1
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Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. Lipid scrambling is a general feature of protein insertases. Proc Natl Acad Sci U S A 2024; 121:e2319476121. [PMID: 38621120 DOI: 10.1073/pnas.2319476121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/13/2024] [Indexed: 04/17/2024] Open
Abstract
Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases." These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far-overlooked role in membrane dynamics as scramblases.
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Affiliation(s)
- Dazhi Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520
| | - Cristian Rocha-Roa
- Department of Biology, University of Fribourg, Fribourg CH-1700, Switzerland
| | - Matthew A Schilling
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520
| | - Karin M Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg CH-1700, Switzerland
- Swiss National Center for Competence in Research Bio-Inspired Materials, University of Fribourg, Fribourg CH-1700, Switzerland
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2
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Zhu Y, Akkaya KC, Ruta J, Yokoyama N, Wang C, Ruwolt M, Lima DB, Lehmann M, Liu F. Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies. Nat Commun 2024; 15:3290. [PMID: 38632225 PMCID: PMC11024108 DOI: 10.1038/s41467-024-47569-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
The functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.
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Affiliation(s)
- Ying Zhu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Kerem Can Akkaya
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Julia Ruta
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Nanako Yokoyama
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Cong Wang
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Max Ruwolt
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Diogo Borges Lima
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Martin Lehmann
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117, Berlin, Germany.
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3
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Li Y, Guo Y, Bröer A, Dai L, Brӧer S, Yan R. Cryo-EM structure of the human Asc-1 transporter complex. Nat Commun 2024; 15:3036. [PMID: 38589439 PMCID: PMC11001984 DOI: 10.1038/s41467-024-47468-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/02/2024] [Indexed: 04/10/2024] Open
Abstract
The Alanine-Serine-Cysteine transporter 1 (Asc-1 or SLC7A10) forms a crucial heterodimeric transporter complex with 4F2hc (SLC3A2) through a covalent disulfide bridge. This complex enables the sodium-independent transport of small neutral amino acids, including L-Alanine (L-Ala), Glycine (Gly), and D-Serine (D-Ser), within the central nervous system (CNS). D-Ser and Gly are two key endogenous glutamate co-agonists that activate N-methyl-d-aspartate (NMDA) receptors by binding to the allosteric site. Mice deficient in Asc-1 display severe symptoms such as tremors, ataxia, and seizures, leading to early postnatal death. Despite its physiological importance, the functional mechanism of the Asc-1-4F2hc complex has remained elusive. Here, we present cryo-electron microscopy (cryo-EM) structures of the human Asc-1-4F2hc complex in its apo state, D-Ser bound state, and L-Ala bound state, resolved at 3.6 Å, 3.5 Å, and 3.4 Å, respectively. Through detailed structural analysis and transport assays, we uncover a comprehensive alternating access mechanism that underlies conformational changes in the complex. In summary, our findings reveal the architecture of the Asc-1 and 4F2hc complex and provide valuable insights into substrate recognition and the functional cycle of this essential transporter complex.
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Affiliation(s)
- Yaning Li
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yingying Guo
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Angelika Bröer
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Lu Dai
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
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4
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Bharambe N, Li Z, Seiferth D, Balakrishna AM, Biggin PC, Basak S. Cryo-EM structures of prokaryotic ligand-gated ion channel GLIC provide insights into gating in a lipid environment. Nat Commun 2024; 15:2967. [PMID: 38580666 PMCID: PMC10997623 DOI: 10.1038/s41467-024-47370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/28/2024] [Indexed: 04/07/2024] Open
Abstract
GLIC, a proton-activated prokaryotic ligand-gated ion channel, served as a model system for understanding the eukaryotic counterparts due to their structural and functional similarities. Despite extensive studies conducted on GLIC, the molecular mechanism of channel gating in the lipid environment requires further investigation. Here, we present the cryo-EM structures of nanodisc-reconstituted GLIC at neutral and acidic pH in the resolution range of 2.6 - 3.4 Å. In our apo state at pH 7.5, the extracellular domain (ECD) displays conformational variations compared to the existing apo structures. At pH 4.0, three distinct conformational states (C1, C2 and O states) are identified. The protonated structures exhibit a compacted and counter-clockwise rotated ECD compared with our apo state. A gradual widening of the pore in the TMD is observed upon reducing the pH, with the widest pore in O state, accompanied by several layers of water pentagons. The pore radius and molecular dynamics (MD) simulations suggest that the O state represents an open conductive state. We also observe state-dependent interactions between several lipids and proteins that may be involved in the regulation of channel gating. Our results provide comprehensive insights into the importance of lipids impact on gating.
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Affiliation(s)
- Nikhil Bharambe
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Zhuowen Li
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - David Seiferth
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Sandip Basak
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 639798, Singapore.
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5
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Torkamannejad S, Chang G, Aroge FA, Sun B. Single Isotopologue for In-Sample Calibration and Absolute Quantitation by LC-MS/MS. J Proteome Res 2024; 23:1351-1359. [PMID: 38445850 DOI: 10.1021/acs.jproteome.3c00848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Targeted mass spectrometry (MS)-based absolute quantitative analysis has been increasingly used in biomarker discovery. The ability to accurately measure the masses by MS enabled the use of isotope-incorporated surrogates having virtually identical physiochemical properties with the target analytes as calibrators. Such a unique capacity allowed for accurate in-sample calibration. Current in-sample calibration uses multiple isotopologues or structural analogues for both the surrogate and the internal standard. Here, we simplified this common practice by using endogenous light peptides as the internal standards and used a mathematical deduction of "heavy matching light, HML" to directly quantify an endogenous analyte. This method provides all necessary assay performance parameters in the authentic matrix, including the lower limit of quantitation (LLOQ) and intercept of the calibration curve, by using only a single isotopologue of the analyte. This method can be applied to the quantitation of proteins, peptides, and small molecules. Using this method, we quantified the efficiency of heart tissue digestion and recovery using sodium deoxycholate as a detergent and two spiked exogenous proteins as mimics of heart proteins. The results demonstrated the robustness of the assay.
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Affiliation(s)
- Soroush Torkamannejad
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Ge Chang
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Fabusuyi A Aroge
- School of Mechatronic Systems Engineering, Simon Fraser University, Surrey, British Columbia V3T0A3, Canada
| | - Bingyun Sun
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
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6
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Pabst G, Keller S. Exploring membrane asymmetry and its effects on membrane proteins. Trends Biochem Sci 2024; 49:333-345. [PMID: 38355393 DOI: 10.1016/j.tibs.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/08/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Plasma membranes utilize free energy to maintain highly asymmetric, non-equilibrium distributions of lipids and proteins between their two leaflets. In this review we discuss recent progress in quantitative research enabled by using compositionally controlled asymmetric model membranes. Both experimental and computational studies have shed light on the nuanced mechanisms that govern the structural and dynamic coupling between compositionally distinct bilayer leaflets. This coupling can increase the membrane bending rigidity and induce order - or lipid domains - across the membrane. Furthermore, emerging evidence indicates that integral membrane proteins not only respond to asymmetric lipid distributions but also exhibit intriguing asymmetric properties themselves. We propose strategies to advance experimental research, aiming for a deeper, quantitative understanding of membrane asymmetry, which carries profound implications for cellular physiology.
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Affiliation(s)
- Georg Pabst
- Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Graz 8010, Austria; BioTechMed-Graz, Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria.
| | - Sandro Keller
- Biophysics, Institute of Molecular Bioscience (IMB), NAWI Graz, University of Graz, Graz 8010, Austria; BioTechMed-Graz, Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria
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7
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Nijland M, Lefebvre SN, Thangaratnarajah C, Slotboom DJ. Bidirectional ATP-driven transport of cobalamin by the mycobacterial ABC transporter BacA. Nat Commun 2024; 15:2626. [PMID: 38521790 PMCID: PMC10960864 DOI: 10.1038/s41467-024-46917-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
BacA is a mycobacterial ATP-binding cassette (ABC) transporter involved in the translocation of water-soluble compounds across the lipid bilayer. Whole-cell-based assays have shown that BacA imports cobalamin as well as unrelated hydrophilic compounds such as the antibiotic bleomycin and the antimicrobial peptide Bac7 into the cytoplasm. Surprisingly, there are indications that BacA also mediates the export of different antibacterial compounds, which is difficult to reconcile with the notion that ABC transporters generally operate in a strictly unidirectional manner. Here we resolve this conundrum by developing a fluorescence-based transport assay to monitor the transport of cobalamin across liposomal membranes. We find that BacA transports cobalamin in both the import and export direction. This highly unusual bidirectionality suggests that BacA is mechanistically distinct from other ABC transporters and facilitates ATP-driven diffusion, a function that may be important for the evolvability of specific transporters, and may bring competitive advantages to microbial communities.
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Affiliation(s)
- Mark Nijland
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Solène N Lefebvre
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Chancievan Thangaratnarajah
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Dirk J Slotboom
- Faculty of Science and Engineering, Groningen, Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
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8
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Arratia LM, Bermudes-Contreras JD, Juarez-Monroy JA, Romero-Macías EA, Luna-Rojas JC, López-Hidalgo M, Vega AV, Zamorano-Carrillo A. Experimental and computational evidence that Calpain-10 binds to the carboxy terminus of Na V1.2 and Na V1.6. Sci Rep 2024; 14:6761. [PMID: 38514708 PMCID: PMC10957924 DOI: 10.1038/s41598-024-57117-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Voltage-gated sodium channels (NaV) are pivotal proteins responsible for initiating and transmitting action potentials. Emerging evidence suggests that proteolytic cleavage of sodium channels by calpains is pivotal in diverse physiological scenarios, including ischemia, brain injury, and neuropathic pain associated with diabetes. Despite this significance, the precise mechanism by which calpains recognize sodium channels, especially given the multiple calpain isoforms expressed in neurons, remains elusive. In this work, we show the interaction of Calpain-10 with NaV's C-terminus through a yeast 2-hybrid assay screening of a mouse brain cDNA library and in vitro by GST-pulldown. Later, we also obtained a structural and dynamic hypothesis of this interaction by modeling, docking, and molecular dynamics simulation. These results indicate that Calpain-10 interacts differentially with the C-terminus of NaV1.2 and NaV1.6. Calpain-10 interacts with NaV1.2 through domains III and T in a stable manner. In contrast, its interaction with NaV1.6 involves domains II and III, which could promote proteolysis through the Cys-catalytic site and C2 motifs.
