, Paweletz LC, Günther Pomorski T. Determination of membrane protein orientation upon liposomal reconstitution down to the single vesicle level. Biol Chem 2023; 404:647-661. [PMID: 36857289 DOI: 10.1515/hsz-2022-0325] [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: 11/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023]
Abstract
Reconstitution of membrane proteins into liposomal membranes represents a key technique in enabling functional analysis under well-defined conditions. In this review, we provide a brief introduction to selected methods that have been developed to determine membrane protein orientation after reconstitution in liposomes, including approaches based on proteolytic digestion with proteases, site-specific labeling, fluorescence quenching and activity assays. In addition, we briefly highlight new strategies based on single vesicle analysis to address the problem of sample heterogeneity.
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Affiliation(s)
- Sarina Veit
- Department of Molecular Biochemistry , Faculty of Chemistry and Biochemistry , NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Laura Charlotte Paweletz
- Department of Molecular Biochemistry , Faculty of Chemistry and Biochemistry , NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry , Faculty of Chemistry and Biochemistry , NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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Lee S, Lee SB, Sung N, Xu WW, Chang C, Kim HE, Catic A, Tsai FTF. Structural basis of impaired disaggregase function in the oxidation-sensitive SKD3 mutant causing 3-methylglutaconic aciduria. Nat Commun 2023; 14:2028. [PMID: 37041140 PMCID: PMC10090083 DOI: 10.1038/s41467-023-37657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/23/2023] [Indexed: 04/13/2023] Open
Abstract
Mitochondria are critical to cellular and organismal health. To prevent damage, mitochondria have evolved protein quality control machines to survey and maintain the mitochondrial proteome. SKD3, also known as CLPB, is a ring-forming, ATP-fueled protein disaggregase essential for preserving mitochondrial integrity and structure. SKD3 deficiency causes 3-methylglutaconic aciduria type VII (MGCA7) and early death in infants, while mutations in the ATPase domain impair protein disaggregation with the observed loss-of-function correlating with disease severity. How mutations in the non-catalytic N-domain cause disease is unknown. Here, we show that the disease-associated N-domain mutation, Y272C, forms an intramolecular disulfide bond with Cys267 and severely impairs SKD3Y272C function under oxidizing conditions and in living cells. While Cys267 and Tyr272 are found in all SKD3 isoforms, isoform-1 features an additional α-helix that may compete with substrate-binding as suggested by crystal structure analyses and in silico modeling, underscoring the importance of the N-domain to SKD3 function.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sang Bum Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nuri Sung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wendy W Xu
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
- Louisiana State University Health New Orleans School of Medicine, New Orleans, LA, 70112, USA
| | - Changsoo Chang
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Hyun-Eui Kim
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Andre Catic
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
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Modeling the cellular fate of alpha-synuclein aggregates: A pathway to pathology. Curr Opin Neurobiol 2022; 72:171-177. [PMID: 35131527 PMCID: PMC9235864 DOI: 10.1016/j.conb.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 01/07/2022] [Accepted: 01/20/2022] [Indexed: 02/06/2023]
Abstract
Parkinson's disease is a progressive neurodegenerative disorder that is characterized by pathological protein inclusions that form in the brains of patients, leading to neuron loss and the observed clinical symptoms. These inclusions, containing aggregates of the protein α-Synuclein, spread throughout the brain as the disease progresses. This spreading follows patterns that inform our understanding of the disease. One way to further our understanding of disease progression is to model the discrete steps from when a cell first encounters an aggregate to when those aggregates propagate to new cells. This review will serve to highlight the recent progress made in the effort to better understand the mechanistic steps that determine how this propagation happens at the cellular level.
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Shillcock JC, Hastings J, Riguet N, Lashuel HA. Non-monotonic fibril surface occlusion by GFP tags from coarse-grained molecular simulations. Comput Struct Biotechnol J 2021; 20:309-321. [PMID: 35070162 PMCID: PMC8753129 DOI: 10.1016/j.csbj.2021.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/23/2022] Open
Abstract
The pathological growth of amyloid fibrils in neurons underlies the progression of neurodegenerative diseases including Alzheimer's and Parkinson's disease. Fibrils form when soluble monomers oligomerise in the cytoplasm. Their subsequent growth occurs via nucleated polymerization mechanisms involving the free ends of the fibrils augmented by secondary nucleation of new oligomers at their surface. Amyloid fibrils possess a complex interactome with diffusing cytoplasmic proteins that regulates many aspects of their growth, seeding capacity, biochemical activity and transition to pathological inclusions in diseased brains. Changes to their surface are also expected to modify their interactome, pathogenicity and spreading in the brain. Many assays visualise fibril formation, growth and inclusion formation by decorating monomeric proteins with fluorescent tags such as GFP. Recent studies from our group suggest that tags with sizes comparable to the fibril radius may modify the fibril surface accessibility and thus their PTM pattern, interactome and ability to form inclusions. Using coarse-grained molecular simulations of a single alpha synuclein fibril tagged with GFP we find that thermal fluctuations of the tags create a non-monotonic, size-dependent sieve around the fibril that perturbs its interactome with diffusing species. Our results indicate that experiments using tagged and untagged monomers to study the growth and interactome of fibrils should be compared with caution, and the confounding effects of the tags are more complex than a reduction in surface accessibility. The prevalence of fluorescent tags in amyloid fibril growth experiments suggests this has implications beyond the specific alpha synuclein fibrils we model here.
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Affiliation(s)
- Julian C. Shillcock
- Blue Brain Project, Ecole polytechnique fédérale de Lausanne, CH-1202 Geneva, Switzerland
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Janna Hastings
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Bioinformatics Competence Center, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Nathan Riguet
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Hilal A. Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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