1
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Cereghetti G, Kissling VM, Koch LM, Arm A, Schmidt CC, Thüringer Y, Zamboni N, Afanasyev P, Linsenmeier M, Eichmann C, Kroschwald S, Zhou J, Cao Y, Pfizenmaier DM, Wiegand T, Cadalbert R, Gupta G, Boehringer D, Knowles TPJ, Mezzenga R, Arosio P, Riek R, Peter M. An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions. Dev Cell 2024:S1534-5807(24)00271-5. [PMID: 38788715 DOI: 10.1016/j.devcel.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/15/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024]
Abstract
Amyloids are known as irreversible aggregates associated with neurodegenerative diseases. However, recent evidence shows that a subset of amyloids can form reversibly and fulfill essential cellular functions. Yet, the molecular mechanisms regulating functional amyloids and distinguishing them from pathological aggregates remain unclear. Here, we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that yeast PK (Cdc19) and human PK (PKM2) form reversible amyloids through a pH-sensitive amyloid core. Stress-induced cytosolic acidification promotes aggregation via protonation of specific glutamate (yeast) or histidine (human) residues within the amyloid core. Mutations mimicking protonation cause constitutive PK aggregation, while non-protonatable PK mutants remain soluble even upon stress. Physiological PK aggregation is coupled to metabolic rewiring and glycolysis arrest, causing severe growth defects when misregulated. Our work thus identifies an evolutionarily conserved, potentially widespread mechanism regulating functional amyloids during stress.
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Affiliation(s)
- Gea Cereghetti
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK.
| | - Vera M Kissling
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | - Lisa M Koch
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Alexandra Arm
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Claudia C Schmidt
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Yannik Thüringer
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, 8093 Zürich, Switzerland
| | - Miriam Linsenmeier
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Sonja Kroschwald
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiangtao Zhou
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Yiping Cao
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Dorota M Pfizenmaier
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland; Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Govind Gupta
- Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | | | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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2
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Xue Y, Yu C, Ouyang H, Huang J, Kang X. Uncovering the Molecular Composition and Architecture of the Bacillus subtilis Biofilm via Solid-State NMR Spectroscopy. J Am Chem Soc 2024; 146:11906-11923. [PMID: 38629727 DOI: 10.1021/jacs.4c00889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The complex and dynamic compositions of biofilms, along with their sophisticated structural assembly mechanisms, endow them with exceptional capabilities to thrive in diverse conditions that are typically unfavorable for individual cells. Characterizing biofilms in their native state is significantly challenging due to their intrinsic complexities and the limited availability of noninvasive techniques. Here, we utilized solid-state nuclear magnetic resonance (NMR) spectroscopy to analyze Bacillus subtilis biofilms in-depth. Our data uncover a dynamically distinct organization within the biofilm: a dominant, hydrophilic, and mobile framework interspersed with minor, rigid cores of limited water accessibility. In these heterogeneous rigid cores, the major components are largely self-assembled. TasA fibers, the most robust elements, further provide a degree of mechanical support for the cell aggregates and some lipid vesicles. Notably, rigid cell aggregates can persist even without the major extracellular polymeric substance (EPS) polymers, although this leads to slight variations in their rigidity and water accessibility. Exopolysaccharides are exclusively present in the mobile domain, playing a pivotal role in its water retention property. Specifically, all water molecules are tightly bound within the biofilm matrix. These findings reveal a dual-layered defensive strategy within the biofilm: a diffusion barrier through limited water mobility in the mobile phase and a physical barrier posed by limited water accessibility in the rigid phase. Complementing these discoveries, our comprehensive, in situ compositional analysis is not only essential for delineating the sophisticated biofilm architecture but also reveals the presence of alternative genetic mechanisms for synthesizing exopolysaccharides beyond the known pathway.