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Affiliation(s)
- Luis Manuel Arratia
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Juan David Bermudes-Contreras
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Jorge Armando Juarez-Monroy
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Erik Alan Romero-Macías
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico
- Doctorado en Ciencias Biomédicas, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla Edo, Mexico City, Mexico
| | - Julio Cesar Luna-Rojas
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico
- Maestría en Neurobiología, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla Edo, Mexico City, Mexico
| | - Marisol López-Hidalgo
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Ana Victoria Vega
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico.
| | - Absalom Zamorano-Carrillo
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico.
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9
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Liu H, Zakrzewicz D, Nosol K, Irobalieva RN, Mukherjee S, Bang-Sørensen R, Goldmann N, Kunz S, Rossi L, Kossiakoff AA, Urban S, Glebe D, Geyer J, Locher KP. Structure of antiviral drug bulevirtide bound to hepatitis B and D virus receptor protein NTCP. Nat Commun 2024; 15:2476. [PMID: 38509088 PMCID: PMC10954734 DOI: 10.1038/s41467-024-46706-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Cellular entry of the hepatitis B and D viruses (HBV/HDV) requires binding of the viral surface polypeptide preS1 to the hepatobiliary transporter Na+-taurocholate co-transporting polypeptide (NTCP). This interaction can be blocked by bulevirtide (BLV, formerly Myrcludex B), a preS1 derivative and approved drug for treating HDV infection. Here, to elucidate the basis of this inhibitory function, we determined a cryo-EM structure of BLV-bound human NTCP. BLV forms two domains, a plug lodged in the bile salt transport tunnel of NTCP and a string that covers the receptor's extracellular surface. The N-terminally attached myristoyl group of BLV interacts with the lipid-exposed surface of NTCP. Our structure reveals how BLV inhibits bile salt transport, rationalizes NTCP mutations that decrease the risk of HBV/HDV infection, and provides a basis for understanding the host specificity of HBV/HDV. Our results provide opportunities for structure-guided development of inhibitors that target HBV/HDV docking to NTCP.
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Affiliation(s)
- Hongtao Liu
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Dariusz Zakrzewicz
- Institute of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Kamil Nosol
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | | | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Rose Bang-Sørensen
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Nora Goldmann
- Institute of Medical Virology, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF) - Giessen-Marburg-Langen Partner Site, Giessen, Germany
| | - Sebastian Kunz
- Institute of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Lorenzo Rossi
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany.
- German Center for Infection Research (DZIF) - partner site Heidelberg, Heidelberg, Germany.
| | - Dieter Glebe
- Institute of Medical Virology, National Reference Centre for Hepatitis B Viruses and Hepatitis D Viruses, Justus Liebig University Giessen, Giessen, Germany.
- German Center for Infection Research (DZIF) - Giessen-Marburg-Langen Partner Site, Giessen, Germany.
| | - Joachim Geyer
- Institute of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany.
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
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10
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Sadhu RK, Luciano M, Xi W, Martinez-Torres C, Schröder M, Blum C, Tarantola M, Villa S, Penič S, Iglič A, Beta C, Steinbock O, Bodenschatz E, Ladoux B, Gabriele S, Gov NS. A minimal physical model for curvotaxis driven by curved protein complexes at the cell's leading edge. Proc Natl Acad Sci U S A 2024; 121:e2306818121. [PMID: 38489386 PMCID: PMC10963004 DOI: 10.1073/pnas.2306818121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/29/2024] [Indexed: 03/17/2024] Open
Abstract
Cells often migrate on curved surfaces inside the body, such as curved tissues, blood vessels, or highly curved protrusions of other cells. Recent in vitro experiments provide clear evidence that motile cells are affected by the curvature of the substrate on which they migrate, preferring certain curvatures to others, termed "curvotaxis." The origin and underlying mechanism that gives rise to this curvature sensitivity are not well understood. Here, we employ a "minimal cell" model which is composed of a vesicle that contains curved membrane protein complexes, that exert protrusive forces on the membrane (representing the pressure due to actin polymerization). This minimal-cell model gives rise to spontaneous emergence of a motile phenotype, driven by a lamellipodia-like leading edge. By systematically screening the behavior of this model on different types of curved substrates (sinusoidal, cylinder, and tube), we show that minimal ingredients and energy terms capture the experimental data. The model recovers the observed migration on the sinusoidal substrate, where cells move along the grooves (minima), while avoiding motion along the ridges. In addition, the model predicts the tendency of cells to migrate circumferentially on convex substrates and axially on concave ones. Both of these predictions are verified experimentally, on several cell types. Altogether, our results identify the minimization of membrane-substrate adhesion energy and binding energy between the membrane protein complexes as key players of curvotaxis in cell migration.
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Affiliation(s)
- Raj Kumar Sadhu
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Marine Luciano
- Department of Biochemistry, University of Geneva, Geneva4 CH-1211, Switzerland
- Mechanobiology & Biomaterials Group, Research Institute for Biosciences, Center of Innovation and Research in Materials and Polymers, University of Mons, MonsB-7000, Belgium
| | - Wang Xi
- Universite Paris Cite, CNRS, Institut Jacques Monod, ParisF-75013, France
| | | | - Marcel Schröder
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Christoph Blum
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Marco Tarantola
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Stefano Villa
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Samo Penič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana1000, Slovenia
| | - Aleš Iglič
- Laboratory of Physics, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana1000, Slovenia
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Potsdam14476, Germany
- Nano Life Science Institute, Kanazawa University, Kanazawa920-1192, Japan
| | - Oliver Steinbock
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL32306-4390
| | - Eberhard Bodenschatz
- Department of Fluid Physics, Pattern Formation and Biocomplexity, Max Planck Institute for Dynamics and Self-Organization, Göttingen37077, Germany
| | - Benoît Ladoux
- Universite Paris Cite, CNRS, Institut Jacques Monod, ParisF-75013, France
| | - Sylvain Gabriele
- Mechanobiology & Biomaterials Group, Research Institute for Biosciences, Center of Innovation and Research in Materials and Polymers, University of Mons, MonsB-7000, Belgium
| | - Nir S. Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot7610001, Israel
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11
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Floch A, Galochkina T, Pirenne F, Tournamille C, de Brevern AG. Molecular dynamics of the human RhD and RhAG blood group proteins. Front Chem 2024; 12:1360392. [PMID: 38566898 PMCID: PMC10985258 DOI: 10.3389/fchem.2024.1360392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction: Blood group antigens of the RH system (formerly known as "Rhesus") play an important role in transfusion medicine because of the severe haemolytic consequences of antibodies to these antigens. No crystal structure is available for RhD proteins with its partner RhAG, and the precise stoichiometry of the trimer complex remains unknown. Methods: To analyse their structural properties, the trimers formed by RhD and/or RhAG subunits were generated by protein modelling and molecular dynamics simulations were performed. Results: No major differences in structural behaviour were found between trimers of different compositions. The conformation of the subunits is relatively constant during molecular dynamics simulations, except for three large disordered loops. Discussion: This work makes it possible to propose a reasonable stoichiometry and demonstrates the potential of studying the structural behaviour of these proteins to investigate the hundreds of genetic variants relevant to transfusion medicine.
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Affiliation(s)
- Aline Floch
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
| | - France Pirenne
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Christophe Tournamille
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
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12
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Iyer RS, Needham SR, Galdadas I, Davis BM, Roberts SK, Man RCH, Zanetti-Domingues LC, Clarke DT, Fruhwirth GO, Parker PJ, Rolfe DJ, Gervasio FL, Martin-Fernandez ML. Drug-resistant EGFR mutations promote lung cancer by stabilizing interfaces in ligand-free kinase-active EGFR oligomers. Nat Commun 2024; 15:2130. [PMID: 38503739 PMCID: PMC10951324 DOI: 10.1038/s41467-024-46284-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
The Epidermal Growth Factor Receptor (EGFR) is frequently found to be mutated in non-small cell lung cancer. Oncogenic EGFR has been successfully targeted by tyrosine kinase inhibitors, but acquired drug resistance eventually overcomes the efficacy of these treatments. Attempts to surmount this therapeutic challenge are hindered by a poor understanding of how and why cancer mutations specifically amplify ligand-independent EGFR auto-phosphorylation signals to enhance cell survival and how this amplification is related to ligand-dependent cell proliferation. Here we show that drug-resistant EGFR mutations manipulate the assembly of ligand-free, kinase-active oligomers to promote and stabilize the assembly of oligomer-obligate active dimer sub-units and circumvent the need for ligand binding. We reveal the structure and assembly mechanisms of these ligand-free, kinase-active oligomers, uncovering oncogenic functions for hitherto orphan transmembrane and kinase interfaces, and for the ectodomain tethered conformation of EGFR. Importantly, we find that the active dimer sub-units within ligand-free oligomers are the high affinity binding sites competent to bind physiological ligand concentrations and thus drive tumor growth, revealing a link with tumor proliferation. Our findings provide a framework for future drug discovery directed at tackling oncogenic EGFR mutations by disabling oligomer-assembling interactions.
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Affiliation(s)
- R Sumanth Iyer
- Central Laser Facility, UKRI-STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
- Immunocore Limited, 92 Park Drive, Milton Park, Abingdon, UK
| | - Sarah R Needham
- Central Laser Facility, UKRI-STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Ioannis Galdadas
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- ISPSO, University of Geneva, Geneva, Switzerland
| | - Benjamin M Davis
- Central Laser Facility, UKRI-STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Selene K Roberts
- Central Laser Facility, UKRI-STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Rico C H Man
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Guy's Campus, King's College London, London, UK
| | | | - David T Clarke
- Central Laser Facility, UKRI-STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK
| | - Gilbert O Fruhwirth
- Imaging Therapies and Cancer Group, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Guy's Campus, King's College London, London, UK
| | - Peter J Parker
- Protein Phosphorylation Laboratory, The Francis Crick Institute, London, UK
- School of Cancer and Pharmaceutical Sciences, Guy's Campus, King's College London, London, UK
| | - Daniel J Rolfe
- Central Laser Facility, UKRI-STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK.
| | - Francesco L Gervasio
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
- ISPSO, University of Geneva, Geneva, Switzerland.
- Chemistry Department, University College London, London, UK.
- Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland.
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13
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Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K. Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport. Nat Commun 2024; 15:2404. [PMID: 38493152 PMCID: PMC10944485 DOI: 10.1038/s41467-024-46747-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
ERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional studies since its identification, the overall architecture and mechanism of action of ERGIC-53 remain unclear. Here we present cryo-EM structures of full-length ERGIC-53 in complex with its functional partner MCFD2. These structures reveal that ERGIC-53 exists as a homotetramer, not a homohexamer as previously suggested, and comprises a four-leaf clover-like head and a long stalk composed of three sets of four-helix coiled-coil followed by a transmembrane domain. 3D variability analysis visualizes the flexible motion of the long stalk and local plasticity of the head region. Notably, MCFD2 is shown to possess a Zn2+-binding site in its N-terminal lid, which appears to modulate cargo binding. Altogether, distinct mechanisms of cargo capture and release by ERGIC- 53 via the stalk bending and metal binding are proposed.
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Affiliation(s)
- Satoshi Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
| | - Yoshiaki Kise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kento Yonezawa
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Mariko Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Nobutaka Shimizu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
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14
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Bestsennaia E, Maslov I, Balandin T, Alekseev A, Yudenko A, Abu Shamseye A, Zabelskii D, Baumann A, Catapano C, Karathanasis C, Gordeliy V, Heilemann M, Gensch T, Borshchevskiy V. Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy. Angew Chem Int Ed Engl 2024; 63:e202307555. [PMID: 38226794 DOI: 10.1002/anie.202307555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 01/03/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
Microbial rhodopsins are retinal membrane proteins that found a broad application in optogenetics. The oligomeric state of rhodopsins is important for their functionality and stability. Of particular interest is the oligomeric state in the cellular native membrane environment. Fluorescence microscopy provides powerful tools to determine the oligomeric state of membrane proteins directly in cells. Among these methods is quantitative photoactivated localization microscopy (qPALM) allowing the investigation of molecular organization at the level of single protein clusters. Here, we apply qPALM to investigate the oligomeric state of the first and most used optogenetic tool Channelrhodopsin-2 (ChR2) in the plasma membrane of eukaryotic cells. ChR2 appeared predominantly as a dimer in the cell membrane and did not form higher oligomers. The disulfide bonds between Cys34 and Cys36 of adjacent ChR2 monomers were not required for dimer formation and mutations disrupting these bonds resulted in only partial monomerization of ChR2. The monomeric fraction increased when the total concentration of mutant ChR2 in the membrane was low. The dissociation constant was estimated for this partially monomerized mutant ChR2 as 2.2±0.9 proteins/μm2 . Our findings are important for understanding the mechanistic basis of ChR2 activity as well as for improving existing and developing future optogenetic tools.
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Affiliation(s)
- Ekaterina Bestsennaia
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ivan Maslov
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and the Biomedical Research Institute, Hasselt University, B3590, Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium
| | - Taras Balandin
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alexey Alekseev
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Anna Yudenko
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Assalla Abu Shamseye
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Dmitrii Zabelskii
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
- European XFEL, 22869, Schenefeld, Germany
| | - Arnd Baumann
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Claudia Catapano
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Christos Karathanasis
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Thomas Gensch
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
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15
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Hořejší V, Angelisová P, Pokorná J, Charnavets T, Benada O, Čajka T, Brdička T. Novel class of peptides disintegrating biological membranes to aid in the characterization of membrane proteins. J Biol Chem 2024; 300:107154. [PMID: 38479603 PMCID: PMC11002605 DOI: 10.1016/j.jbc.2024.107154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 04/09/2024] Open
Abstract
Styrene-maleic acid (SMA) and similar amphiphilic copolymers are known to cut biological membranes into lipid nanoparticles/nanodiscs containing membrane proteins apparently in their relatively native membrane lipid environment. Our previous work demonstrated that membrane raft microdomains resist such disintegration by SMA. The use of SMA in studying membrane proteins is limited by its heterogeneity and the inability to prepare defined derivatives. In the present paper, we demonstrate that some amphiphilic peptides structurally mimicking SMA also similarly disintegrate cell membranes. In contrast to the previously used copolymers, the simple peptides are structurally homogeneous. We found that their membrane-disintegrating activity increases with their length (reaching optimum at 24 amino acids) and requires a basic primary structure, that is, (XXD)n, where X represents a hydrophobic amino acid (optimally phenylalanine), D aspartic acid, and n is the number of repeats of these triplets. These peptides may provide opportunities for various well-defined potentially useful modifications in the study of membrane protein biochemistry. Our present results confirm a specific character of membrane raft microdomains.
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Affiliation(s)
- Václav Hořejší
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Pavla Angelisová
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Pokorná
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tatsiana Charnavets
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Oldřich Benada
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Čajka
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Brdička
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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16
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Mazza T, Roumeliotis TI, Garitta E, Drew D, Rashid ST, Indiveri C, Choudhary JS, Linton KJ, Beis K. Structural basis for the modulation of MRP2 activity by phosphorylation and drugs. Nat Commun 2024; 15:1983. [PMID: 38438394 PMCID: PMC10912322 DOI: 10.1038/s41467-024-46392-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
Multidrug resistance-associated protein 2 (MRP2/ABCC2) is a polyspecific efflux transporter of organic anions expressed in hepatocyte canalicular membranes. MRP2 dysfunction, in Dubin-Johnson syndrome or by off-target inhibition, for example by the uricosuric drug probenecid, elevates circulating bilirubin glucuronide and is a cause of jaundice. Here, we determine the cryo-EM structure of rat Mrp2 (rMrp2) in an autoinhibited state and in complex with probenecid. The autoinhibited state exhibits an unusual conformation for this class of transporter in which the regulatory domain is folded within the transmembrane domain cavity. In vitro phosphorylation, mass spectrometry and transport assays show that phosphorylation of the regulatory domain relieves this autoinhibition and enhances rMrp2 transport activity. The in vitro data is confirmed in human hepatocyte-like cells, in which inhibition of endogenous kinases also reduces human MRP2 transport activity. The drug-bound state reveals two probenecid binding sites that suggest a dynamic interplay with autoinhibition. Mapping of the Dubin-Johnson mutations onto the rodent structure indicates that many may interfere with the transition between conformational states.
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Affiliation(s)
- Tiziano Mazza
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK
- Department DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036, Arcavacata di Rende, Italy
| | - Theodoros I Roumeliotis
- Functional Proteomics group, Chester Beatty Laboratories, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Elena Garitta
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, E1 2A, London, UK
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - S Tamir Rashid
- Department of Metabolism, Digestion & Reproduction, Imperial College London, W12 0NN, London, UK
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036, Arcavacata di Rende, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), 70126, Bari, Italy
| | - Jyoti S Choudhary
- Functional Proteomics group, Chester Beatty Laboratories, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Kenneth J Linton
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, E1 2A, London, UK
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK.
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK.
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17
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Woods H, Leman JK, Meiler J. Modeling membrane geometries implicitly in Rosetta. Protein Sci 2024; 33:e4908. [PMID: 38358133 PMCID: PMC10868433 DOI: 10.1002/pro.4908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
Interactions between membrane proteins (MPs) and lipid bilayers are critical for many cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy function is based on a "slab" model, which represent the membrane as a flat bilayer. However, in nature membranes often have a curvature that is important for function and/or stability. Even more prevalent, in structural biology research MPs are reconstituted in model membrane systems such as micelles, bicelles, nanodiscs, or liposomes. Thus, we have modified the existing membrane energy potentials within the RosettaMP framework to allow users to model MPs in different membrane geometries. We show that these modifications can be utilized in core applications within Rosetta such as structure refinement, protein-protein docking, and protein design. For MP structures found in curved membranes, refining these structures in curved, implicit membranes produces higher quality models with structures closer to experimentally determined structures. For MP systems embedded in multiple membranes, representing both membranes results in more favorable scores compared to only representing one of the membranes. Modeling MPs in geometries mimicking the membrane model system used in structure determination can improve model quality and model discrimination.