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Affiliation(s)
- Yi Xue
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chenjie Yu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Han Ouyang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jiaofang Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xue Kang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
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3
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Duan P, El Mammeri N, Hong M. Milligram-scale assembly and NMR fingerprint of tau fibrils adopting the Alzheimer's disease fold. J Biol Chem 2024; 300:107326. [PMID: 38679331 PMCID: PMC11145547 DOI: 10.1016/j.jbc.2024.107326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
In the Alzheimer's disease (AD) brain, the microtubule-associated protein tau aggregates into paired helical filaments in which each protofilament has a C-shaped conformation. In vitro assembly of tau fibrils adopting this fold is highly valuable for both fundamental and applied studies of AD without requiring patient-brain extracted fibrils. To date, reported methods for forming AD-fold tau fibrils have been irreproducible and sensitive to subtle variations in fibrillization conditions. Here, we describe a route to reproducibly assemble tau fibrils adopting the AD fold on the multi-milligram scale. We investigated the fibrillization conditions of two constructs and found that a tau (297-407) construct that contains four AD phospho-mimetic glutamate mutations robustly formed the C-shaped conformation. 2D and 3D correlation solid-state NMR spectra show a single predominant set of chemical shifts, indicating a single molecular conformation. Negative-stain electron microscopy and cryo-EM data confirm that the protofilament formed by 4E-tau (297-407) adopts the C-shaped conformation, which associates into paired, triple, and quadruple helical filaments. In comparison, NMR spectra indicate that a previously reported construct, tau (297-391), forms a mixture of a four-layered dimer structure and the C-shaped structure, whose populations are sensitive to the environmental conditions. The determination of the NMR chemical shifts of the AD-fold tau opens the possibility for future studies of tau fibril conformations and ligand binding by NMR. The quantitative assembly of tau fibrils adopting the AD fold should facilitate the development of diagnostic and therapeutic compounds that target AD tau.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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4
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Wu P, Zehnder J, Schröder N, Blümmel PEW, Salmon L, Damberger FF, Lipps G, Allain FHT, Wiegand T. Initial Primer Synthesis of a DNA Primase Monitored by Real-Time NMR Spectroscopy. J Am Chem Soc 2024; 146:9583-9596. [PMID: 38538061 PMCID: PMC11009956 DOI: 10.1021/jacs.3c11836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Primases are crucial enzymes for DNA replication, as they synthesize a short primer required for initiating DNA replication. We herein present time-resolved nuclear magnetic resonance (NMR) spectroscopy in solution and in the solid state to study the initial dinucleotide formation reaction of archaeal pRN1 primase. Our findings show that the helix-bundle domain (HBD) of pRN1 primase prepares the two substrates and then hands them over to the catalytic domain to initiate the reaction. By using nucleotide triphosphate analogues, the reaction is substantially slowed down, allowing us to study the initial dinucleotide formation in real time. We show that the sedimented protein-DNA complex remains active in the solid-state NMR rotor and that time-resolved 31P-detected cross-polarization experiments allow monitoring the kinetics of dinucleotide formation. The kinetics in the sedimented protein sample are comparable to those determined by solution-state NMR. Protein conformational changes during primer synthesis are observed in time-resolved 1H-detected experiments at fast magic-angle spinning frequencies (100 kHz). A significant number of spectral changes cluster in the HBD pointing to the importance of the HBD for positioning the nucleotides and the dinucleotide.
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Affiliation(s)
- Pengzhi Wu
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Johannes Zehnder
- Laboratory
of Physical Chemistry, ETH Zürich, 8093 Zurich, Switzerland
| | - Nina Schröder
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Pascal E. W. Blümmel
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Loïc Salmon
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Fred. F. Damberger
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Georg Lipps
- Institute
of Chemistry and Bioanalytics, University
of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland
| | - Frédéric H.-T. Allain
- Department
of Biology, Institute of Biochemistry, ETH
Zürich, 8093 Zurich, Switzerland
| | - Thomas Wiegand
- Laboratory
of Physical Chemistry, ETH Zürich, 8093 Zurich, Switzerland
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
- Max-Planck-Institute
for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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5
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Zyla DS, Wiegand T, Bachmann P, Zdanowicz R, Giese C, Meier BH, Waksman G, Hospenthal MK, Glockshuber R. The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili. Nat Commun 2024; 15:3032. [PMID: 38589417 PMCID: PMC11001860 DOI: 10.1038/s41467-024-47212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
Type 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of copies of the main structural subunit FimA and is assembled in vivo by the assembly platform FimD. Although type 1 pilus rods can self-assemble from FimA in vitro, this reaction is slower and produces structures with lower kinetic stability against denaturants compared to in vivo-assembled rods. Our study reveals that FimD-catalysed in vitro-assembled type 1 pilus rods attain a similar stability as pilus rods assembled in vivo. Employing structural, biophysical and biochemical analyses, we show that in vitro assembly reactions lacking FimD produce pilus rods with structural defects, reducing their stability against dissociation. Overall, our results indicate that FimD is not only required for the catalysis of pilus assembly, but also to control the assembly of the most stable quaternary structure.