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Affiliation(s)
- Hope Woods
- Center of Structural Biology, Vanderbilt UniversityNashvilleTennesseeUSA
- Chemical and Physical Biology ProgramVanderbilt UniversityNashvilleTennesseeUSA
| | | | - Jens Meiler
- Center of Structural Biology, Vanderbilt UniversityNashvilleTennesseeUSA
- Department of ChemistryVanderbilt UniversityNashvilleTennesseeUSA
- Institute for Drug Discovery, Leipzig University Medical SchoolLeipzigGermany
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18
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Lee A, Sung G, Shin S, Lee SY, Sim J, Nhung TTM, Nghi TD, Park SK, Sathieshkumar PP, Kang I, Mun JY, Kim JS, Rhee HW, Park KM, Kim K. OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools. Nat Commun 2024; 15:1851. [PMID: 38424052 PMCID: PMC10904832 DOI: 10.1038/s41467-024-46034-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Identifying proteins at organelle contact sites, such as mitochondria-associated endoplasmic reticulum membranes (MAM), is essential for understanding vital cellular processes, yet challenging due to their dynamic nature. Here we report "OrthoID", a proteomic method utilizing engineered enzymes, TurboID and APEX2, for the biotinylation (Bt) and adamantylation (Ad) of proteins close to the mitochondria and endoplasmic reticulum (ER), respectively, in conjunction with high-affinity binding pairs, streptavidin-biotin (SA-Bt) and cucurbit[7]uril-adamantane (CB[7]-Ad), for selective orthogonal enrichment of Bt- and Ad-labeled proteins. This approach effectively identifies protein candidates associated with the ER-mitochondria contact, including LRC59, whose roles at the contact site were-to the best of our knowledge-previously unknown, and tracks multiple protein sets undergoing structural and locational changes at MAM during mitophagy. These findings demonstrate that OrthoID could be a powerful proteomics tool for the identification and analysis of spatiotemporal proteins at organelle contact sites and revealing their dynamic behaviors in vital cellular processes.
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Affiliation(s)
- Ara Lee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea
- Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Gihyun Sung
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea
- Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Song-Yi Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jaehwan Sim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Truong Thi My Nhung
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Tran Diem Nghi
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | | | - Imkyeung Kang
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
- Department of Microbiology, University of Ulsan College of Medicine, Ulsan, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
| | - Kyeng Min Park
- Department of Biochemistry, Daegu Catholic University School of Medicine, Daegu, Republic of Korea.
| | - Kimoon Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, Republic of Korea.
- Division of Advanced Materials Science (AMS), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
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19
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Mori S, Shionyu M, Shimamoto K, Nomura K. Bacterial Glycolipid Acting on Protein Transport Across Membranes. Chembiochem 2024:e202300808. [PMID: 38400776 DOI: 10.1002/cbic.202300808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/11/2024] [Accepted: 02/22/2024] [Indexed: 02/26/2024]
Abstract
The process of protein transport across membranes involves a variety of factors and has been extensively investigated. Traditionally, proteinaceous translocons and chaperones have been recognized as crucial factors in this process. However, recent studies have highlighted the significant roles played by lipids and a glycolipid present in biological membranes in membrane protein transport. Membrane lipids can influence transport efficiency by altering the physicochemical properties of membranes. Notably, our studies have revealed that diacylglycerol (DAG) attenuates mobility in the membrane core region, leading to a dramatic suppression of membrane protein integration. Conversely, a glycolipid in Escherichia coli inner membranes, named membrane protein integrase (MPIase), enhances integration not only through the alteration of membrane properties but also via direct interactions with membrane proteins. This review explores the mechanisms of membrane protein integration mediated by membrane lipids, specifically DAG, and MPIase. Our results, along with the employed physicochemical analysis methods such as fluorescence measurements, nuclear magnetic resonance, surface plasmon resonance, and docking simulation, are presented to elucidate these mechanisms.
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Affiliation(s)
- Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
| | - Masafumi Shionyu
- Department of Frontier Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
- Department of Chemistry Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
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20
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Wang Q, Yang X, Yuan R, Shen A, Wang P, Li H, Zhang J, Tian C, Jiang Z, Li W, Dong S. A co-assembly platform engaging macrophage scavenger receptor A for lysosome-targeting protein degradation. Nat Commun 2024; 15:1663. [PMID: 38396109 PMCID: PMC10891067 DOI: 10.1038/s41467-024-46130-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Targeted degradation of proteins has emerged as a powerful method for modulating protein homeostasis. Identification of suitable degraders is essential for achieving effective protein degradation. Here, we present a non-covalent degrader construction strategy, based on a modular supramolecular co-assembly system consisting of two self-assembling peptide ligands that bind cell membrane receptors and the protein of interest simultaneously, resulting in targeted protein degradation. The developed lysosome-targeting co-assemblies (LYTACAs) can induce lysosomal degradation of extracellular protein IL-17A and membrane protein PD-L1 in several scavenger receptor A-expressing cell lines. The IL-17A-degrading co-assembly has been applied in an imiquimod-induced psoriasis mouse model, where it decreases IL-17A levels in the skin lesion and alleviates psoriasis-like inflammation. Extending to asialoglycoprotein receptor-related protein degradation, LYTACAs have demonstrated the versatility and potential in streamlining degraders for extracellular and membrane proteins.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xingyue Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Ruixin Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Ao Shen
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Pushu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Haoting Li
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Jun Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
- Chemical Biology Center, Peking University, Beijing, China
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Chao Tian
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhujun Jiang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Wenzhe Li
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China.
- Chemical Biology Center, Peking University, Beijing, China.
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
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21
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He Z, Wu M, Tian H, Wang L, Hu Y, Han F, Zhou J, Wang Y, Zhou L. Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nat Commun 2024; 15:1628. [PMID: 38388527 PMCID: PMC10884005 DOI: 10.1038/s41467-024-46018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III2 + IV and supercomplex III2 + IV2. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
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Affiliation(s)
- Zhaoxiang He
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengchen Wu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hongtao Tian
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Liangdong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yiqi Hu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fangzhu Han
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China.
| | - Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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22
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Guo SC, Shen R, Roux B, Dinner AR. Dynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP. Nat Commun 2024; 15:1408. [PMID: 38360718 PMCID: PMC10869754 DOI: 10.1038/s41467-024-45514-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
The Ciona intestinalis voltage-sensing phosphatase (Ci-VSP) is a membrane protein containing a voltage-sensing domain (VSD) that is homologous to VSDs from voltage-gated ion channels responsible for cellular excitability. Previously published crystal structures of Ci-VSD in putative resting and active conformations suggested a helical-screw voltage sensing mechanism in which the S4 helix translocates and rotates to enable exchange of salt-bridge partners, but the microscopic details of the transition between the resting and active conformations remained unknown. Here, by combining extensive molecular dynamics simulations with a recently developed computational framework based on dynamical operators, we elucidate the microscopic mechanism of the resting-active transition at physiological membrane potential. Sparse regression reveals a small set of coordinates that distinguish intermediates that are hidden from electrophysiological measurements. The intermediates arise from a noncanonical helical-screw mechanism in which translocation, rotation, and side-chain movement of the S4 helix are only loosely coupled. These results provide insights into existing experimental and computational findings on voltage sensing and suggest ways of further probing its mechanism.
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Affiliation(s)
- Spencer C Guo
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Rong Shen
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Benoît Roux
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
| | - Aaron R Dinner
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
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23
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Jacobson DR, Perkins TT. Quantifying a light-induced energetic change in bacteriorhodopsin by force spectroscopy. Proc Natl Acad Sci U S A 2024; 121:e2313818121. [PMID: 38324569 PMCID: PMC10873598 DOI: 10.1073/pnas.2313818121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/26/2023] [Indexed: 02/09/2024] Open
Abstract
Ligand-induced conformational changes are critical to the function of many membrane proteins and arise from numerous intramolecular interactions. In the photocycle of the model membrane protein bacteriorhodopsin (bR), absorption of a photon by retinal triggers a conformational cascade that results in pumping a proton across the cell membrane. While decades of spectroscopy and structural studies have probed this photocycle in intricate detail, changes in intramolecular energetics that underlie protein motions have remained elusive to experimental quantification. Here, we measured these energetics on the millisecond time scale using atomic-force-microscopy-based single-molecule force spectroscopy. Precisely, timed light pulses triggered the bR photocycle while we measured the equilibrium unfolding and refolding of the terminal 8-amino-acid region of bR's G-helix. These dynamics changed when the EF-helix pair moved ~9 Å away from this end of the G helix during the "open" portion of bR's photocycle. In ~60% of the data, we observed abrupt light-induced destabilization of 3.4 ± 0.3 kcal/mol, lasting 38 ± 3 ms. The kinetics and pH-dependence of this destabilization were consistent with prior measurements of bR's open phase. The frequency of light-induced destabilization increased with the duration of illumination and was dramatically reduced in the triple mutant (D96G/F171C/F219L) thought to trap bR in its open phase. In the other ~40% of the data, photoexcitation unexpectedly stabilized a longer-lived putative misfolded state. Through this work, we establish a general single-molecule force spectroscopy approach for measuring ligand-induced energetics and lifetimes in membrane proteins.
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Affiliation(s)
- David R. Jacobson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO80309
| | - Thomas T. Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO80309
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO80309
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24
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Antollini SS, Barrantes FJ. Carlos Gutiérrez-Merino: Synergy of Theory and Experimentation in Biological Membrane Research. Molecules 2024; 29:820. [PMID: 38398572 PMCID: PMC10893188 DOI: 10.3390/molecules29040820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Professor Carlos Gutiérrez-Merino, a prominent scientist working in the complex realm of biological membranes, has made significant theoretical and experimental contributions to the field. Contemporaneous with the development of the fluid-mosaic model of Singer and Nicolson, the Förster resonance energy transfer (FRET) approach has become an invaluable tool for studying molecular interactions in membranes, providing structural insights on a scale of 1-10 nm and remaining important alongside evolving perspectives on membrane structures. In the last few decades, Gutiérrez-Merino's work has covered multiple facets in the field of FRET, with his contributions producing significant advances in quantitative membrane biology. His more recent experimental work expanded the ground concepts of FRET to high-resolution cell imaging. Commencing in the late 1980s, a series of collaborations between Gutiérrez-Merino and the authors involved research visits and joint investigations focused on the nicotinic acetylcholine receptor and its relation to membrane lipids, fostering a lasting friendship.