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Affiliation(s)
- Dawid S Zyla
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
- La Jolla Institute for Immunology, 9420 Athena Cir, La Jolla, CA, 92037, USA
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim/Ruhr, Germany
| | - Paul Bachmann
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Rafal Zdanowicz
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK
| | - Manuela K Hospenthal
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland.
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK.
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
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6
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Sučec I, Pankratova Y, Parasar M, Hong M. Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63. Protein Sci 2024; 33:e4923. [PMID: 38501465 PMCID: PMC10949323 DOI: 10.1002/pro.4923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 03/20/2024]
Abstract
The envelope (E) proteins of coronaviruses (CoVs) form cation-conducting channels that are associated with the pathogenicity of these viruses. To date, high-resolution structural information about these viroporins is limited to the SARS-CoV E protein. To broaden our structural knowledge of other members of this family of viroporins, we now investigate the conformation of the E protein of the human coronavirus (hCoV), NL63. Using two- and three-dimensional magic-angle-spinning NMR, we have measured 13 C and 15 N chemical shifts of the transmembrane domain of E (ETM), which yielded backbone (ϕ, ψ) torsion angles. We further measured the water accessibility of NL63 ETM at neutral pH versus acidic pH in the presence of Ca2+ ions. These data show that NL63 ETM adopts a regular α-helical conformation that is unaffected by pH and the N-terminal ectodomain. Interestingly, the water accessibility of NL63 ETM increases only modestly at acidic pH in the presence of Ca2+ compared to neutral pH, in contrast to SARS ETM, which becomes much more hydrated at acidic pH. This difference suggests a structural basis for the weaker channel conductance of α-CoV compared to β-CoV E proteins. The weaker E channel activity may in turn contribute to the reduced virulence of hCoV-NL63 compared to SARS-CoV viruses.
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Affiliation(s)
- Iva Sučec
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Yanina Pankratova
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mriganka Parasar
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mei Hong
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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7
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Duan P, Hong M. Selective Detection of Intermediate-Amplitude Motion by Solid-State NMR. J Phys Chem B 2024; 128:2293-2303. [PMID: 38417154 DOI: 10.1021/acs.jpcb.3c06839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
The coexistence of rigid and mobile molecules or molecular segments abounds in biomolecular assemblies. Examples include the carbohydrate-rich cell walls of plants and intrinsically disordered proteins that contain rigid β-sheet cores. In solid-state nuclear magnetic resonance (NMR) spectroscopy, dipolar polarization transfer experiments are well suited for detecting rigid components, whereas scalar-coupling experiments are well suited for detecting highly mobile components. However, few NMR methods are available to detect the segments that undergo intermediate-amplitude fast motion. Here, we introduce two NMR experiments, a two-dimensional T2H-filtered CP-hCH correlation and a three-dimensional J-INADEQUATE CCH correlation, to observe this intermediate-amplitude motion. Both experiments involve 1H detection under fast magic-angle spinning (MAS). By combining 1H transverse relaxation (T2H) filters with dipolar polarization transfer, we suppress the signals of both highly rigid and highly mobile species, thus revealing the signals of intermediate mobile species. 1H detection under fast MAS is crucial for distinguishing the different motional amplitudes. We demonstrate these techniques on several plant cell wall samples and show that they allow the selective detection and resolution of certain hemicellulose and pectin signals, which are usually masked by the signals of the rigid cellulose and the highly dynamic pectins in purely dipolar and scalar NMR spectra.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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8
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Emmanouilidis L, Bartalucci E, Kan Y, Ijavi M, Pérez ME, Afanasyev P, Boehringer D, Zehnder J, Parekh SH, Bonn M, Michaels TCT, Wiegand T, Allain FHT. A solid beta-sheet structure is formed at the surface of FUS droplets during aging. Nat Chem Biol 2024:10.1038/s41589-024-01573-w. [PMID: 38467846 DOI: 10.1038/s41589-024-01573-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
Phase transitions are important to understand cell dynamics, and the maturation of liquid droplets is relevant to neurodegenerative disorders. We combined NMR and Raman spectroscopies with microscopy to follow, over a period of days to months, droplet maturation of the protein fused in sarcoma (FUS). Our study reveals that the surface of the droplets plays a critical role in this process, while RNA binding prevents it. The maturation kinetics are faster in an agarose-stabilized biphasic sample compared with a monophasic condensed sample, owing to the larger surface-to-volume ratio. In addition, Raman spectroscopy reports structural differences upon maturation between the inside and the surface of droplets, which is comprised of β-sheet content, as revealed by solid-state NMR. In agreement with these observations, a solid crust-like shell is observed at the surface using microaspiration. Ultimately, matured droplets were converted into fibrils involving the prion-like domain as well as the first RGG motif.