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Affiliation(s)
- Silvia S. Antollini
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Instituto de Investigaciones Bioquímicas de Bahía Blanca (CONICET-UNS), Bahía Blanca 8000, Argentina;
| | - Francisco J. Barrantes
- Laboratory of Molecular Neurobiology, BIOMED UCA-CONICET, Buenos Aires C1107AAZ, Argentina
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25
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Sakamoto H, Nishikawa M, Yamada S. Development of tight junction-strengthening compounds using a high-throughput screening system to evaluate cell surface-localized claudin-1 in keratinocytes. Sci Rep 2024; 14:3312. [PMID: 38332234 PMCID: PMC10853544 DOI: 10.1038/s41598-024-53649-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Tight junctions (TJs) are important factors constituting the physical barriers of the skin, and their suppression has been described in various conditions, such as aged skin and atopic dermatitis lesions. However, the methods for improving skin TJ function remain insufficient. Therefore, to obtain compounds that can improve TJ function, we developed a novel high-throughput screening system termed live-cell immunostaining to evaluate cell surface-localized claudin-1 (CLDN1) with high selectivity using normal human epidermal keratinocytes (NHEKs). Heparinoid and phospho-pyridoxal (p-Pyr), a metabolite of pyridoxine, were identified as hit compounds. In addition, heparinoid was strongly suggested to increase CLDN1 expression by inhibiting epidermal growth factor receptor signaling. By contrast, p-Pyr did not enhance CLDN1 expression, but it accelerated the translocation of CLDN1 to the cell surface. Finally, we confirmed that heparinoid and p-Pyr improved barrier function in NHEKs in a transepithelial electrical resistance assay. In conclusion, heparinoid and p-Pyr could potentially ameliorate skin conditions by improving TJ function.
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Affiliation(s)
- Hiroki Sakamoto
- Research and Development Headquarters, Well-Being Research Laboratories, Lion Corporation, 100 Tajima, Odawara, Kanagawa, 256-0811, Japan
| | - Momoyo Nishikawa
- Research and Development Headquarters, Well-Being Research Laboratories, Lion Corporation, 100 Tajima, Odawara, Kanagawa, 256-0811, Japan
| | - Seigo Yamada
- Research and Development Headquarters, Well-Being Research Laboratories, Lion Corporation, 100 Tajima, Odawara, Kanagawa, 256-0811, Japan.
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26
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Szenci G, Glatz G, Takáts S, Juhász G. The Ykt6-Snap29-Syx13 SNARE complex promotes crinophagy via secretory granule fusion with Lamp1 carrier vesicles. Sci Rep 2024; 14:3200. [PMID: 38331993 PMCID: PMC10853563 DOI: 10.1038/s41598-024-53607-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/02/2024] [Indexed: 02/10/2024] Open
Abstract
In the Drosophila larval salivary gland, developmentally programmed fusions between lysosomes and secretory granules (SGs) and their subsequent acidification promote the maturation of SGs that are secreted shortly before puparium formation. Subsequently, ongoing fusions between non-secreted SGs and lysosomes give rise to degradative crinosomes, where the superfluous secretory material is degraded. Lysosomal fusions control both the quality and quantity of SGs, however, its molecular mechanism is incompletely characterized. Here we identify the R-SNARE Ykt6 as a novel regulator of crinosome formation, but not the acidification of maturing SGs. We show that Ykt6 localizes to Lamp1+ carrier vesicles, and forms a SNARE complex with Syntaxin 13 and Snap29 to mediate fusion with SGs. These Lamp1 carriers represent a distinct vesicle population that are functionally different from canonical Arl8+, Cathepsin L+ lysosomes, which also fuse with maturing SGs but are controlled by another SNARE complex composed of Syntaxin 13, Snap29 and Vamp7. Ykt6- and Vamp7-mediated vesicle fusions also determine the fate of SGs, as loss of either of these SNAREs prevents crinosomes from acquiring endosomal PI3P. Our results highlight that fusion events between SGs and different lysosome-related vesicle populations are critical for fine regulation of the maturation and crinophagic degradation of SGs.
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Affiliation(s)
- Győző Szenci
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, 1117, Hungary
- Doctoral School of Biology, Institute of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Gábor Glatz
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Szabolcs Takáts
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, 1117, Hungary.
| | - Gábor Juhász
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, 1117, Hungary.
- Institute of Genetics, HUN-REN Biological Research Centre Szeged, Szeged, 6726, Hungary.
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27
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Sarson-Lawrence KTG, Hardy JM, Iaria J, Stockwell D, Behrens K, Saiyed T, Tan C, Jebeli L, Scott NE, Dite TA, Nicola NA, Leis AP, Babon JJ, Kershaw NJ. Cryo-EM structure of the extracellular domain of murine Thrombopoietin Receptor in complex with Thrombopoietin. Nat Commun 2024; 15:1135. [PMID: 38326297 PMCID: PMC10850085 DOI: 10.1038/s41467-024-45356-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
Thrombopoietin (Tpo) is the primary regulator of megakaryocyte and platelet numbers and is required for haematopoetic stem cell maintenance. Tpo functions by binding its receptor (TpoR, a homodimeric Class I cytokine receptor) and initiating cell proliferation or differentiation. Here we characterise the murine Tpo:TpoR signalling complex biochemically and structurally, using cryo-electron microscopy. Tpo uses opposing surfaces to recruit two copies of receptor, forming a 1:2 complex. Although it binds to the same, membrane-distal site on both receptor chains, it does so with significantly different affinities and its highly glycosylated C-terminal domain is not required. In one receptor chain, a large insertion, unique to TpoR, forms a partially structured loop that contacts cytokine. Tpo binding induces the juxtaposition of the two receptor chains adjacent to the cell membrane. The therapeutic agent romiplostim also targets the cytokine-binding site and the characterisation presented here supports the future development of improved TpoR agonists.
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Affiliation(s)
- Kaiseal T G Sarson-Lawrence
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Joshua M Hardy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
| | - Josephine Iaria
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Dina Stockwell
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Kira Behrens
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Tamanna Saiyed
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Cyrus Tan
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Victoria, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Victoria, Australia
| | - Toby A Dite
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Nicos A Nicola
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Andrew P Leis
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
| | - Jeffrey J Babon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia.
| | - Nadia J Kershaw
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia.
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28
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Mao YX, Chen ZP, Wang L, Wang J, Zhou CZ, Hou WT, Chen Y. Transport mechanism of human bilirubin transporter ABCC2 tuned by the inter-module regulatory domain. Nat Commun 2024; 15:1061. [PMID: 38316776 PMCID: PMC10844203 DOI: 10.1038/s41467-024-45337-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
Bilirubin is mainly generated from the breakdown of heme when red blood cells reach the end of their lifespan. Accumulation of bilirubin in human body usually leads to various disorders, including jaundice and liver disease. Bilirubin is conjugated in hepatocytes and excreted to bile duct via the ATP-binding cassette transporter ABCC2, dysfunction of which would lead to Dubin-Johnson syndrome. Here we determine the structures of ABCC2 in the apo, substrate-bound and ATP/ADP-bound forms using the cryo-electron microscopy, exhibiting a full transporter with a regulatory (R) domain inserted between the two half modules. Combined with substrate-stimulated ATPase and transport activity assays, structural analysis enables us to figure out transport cycle of ABCC2 with the R domain adopting various conformations. At the rest state, the R domain binding to the translocation cavity functions as an affinity filter that allows the substrates of high affinity to be transported in priority. Upon substrate binding, the R domain is expelled from the cavity and docks to the lateral of transmembrane domain following ATP hydrolysis. Our findings provide structural insights into a transport mechanism of ABC transporters finely tuned by the R domain.
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Affiliation(s)
- Yao-Xu Mao
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Zhi-Peng Chen
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Liang Wang
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Jie Wang
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China.
| | - Wen-Tao Hou
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China.
| | - Yuxing Chen
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, 230027, China.
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29
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Said HH, Doucette AA. Enhanced Electrophoretic Depletion of Sodium Dodecyl Sulfate with Methanol for Membrane Proteome Analysis by Mass Spectrometry. Proteomes 2024; 12:5. [PMID: 38390965 PMCID: PMC10885059 DOI: 10.3390/proteomes12010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Membrane proteins are underrepresented during proteome characterizations, primarily owing to their lower solubility. Sodium dodecyl sulfate (SDS) is favored to enhance protein solubility but interferes with downstream analysis by mass spectrometry. Here, we present an improved workflow for SDS depletion using transmembrane electrophoresis (TME) while retaining a higher recovery of membrane proteins. Though higher levels of organic solvent lower proteome solubility, we found that the inclusion of 40% methanol provided optimal solubility of membrane proteins, with 86% recovery relative to extraction with SDS. Incorporating 40% methanol during the electrophoretic depletion of SDS by TME also maximized membrane protein recovery. We further report that methanol accelerates the rate of detergent removal, allowing TME to deplete SDS below 100 ppm in under 3 min. This is attributed to a three-fold elevation in the critical micelle concentration (CMC) of SDS in the presence of methanol, combined with a reduction in the SDS to protein binding ratio in methanol (0.3 g SDS/g protein). MS analysis of membrane proteins isolated from the methanol-assisted workflow revealed enhanced proteome detection, particularly for proteins whose pI contributed a minimal net charge and therefore possessed reduced solubility in a purely aqueous solvent. This protocol presents a robust approach for the preparation of membrane proteins by maximizing their solubility in MS-compatible solvents, offering a tool to advance membrane proteome characterization.
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Affiliation(s)
- Hammam H Said
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS B3H 4R2, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS B3H 4R2, Canada
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30
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Loland CJ, Wellendorph P, Pedersen SF, Gether U. Transmembrane transporter proteins: Capturing transport in motion. Basic Clin Pharmacol Toxicol 2024; 134:203-205. [PMID: 37945540 DOI: 10.1111/bcpt.13960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Affiliation(s)
- Claus J Loland
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Petrine Wellendorph
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stine F Pedersen
- Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Ulrik Gether
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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31
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Davies JS, Currie MJ, Dobson RCJ, Horne CR, North RA. TRAPs: the 'elevator-with-an-operator' mechanism. Trends Biochem Sci 2024; 49:134-144. [PMID: 38102017 DOI: 10.1016/j.tibs.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are nutrient-uptake systems found in bacteria and archaea. These evolutionary divergent transporter systems couple a substrate-binding protein (SBP) to an elevator-type secondary transporter, which is a first-of-its-kind mechanism of transport. Here, we highlight breakthrough TRAP transporter structures and recent functional data that probe the mechanism of transport. Furthermore, we discuss recent structural and biophysical studies of the ion transporter superfamily (ITS) members and highlight mechanistic principles that are relevant for further exploration of the TRAP transporter system.
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Affiliation(s)
- James S Davies
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Michael J Currie
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, Christchurch 8140, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, Maurice Wilkins Centre for Biodiscovery, MacDiarmid Institute for Advanced Materials and Nanotechnology, Christchurch 8140, New Zealand; School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia.
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
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32
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Steinkühler J, Peruzzi JA, Krüger A, Villaseñor CG, Jacobs ML, Jewett MC, Kamat NP. Improving Cell-Free Expression of Model Membrane Proteins by Tuning Ribosome Cotranslational Membrane Association and Nascent Chain Aggregation. ACS Synth Biol 2024; 13:129-140. [PMID: 38150067 DOI: 10.1021/acssynbio.3c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Cell-free gene expression (CFE) systems are powerful tools for transcribing and translating genes outside of a living cell. Synthesis of membrane proteins is of particular interest, but their yield in CFE is substantially lower than that for soluble proteins. In this paper, we study the CFE of membrane proteins and develop a quantitative kinetic model. We identify that ribosome stalling during the translation of membrane proteins is a strong predictor of membrane protein synthesis due to aggregation between the ribosome nascent chains. Synthesis can be improved by the addition of lipid membranes, which incorporate protein nascent chains and, therefore, kinetically compete with aggregation. We show that the balance between peptide-membrane association and peptide aggregation rates determines the yield of the synthesized membrane protein. We define a membrane protein expression score that can be used to rationalize the engineering of lipid composition and the N-terminal domain of a native and computationally designed membrane proteins produced through CFE.
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Affiliation(s)
- Jan Steinkühler
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Bio-Inspired Computation, Kiel University, Kaiserstraße 2, 24143 Kiel, Germany
- Kiel Nano, Surface and Interface Science KiNSIS, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - Justin A Peruzzi
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Citlayi G Villaseñor
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Miranda L Jacobs
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Neha P Kamat
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
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33
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Bongiovanni TR, Latario CJ, Le Cras Y, Trus E, Robitaille S, Swartz K, Schmidtke D, Vincent M, Kosta A, Orth J, Stengel F, Pellarin R, Rocha EPC, Ross BD, Durand E. Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota. Nat Commun 2024; 15:429. [PMID: 38200008 PMCID: PMC10781749 DOI: 10.1038/s41467-023-44426-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitor cells through contact-dependent translocation of toxic effector proteins. In Proteobacteria, the T6SS is anchored to the cell envelope through a megadalton-sized membrane complex (MC). However, the genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of canonical MC components. Here, we identify five genes in Bacteroides fragilis (tssNQOPR) that are essential for T6SS function and encode a Bacteroidota-specific MC. We purify this complex, reveal its dimensions using electron microscopy, and identify a protein-protein interaction network underlying the assembly of the MC including the stoichiometry of the five TssNQOPR components. Protein TssN mediates the connection between the Bacteroidota MC and the conserved baseplate. Although MC gene content and organization varies across the phylum Bacteroidota, no MC homologs are detected outside of T6SS loci, suggesting ancient co-option and functional convergence with the non-homologous MC of Pseudomonadota.
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Affiliation(s)
- Thibault R Bongiovanni
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Casey J Latario
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Youn Le Cras
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Evan Trus
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Sophie Robitaille
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Kerry Swartz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Danica Schmidtke
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA
| | - Maxence Vincent
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Artemis Kosta
- Microscopy Core Facility, Institut de Microbiologie de la Méditerranée (IMM), FR3479, CNRS, Aix-Marseille University, Marseille, France
| | - Jan Orth
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007, Lyon, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA.
| | - Eric Durand
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
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34
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Adrien V, Reffay M, Taulier N, Verchère A, Monlezun L, Picard M, Ducruix A, Broutin I, Pincet F, Urbach W. Kinetic study of membrane protein interactions: from three to two dimensions. Sci Rep 2024; 14:882. [PMID: 38195620 PMCID: PMC10776792 DOI: 10.1038/s41598-023-50827-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 12/26/2023] [Indexed: 01/11/2024] Open
Abstract
Molecular interactions are contingent upon the system's dimensionality. Notably, comprehending the impact of dimensionality on protein-protein interactions holds paramount importance in foreseeing protein behaviour across diverse scenarios, encompassing both solution and membrane environments. Here, we unravel interactions among membrane proteins across various dimensionalities by quantifying their binding rates through fluorescence recovery experiments. Our findings are presented through the examination of two protein systems: streptavidin-biotin and a protein complex constituting a bacterial efflux pump. We present here an original approach for gauging a two-dimensional binding constant between membrane proteins embedded in two opposite membranes. The quotient of protein binding rates in solution and on the membrane represents a metric denoting the exploration distance of the interacting sites-a novel interpretation.
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Affiliation(s)
- Vladimir Adrien
- Laboratoire de Physique de l'École normale superieure, École Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
- Department of Infectious Diseases, Avicenne Hospital, AP-HP, Université Sorbonne Paris Nord, Bobigny, France.
- Université Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and Neuroscience of Paris (IPNP), Paris, France.
| | - Myriam Reffay
- Laboratoire Matière et Systèmes Complexes, UMR 7057, CNRS and Université de Paris Cité, 75205, Paris Cedex 13, France
| | - Nicolas Taulier
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale-LIB, 75006, Paris, France
| | - Alice Verchère
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
| | - Laura Monlezun
- Université Paris Cité, CNRS, Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris, France
| | - Martin Picard
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, 75005, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 75005, Paris, France
| | - Arnaud Ducruix
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
| | - Isabelle Broutin
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
| | - Frédéric Pincet
- Laboratoire de Physique de l'École normale superieure, École Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
| | - Wladimir Urbach
- Laboratoire de Physique de l'École normale superieure, École Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale-LIB, 75006, Paris, France.
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35
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Wang L, Hoang A, Gil-Iturbe E, Laganowsky A, Quick M, Zhou M. Mechanism of anion exchange and small-molecule inhibition of pendrin. Nat Commun 2024; 15:346. [PMID: 38184688 PMCID: PMC10771415 DOI: 10.1038/s41467-023-44612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024] Open
Abstract
Pendrin (SLC26A4) is an anion exchanger that mediates bicarbonate (HCO3-) exchange for chloride (Cl-) and is crucial for maintaining pH and salt homeostasis in the kidney, lung, and cochlea. Pendrin also exports iodide (I-) in the thyroid gland. Pendrin mutations in humans lead to Pendred syndrome, causing hearing loss and goiter. Inhibition of pendrin is a validated approach for attenuating airway hyperresponsiveness in asthma and for treating hypertension. However, the mechanism of anion exchange and its inhibition by drugs remains poorly understood. We applied cryo-electron microscopy to determine structures of pendrin from Sus scrofa in the presence of either Cl-, I-, HCO3- or in the apo-state. The structures reveal two anion-binding sites in each protomer, and functional analyses show both sites are involved in anion exchange. The structures also show interactions between the Sulfate Transporter and Anti-Sigma factor antagonist (STAS) and transmembrane domains, and mutational studies suggest a regulatory role. We also determine the structure of pendrin in a complex with niflumic acid (NFA), which uncovers a mechanism of inhibition by competing with anion binding and impeding the structural changes necessary for anion exchange. These results reveal directions for understanding the mechanisms of anion selectivity and exchange and their regulations by the STAS domain. This work also establishes a foundation for analyzing the pathophysiology of mutations associated with Pendred syndrome.
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Affiliation(s)
- Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony Hoang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
- Area Neuroscience - Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
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36
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Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N. Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake. Nat Commun 2024; 15:331. [PMID: 38184686 PMCID: PMC10771500 DOI: 10.1038/s41467-023-44606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
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Affiliation(s)
- Maximilian Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, F-75015, Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne, F-75015, Paris, France
| | - Philippe Delepelaire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université Paris Cité, UMR7099 CNRS, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, F-75005, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France.
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37
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Novischi SYP, Karoly-Lakatos A, Chok K, Bonifer C, Becker-Baldus J, Glaubitz C. Probing the allosteric NBD-TMD crosstalk in the ABC transporter MsbA by solid-state NMR. Commun Biol 2024; 7:43. [PMID: 38182790 PMCID: PMC10770068 DOI: 10.1038/s42003-023-05617-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 11/21/2023] [Indexed: 01/07/2024] Open
Abstract
The ABC transporter MsbA plays a critical role in Gram-negative bacteria in the regulation of the outer membrane by translocating core-LPS across the inner membrane. Additionally, a broad substrate specificity for lipophilic drugs has been shown. The allosteric interplay between substrate binding in the transmembrane domains and ATP binding and turnover in the nucleotide-binding domains must be mediated via the NBD/TMD interface. Previous studies suggested the involvement of two intracellular loops called coupling helix 1 and 2 (CH1, CH2). Here, we demonstrate by solid-state NMR spectroscopy that substantial chemical shift changes within both CH1 and CH2 occur upon substrate binding, in the ATP hydrolysis transition state, and upon inhibitor binding. CH2 is domain-swapped within the MsbA structure, and it is noteworthy that substrate binding induces a larger response in CH2 compared to CH1. Our data demonstrate that CH1 and CH2 undergo structural changes as part of the TMD-NBD cross-talk.