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Affiliation(s)
- Leonidas Emmanouilidis
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
- Bringing Materials to Life Initiative, ETH Zurich, Zurich, Switzerland.
| | - Ettore Bartalucci
- Max Planck Institute for Chemical Energy Conversion, Mülheim/Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany
| | - Yelena Kan
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Mahdiye Ijavi
- Department of Materials, ETH Zurich, Zurich, Switzerland
| | - Maria Escura Pérez
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | | | - Johannes Zehnder
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sapun H Parekh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Thomas C T Michaels
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Bringing Materials to Life Initiative, ETH Zurich, Zurich, Switzerland
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Mülheim/Ruhr, Germany.
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany.
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland.
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.
- Bringing Materials to Life Initiative, ETH Zurich, Zurich, Switzerland.
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9
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Medeiros-Silva J, Dregni AJ, Hong M. Distinguishing Different Hydrogen-Bonded Helices in Proteins by Efficient 1H-Detected Three-Dimensional Solid-State NMR. Biochemistry 2024; 63:181-190. [PMID: 38127783 PMCID: PMC10880114 DOI: 10.1021/acs.biochem.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Helical structures in proteins include not only α-helices but also 310 and π helices. These secondary structures differ in the registry of the C═O···H-N hydrogen bonds, which are i to i + 4 for α-helices, i to i + 3 for 310 helices, and i to i + 5 for π-helices. The standard NMR observable of protein secondary structures are chemical shifts, which are, however, insensitive to the precise type of helices. Here, we introduce a three-dimensional (3D) 1H-detected experiment that measures and assigns CO-HN cross-peaks to distinguish the different types of hydrogen-bonded helices. This hCOhNH experiment combines efficient cross-polarization from CO to HN with 13C, 15N, and 1H chemical shift correlation to detect the relative proximities of the COi-Hi+jN spin pairs. We demonstrate this experiment on the membrane-bound transmembrane domain of the SARS-CoV-2 envelope (E) protein (ETM). We show that the C-terminal five residues of ETM form a 310-helix, whereas the rest of the transmembrane domain have COi-Hi+4N hydrogen bonds that are characteristic of α-helices. This result confirms the recent high-resolution solid-state NMR structure of the open state of ETM, which was solved in the absence of explicit hydrogen-bonding restraints. This C-terminal 310 helix may facilitate proton and calcium conduction across the hydrophobic gate of the channel. This hCOhNH experiment is generally applicable and can be used to distinguish not only different types of helices but also different types of β-strands and other hydrogen-bonded conformations in proteins.
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Affiliation(s)
- Joao Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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10
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Paschke RR, Mohr S, Lange S, Lange A, Kozuch J. In Situ Spectroscopic Detection of Large-Scale Reorientations of Transmembrane Helices During Influenza A M2 Channel Opening. Angew Chem Int Ed Engl 2023; 62:e202309069. [PMID: 37733579 DOI: 10.1002/anie.202309069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 09/23/2023]
Abstract
Viroporins are small ion channels in membranes of enveloped viruses that play key roles during viral life cycles. To use viroporins as drug targets against viral infection requires in-depth mechanistic understanding and, with that, methods that enable investigations under in situ conditions. Here, we apply surface-enhanced infrared absorption (SEIRA) spectroscopy to Influenza A M2 reconstituted within a solid-supported membrane, to shed light on the mechanics of its viroporin function. M2 is a paradigm of pH-activated proton channels and controls the proton flux into the viral interior during viral infection. We use SEIRA to track the large-scale reorientation of M2's transmembrane α-helices in situ during pH-activated channel opening. We quantify this event as a helical tilt from 26° to 40° by correlating the experimental results with solid-state nuclear magnetic resonance-informed computational spectroscopy. This mechanical motion is impeded upon addition of the inhibitor rimantadine, giving a direct spectroscopic marker to test antiviral activity. The presented approach provides a spectroscopic tool to quantify large-scale structural changes and to track the function and inhibition of the growing number of viroporins from pathogenic viruses in future studies.