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Affiliation(s)
- S Y Phoebe Novischi
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Andrea Karoly-Lakatos
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Kerby Chok
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Christian Bonifer
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany.
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Alotaibi MO, Alotaibi NM, Alwaili MA, Alshammari N, Adnan M, Patel M. Natural sapogenins as potential inhibitors of aquaporins for targeted cancer therapy: computational insights into binding and inhibition mechanism. J Biomol Struct Dyn 2024:1-22. [PMID: 38174738 DOI: 10.1080/07391102.2023.2299743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Aquaporins (AQPs) are membrane proteins that facilitate the transport of water and other small molecules across biological membranes. AQPs are involved in various physiological processes and pathological conditions, including cancer, making them as potential targets for anticancer therapy. However, the development of selective and effective inhibitors of AQPs remains a challenge. In this study, we explored the possibility of using natural sapogenins, a class of plant-derived aglycones of saponins with diverse biological activities, as potential inhibitors of AQPs. We performed molecular docking, dynamics simulation and binding energy calculation to investigate the binding and inhibition mechanism of 19 sapogenins against 13 AQPs (AQP0-AQP13) that are overexpressed in various cancers. Our results showed that out of 19 sapogenins, 8 (Diosgenin, Gitogenin, Tigogenin, Ruscogenin, Yamogenin, Hecogenin, Sarsasapogenin and Smilagenin) exhibited acceptable drug-like characteristics. These sapogenin also exhibited favourable binding affinities in the range of -7.6 to -13.4 kcal/mol, and interactions within the AQP binding sites. Furthermore, MD simulations provided insights into stability and dynamics of the sapogenin-AQP complexes. Most of the fluctuations in binding pocket were observed for AQP0-Gitogenin and AQP4-Diosgenin. However, remaining protein-ligand complex showed stable root mean square deviation (RMSD) plots, strong hydrogen bonding interactions, stable solvent-accessible surface area (SASA) values and minimum distance to the receptor. These observations suggest that natural sapogenin hold promise as novel inhibitors of AQPs, offering a basis for the development of innovative therapeutic agents for cancer treatment. However, further validation of the identified compounds through experiments is essential for translating these findings into therapeutic applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Modhi O Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nahaa M Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Maha Abdullah Alwaili
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mitesh Patel
- Research and Development Cell, Department of Biotechnology, Parul Institute of Applied Sciences, Parul University, Vadodara, India
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Mehta N, Mondal S, Watson ET, Cui Q, Chapman ER. The juxtamembrane linker of synaptotagmin 1 regulates Ca 2+ binding via liquid-liquid phase separation. Nat Commun 2024; 15:262. [PMID: 38177243 PMCID: PMC10766989 DOI: 10.1038/s41467-023-44414-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024] Open
Abstract
Synaptotagmin (syt) 1, a Ca2+ sensor for synaptic vesicle exocytosis, functions in vivo as a multimer. Syt1 senses Ca2+ via tandem C2-domains that are connected to a single transmembrane domain via a juxtamembrane linker. Here, we show that this linker segment harbors a lysine-rich, intrinsically disordered region that is necessary and sufficient to mediate liquid-liquid phase separation (LLPS). Interestingly, condensate formation negatively regulates the Ca2+-sensitivity of syt1. Moreover, Ca2+ and anionic phospholipids facilitate the observed phase separation, and increases in [Ca2+]i promote the fusion of syt1 droplets in living cells. Together, these observations suggest a condensate-mediated feedback loop that serves to fine-tune the ability of syt1 to trigger release, via alterations in Ca2+ binding activity and potentially through the impact of LLPS on membrane curvature during fusion reactions. In summary, the juxtamembrane linker of syt1 emerges as a regulator of syt1 function by driving self-association via LLPS.
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Affiliation(s)
- Nikunj Mehta
- Howard Hughes Medical Institute, Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Sayantan Mondal
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Emma T Watson
- Howard Hughes Medical Institute, Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Edwin R Chapman
- Howard Hughes Medical Institute, Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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40
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Eria-Oliveira AS, Folacci M, Chassot AA, Fedou S, Thézé N, Zabelskii D, Alekseev A, Bamberg E, Gordeliy V, Sandoz G, Vivaudou M. Hijacking of internal calcium dynamics by intracellularly residing viral rhodopsins. Nat Commun 2024; 15:65. [PMID: 38167346 PMCID: PMC10761956 DOI: 10.1038/s41467-023-44548-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
Rhodopsins are ubiquitous light-driven membrane proteins with diverse functions, including ion transport. Widely distributed, they are also coded in the genomes of giant viruses infecting phytoplankton where their function is not settled. Here, we examine the properties of OLPVR1 (Organic Lake Phycodnavirus Rhodopsin) and two other type 1 viral channelrhodopsins (VCR1s), and demonstrate that VCR1s accumulate exclusively intracellularly, and, upon illumination, induce calcium release from intracellular IP3-dependent stores. In vivo, this light-induced calcium release is sufficient to remote control muscle contraction in VCR1-expressing tadpoles. VCR1s natively confer light-induced Ca2+ release, suggesting a distinct mechanism for reshaping the response to light of virus-infected algae. The ability of VCR1s to photorelease calcium without altering plasma membrane electrical properties marks them as potential precursors for optogenetics tools, with potential applications in basic research and medicine.
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Affiliation(s)
- Ana-Sofia Eria-Oliveira
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Université Côte d'Azur, CNRS, INSERM, iBV, Nice, France
- Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France
- Fédération Hospitalo-Universitaire InovPain, Cote d'Azur University, University Hospital Center Nice, Nice, France
| | - Mathilde Folacci
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Anne Amandine Chassot
- Université Côte d'Azur, CNRS, INSERM, iBV, Nice, France
- Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France
- Fédération Hospitalo-Universitaire InovPain, Cote d'Azur University, University Hospital Center Nice, Nice, France
| | - Sandrine Fedou
- Univ. Bordeaux, Inserm, BRIC, UMR, 1312, Bordeaux, France
| | - Nadine Thézé
- Univ. Bordeaux, Inserm, BRIC, UMR, 1312, Bordeaux, France
| | | | - Alexey Alekseev
- Advanced Optogenes Group, Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Guillaume Sandoz
- Université Côte d'Azur, CNRS, INSERM, iBV, Nice, France.
- Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France.
- Fédération Hospitalo-Universitaire InovPain, Cote d'Azur University, University Hospital Center Nice, Nice, France.
| | - Michel Vivaudou
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France.
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Pérez-Jover I, Rochon K, Hu D, Mahajan M, Madan Mohan P, Santos-Pérez I, Ormaetxea Gisasola J, Martinez Galvez JM, Agirre J, Qi X, Mears JA, Shnyrova AV, Ramachandran R. Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nat Commun 2024; 15:52. [PMID: 38168038 PMCID: PMC10761769 DOI: 10.1038/s41467-023-44413-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial and peroxisomal fission, but the regulatory mechanisms remain ambiguous. Here we find that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, surprisingly leading to the fission of model membranes in vitro. In vivo, the involvement of the native CT-SLiM is critical for productive mitochondrial and peroxisomal fission, as both deletion and non-native extension of the CT-SLiM severely impair their progression. Thus, contrary to prevailing models, Drp1-catalyzed membrane fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.
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Affiliation(s)
- Isabel Pérez-Jover
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Di Hu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Mukesh Mahajan
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Pooja Madan Mohan
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Isaac Santos-Pérez
- Electron Microscopy and Crystallography Center for Cooperative Research in Biosciences (CIC bioGUNE), Bizkaia Science and Technology, Park Bld 800, 48160-Derio, Bizkaia, Spain
| | - Julene Ormaetxea Gisasola
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain
| | - Juan Manuel Martinez Galvez
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK
| | - Xin Qi
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anna V Shnyrova
- Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain.
- Instituto Biofisika, CSIC, UPV/EHU, 48940, Leioa, Spain.
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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Wu H, Smalinskaitė L, Hegde RS. EMC rectifies the topology of multipass membrane proteins. Nat Struct Mol Biol 2024; 31:32-41. [PMID: 37957425 PMCID: PMC10803268 DOI: 10.1038/s41594-023-01120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/08/2023] [Indexed: 11/15/2023]
Abstract
Most eukaryotic multipass membrane proteins are inserted into the membrane of the endoplasmic reticulum. Their transmembrane domains (TMDs) are thought to be inserted co-translationally as they emerge from a membrane-bound ribosome. Here we find that TMDs near the carboxyl terminus of mammalian multipass proteins are inserted post-translationally by the endoplasmic reticulum membrane protein complex (EMC). Site-specific crosslinking shows that the EMC's cytosol-facing hydrophilic vestibule is adjacent to a pre-translocated C-terminal tail. EMC-mediated insertion is mostly agnostic to TMD hydrophobicity, favored for short uncharged C-tails and stimulated by a preceding unassembled TMD bundle. Thus, multipass membrane proteins can be released by the ribosome-translocon complex in an incompletely inserted state, requiring a separate EMC-mediated post-translational insertion step to rectify their topology, complete biogenesis and evade quality control. This sequential co-translational and post-translational mechanism may apply to ~250 diverse multipass proteins, including subunits of the pentameric ion channel family that are crucial for neurotransmission.