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Affiliation(s)
- Ronja Rabea Paschke
- Physics Department, Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195, Berlin, Germany
- Research Building SupraFAB, Freie Universität Berlin, Altensteinstr. 23a, 14195, Berlin, Germany
| | - Swantje Mohr
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Sascha Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Adam Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Jacek Kozuch
- Physics Department, Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195, Berlin, Germany
- Research Building SupraFAB, Freie Universität Berlin, Altensteinstr. 23a, 14195, Berlin, Germany
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11
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Medeiros-Silva J, Dregni AJ, Somberg NH, Duan P, Hong M. Atomic structure of the open SARS-CoV-2 E viroporin. SCIENCE ADVANCES 2023; 9:eadi9007. [PMID: 37831764 PMCID: PMC10575589 DOI: 10.1126/sciadv.adi9007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
Abstract
The envelope (E) protein of the SARS-CoV-2 virus forms cation-conducting channels in the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of infected cells. The calcium channel activity of E is associated with the inflammatory responses of COVID-19. Using solid-state NMR (ssNMR) spectroscopy, we have determined the open-state structure of E's transmembrane domain (ETM) in lipid bilayers. Compared to the closed state, open ETM has an expansive water-filled amino-terminal chamber capped by key glutamate and threonine residues, a loose phenylalanine aromatic belt in the middle, and a constricted polar carboxyl-terminal pore filled with an arginine and a threonine residue. This structure gives insights into how protons and calcium ions are selected by ETM and how they permeate across the hydrophobic gate of this viroporin.
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Affiliation(s)
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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12
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Callon M, Luder D, Malär AA, Wiegand T, Římal V, Lecoq L, Böckmann A, Samoson A, Meier BH. High and fast: NMR protein-proton side-chain assignments at 160 kHz and 1.2 GHz. Chem Sci 2023; 14:10824-10834. [PMID: 37829013 PMCID: PMC10566471 DOI: 10.1039/d3sc03539e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/16/2023] [Indexed: 10/14/2023] Open
Abstract
The NMR spectra of side-chain protons in proteins provide important information, not only about their structure and dynamics, but also about the mechanisms that regulate interactions between macromolecules. However, in the solid-state, these resonances are particularly difficult to resolve, even in relatively small proteins. We show that magic-angle-spinning (MAS) frequencies of 160 kHz, combined with a high magnetic field of 1200 MHz proton Larmor frequency, significantly improve their spectral resolution. We investigate in detail the gain for MAS frequencies between 110 and 160 kHz MAS for a model sample as well as for the hepatitis B viral capsid assembled from 120 core-protein (Cp) dimers. For both systems, we found a significantly improved spectral resolution of the side-chain region in the 1H-13C 2D spectra. The combination of 160 kHz MAS frequency with a magnetic field of 1200 MHz, allowed us to assign 61% of the aliphatic protons of Cp. The side-chain proton assignment opens up new possibilities for structural studies and further characterization of protein-protein or protein-nucleic acid interactions.