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Affiliation(s)
- Haoxi Wu
- MRC Laboratory of Molecular Biology, Cambridge, UK
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43
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Wycisk V, Wagner MC, Urner LH. Trends in the Diversification of the Detergentome. Chempluschem 2024; 89:e202300386. [PMID: 37668309 DOI: 10.1002/cplu.202300386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/06/2023]
Abstract
Detergents are amphiphilic molecules that serve as enabling steps for today's world applications. The increasing diversity of the detergentome is key to applications enabled by detergent science. Regardless of the application, the optimal design of detergents is determined empirically, which leads to failed preparations, and raising costs. To facilitate project planning, here we review synthesis strategies that drive the diversification of the detergentome. Synthesis strategies relevant for industrial and academic applications include linear, modular, combinatorial, bio-based, and metric-assisted detergent synthesis. Scopes and limitations of individual synthesis strategies in context with industrial product development and academic research are discussed. Furthermore, when designing detergents, the selection of molecular building blocks, i. e., head, linker, tail, is as important as the employed synthesis strategy. To facilitate the design of safe-to-use and tailor-made detergents, we provide an overview of established head, linker, and tail groups and highlight selected scopes and limitations for applications. It becomes apparent that most recent contributions to the increasing chemical diversity of detergent building blocks originate from the development of detergents for membrane protein studies. The overview of synthesis strategies and molecular blocks will bring us closer to the ability to predictably design and synthesize optimal detergents for challenging future applications.
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Affiliation(s)
- Virginia Wycisk
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Marc-Christian Wagner
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Leonhard H Urner
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
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44
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Jormakka M. Structural insights into ferroportin mediated iron transport. Biochem Soc Trans 2023; 51:BST20230594. [PMID: 38115725 DOI: 10.1042/bst20230594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Iron is a vital trace element for almost all organisms, and maintaining iron homeostasis is critical for human health. In mammals, the only known gatekeeper between intestinally absorbed iron and circulatory blood plasma is the membrane transporter ferroportin (Fpn). As such, dysfunction of Fpn or its regulation is a key driver of iron-related pathophysiology. This review focuses on discussing recent insights from high-resolution structural studies of the Fpn protein family. While these studies have unveiled crucial details of Fpn regulation and structural architecture, the associated functional studies have also at times provided conflicting data provoking more questions than answers. Here, we summarize key findings and illuminate important remaining questions and contradictions.
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Affiliation(s)
- Mika Jormakka
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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45
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Xiao L, Yang Q, Tan J, Ma B, Chen D. Engineering a Cl - -Modulated Light-Driven Na + Pump. Chemistry 2023; 29:e202302543. [PMID: 37833829 DOI: 10.1002/chem.202302543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 10/15/2023]
Abstract
Microbial Na+ -pumping rhodopsin (NaR) is a promising optogenetic tool due to its unique ability to transport Na+ . Like most rhodopsin-based tools, NaR is limited to light-based control. In this study, our objective was to develop a novel mode of modulation for NaR beyond light control. By introducing a potential Cl- binding site near the putative Na+ release cavity, we engineered Nonlabens dokdonensis rhodopsin 2 (NdR2) to be modulated by Cl- , an essential chemical in organisms. The engineered NdR2 demonstrated an approximately two-fold increase in Na+ pump activity in the presence of 100 mM Cl- compared to Cl- -free solution. Increasing Cl- concentration decreased the lifetimes of the M and O intermediates accordingly. The analysis of competitive ion uptake suggested the bound Cl- may increase the Na+ affinity and selectivity. This chemical modulation allows for more diverse and precise control over cellular processes, advancing the development of next-generation optogenetic tools. Notably, our Cl- -modulated NdR2 establishes an innovative mechanism for linking Cl- to Na+ -related processes, with potential applications in optogenetic therapies for related diseases.
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Affiliation(s)
- Lan Xiao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qifan Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingjing Tan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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46
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Yeow J, Luo M, Chng SS. Molecular mechanism of phospholipid transport at the bacterial outer membrane interface. Nat Commun 2023; 14:8285. [PMID: 38092770 PMCID: PMC10719372 DOI: 10.1038/s41467-023-44144-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. To maintain this barrier, the OmpC-Mla system removes mislocalized PLs from the OM outer leaflet, and transports them to the inner membrane (IM); in the first step, the OmpC-MlaA complex transfers PLs to the periplasmic chaperone MlaC, but mechanistic details are lacking. Here, we biochemically and structurally characterize the MlaA-MlaC transient complex. We map the interaction surfaces between MlaA and MlaC in Escherichia coli, and show that electrostatic interactions are important for MlaC recruitment to the OM. We further demonstrate that interactions with MlaC modulate conformational states in MlaA. Finally, we solve a 2.9-Å cryo-EM structure of a disulfide-trapped OmpC-MlaA-MlaC complex in nanodiscs, reinforcing the mechanism of MlaC recruitment, and highlighting membrane thinning as a plausible strategy for directing lipids for transport. Our work offers critical insights into retrograde PL transport by the OmpC-Mla system in maintaining OM lipid asymmetry.
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Affiliation(s)
- Jiang Yeow
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117558, Singapore
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore, 117456, Singapore.
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Habenicht T, Weidenbach K, Velazquez-Campoy A, Buey RM, Balsera M, Schmitz RA. Small protein mediates inhibition of ammonium transport in Methanosarcina mazei-an ancient mechanism? Microbiol Spectr 2023; 11:e0281123. [PMID: 37909787 PMCID: PMC10714827 DOI: 10.1128/spectrum.02811-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Small proteins containing fewer than 70 amino acids, which were previously disregarded due to computational prediction and biochemical detection challenges, have gained increased attention in the scientific community in recent years. However, the number of functionally characterized small proteins, especially in archaea, is still limited. Here, by using biochemical and genetic approaches, we demonstrate a crucial role of the small protein sP36 in the nitrogen metabolism of M. mazei, which modulates the ammonium transporter AmtB1 according to nitrogen availability. This modulation might represent an ancient archaeal mechanism of AmtB1 inhibition, in contrast to the well-studied uridylylation-dependent regulation in bacteria.
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Affiliation(s)
- Tim Habenicht
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katrin Weidenbach
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Investigaciones Sanitarias de Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Ruben M. Buey
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Monica Balsera
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Spanish National Research Council (IRNASA-CSIC), Salamanca, Spain
| | - Ruth A. Schmitz
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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48
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Jahn H, Bartoš L, Dearden GI, Dittman JS, Holthuis JCM, Vácha R, Menon AK. Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase. Nat Commun 2023; 14:8115. [PMID: 38065946 PMCID: PMC10709637 DOI: 10.1038/s41467-023-43570-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Mitochondria are double-membrane-bounded organelles that depend critically on phospholipids supplied by the endoplasmic reticulum. These lipids must cross the outer membrane to support mitochondrial function, but how they do this is unclear. We identify the Voltage Dependent Anion Channel (VDAC), an abundant outer membrane protein, as a scramblase-type lipid transporter that catalyzes lipid entry. On reconstitution into membrane vesicles, dimers of human VDAC1 and VDAC2 catalyze rapid transbilayer translocation of phospholipids by a mechanism that is unrelated to their channel activity. Coarse-grained molecular dynamics simulations of VDAC1 reveal that lipid scrambling occurs at a specific dimer interface where polar residues induce large water defects and bilayer thinning. The rate of phospholipid import into yeast mitochondria is an order of magnitude lower in the absence of VDAC homologs, indicating that VDACs provide the main pathway for lipid entry. Thus, VDAC isoforms, members of a superfamily of beta barrel proteins, moonlight as a class of phospholipid scramblases - distinct from alpha-helical scramblase proteins - that act to import lipids into mitochondria.
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Affiliation(s)
- Helene Jahn
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Ladislav Bartoš
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Grace I Dearden
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jeremy S Dittman
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Joost C M Holthuis
- Department of Molecular Cell Biology, University of Osnabrück, Osnabrück, 49076, Germany
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
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Karki S, Javanainen M, Rehan S, Tranter D, Kellosalo J, Huiskonen JT, Happonen L, Paavilainen V. Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. EMBO Rep 2023; 24:e57910. [PMID: 37983950 DOI: 10.15252/embr.202357910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. Here, we present the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by cryogenic electron microscopy (cryo-EM). Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions.
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Affiliation(s)
- Sudeep Karki
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Shahid Rehan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Protein Biochemistry and Structural Biology, Omass Therapeutics Ltd, Oxford, UK
| | - Dale Tranter
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juho Kellosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ville Paavilainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Lee Y, Park S, Yuan F, Hayden CC, Wang L, Lafer EM, Choi SQ, Stachowiak JC. Transmembrane coupling of liquid-like protein condensates. Nat Commun 2023; 14:8015. [PMID: 38049424 PMCID: PMC10696066 DOI: 10.1038/s41467-023-43332-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
Liquid-liquid phase separation of proteins occurs on both surfaces of cellular membranes during diverse physiological processes. In vitro reconstitution could provide insight into the mechanisms underlying these events. However, most existing reconstitution techniques provide access to only one membrane surface, making it difficult to probe transmembrane phenomena. To study protein phase separation simultaneously on both membrane surfaces, we developed an array of freestanding planar lipid membranes. Interestingly, we observed that liquid-like protein condensates on one side of the membrane colocalized with those on the other side, resulting in transmembrane coupling. Our results, based on lipid probe partitioning and mobility of lipids, suggest that protein condensates locally reorganize membrane lipids, a process which could be explained by multiple effects. These findings suggest a mechanism by which signals originating on one side of a biological membrane, triggered by protein phase separation, can be transferred to the opposite side.
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Affiliation(s)
- Yohan Lee
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Sujin Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Feng Yuan
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Carl C Hayden
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Liping Wang
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Eileen M Lafer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
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