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Affiliation(s)
| | | | | | | | - Václav Římal
- Physical Chemistry, ETH Zürich 8093 Zürich Switzerland
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086, CNRS, Université de Lyon, Labex Ecofect 7 passage du Vercors 69367 Lyon France
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086, CNRS, Université de Lyon, Labex Ecofect 7 passage du Vercors 69367 Lyon France
| | - Ago Samoson
- Institute of Cybernetics, Spin Design Laboratory, Tallinn University of Technology Tallinn Estonia
| | - Beat H Meier
- Physical Chemistry, ETH Zürich 8093 Zürich Switzerland
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13
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Somberg NH, Medeiros‐Silva J, Jo H, Wang J, DeGrado WF, Hong M. Hexamethylene amiloride binds the SARS-CoV-2 envelope protein at the protein-lipid interface. Protein Sci 2023; 32:e4755. [PMID: 37632140 PMCID: PMC10503410 DOI: 10.1002/pro.4755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
The SARS-CoV-2 envelope (E) protein forms a five-helix bundle in lipid bilayers whose cation-conducting activity is associated with the inflammatory response and respiratory distress symptoms of COVID-19. E channel activity is inhibited by the drug 5-(N,N-hexamethylene) amiloride (HMA). However, the binding site of HMA in E has not been determined. Here we use solid-state NMR to measure distances between HMA and the E transmembrane domain (ETM) in lipid bilayers. 13 C, 15 N-labeled HMA is combined with fluorinated or 13 C-labeled ETM. Conversely, fluorinated HMA is combined with 13 C, 15 N-labeled ETM. These orthogonal isotopic labeling patterns allow us to conduct dipolar recoupling NMR experiments to determine the HMA binding stoichiometry to ETM as well as HMA-protein distances. We find that HMA binds ETM with a stoichiometry of one drug per pentamer. Unexpectedly, the bound HMA is not centrally located within the channel pore, but lies on the lipid-facing surface in the middle of the TM domain. This result suggests that HMA may inhibit the E channel activity by interfering with the gating function of an aromatic network. These distance data are obtained under much lower drug concentrations than in previous chemical shift perturbation data, which showed the largest perturbation for N-terminal residues. This difference suggests that HMA has higher affinity for the protein-lipid interface than the channel pore. These results give insight into the inhibition mechanism of HMA for SARS-CoV-2 E.
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Affiliation(s)
- Noah H. Somberg
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - João Medeiros‐Silva
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Hyunil Jo
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgersthe State University of New JerseyPiscatawayNew JerseyUSA
| | - William F. DeGrado
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Mei Hong
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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14
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Lipiński WP, Zehnder J, Abbas M, Güntert P, Spruijt E, Wiegand T. Fibrils Emerging from Droplets: Molecular Guiding Principles behind Phase Transitions of a Short Peptide-Based Condensate Studied by Solid-State NMR. Chemistry 2023; 29:e202301159. [PMID: 37310801 DOI: 10.1002/chem.202301159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid-liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid-to-solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid-liquid and subsequent liquid-to-solid phase transition as model systems to study both processes. Using solid-state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid-like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR-based structure calculation. The fibrils are stabilised by hydrogen bonds and side-chain π-π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid-to-solid transition of proteins, particularly those related to neurodegenerative diseases.
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Affiliation(s)
- Wojciech P Lipiński
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Johannes Zehnder
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Manzar Abbas
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Peter Güntert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, 192-0397, Tokyo, Japan
| | - Evan Spruijt
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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15
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Osborn Popp TM, Matchett BT, Green RG, Chhabra I, Mumudi S, Bernstein AD, Perodeau JR, Nieuwkoop AJ. 3D-Printable centrifugal devices for biomolecular solid state NMR rotors. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 354:107524. [PMID: 37481918 PMCID: PMC10528322 DOI: 10.1016/j.jmr.2023.107524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
The advent of magic angle spinning (MAS) rates exceeding 100 kHz has facilitated the acquisition of 1H-detected solid-state NMR spectra of biomolecules with high resolution. However, challenges can arise when preparing rotors for these experiments, due to the physical properties of biomolecular solid samples and the small dimensions of the rotors. In this study, we have designed 3D-printable centrifugal devices that facilitate efficient and consistent packing of crystalline protein slurries or viscous phospholipids into 0.7 mm rotors. We demonstrate the efficacy of these packing devices using 1H-detected solid state NMR at 105 kHz. In addition to devices for 0.7 mm rotors, we have also developed devices for other frequently employed rotor sizes and styles. We have made all our designs openly accessible, and we encourage their usage and ongoing development as a shared effort within the solid state NMR community.
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Affiliation(s)
- Thomas M Osborn Popp
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States.
| | - Brandon T Matchett
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Rashawn G Green
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Insha Chhabra
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Smriti Mumudi
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Ashley D Bernstein
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Jacqueline R Perodeau
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New, Jersey, Piscataway, NJ 08854, United States.
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16
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Sučec I, Mammeri NE, Dregni AJ, Hong M. Rapid Determination of the Topology of Oligomeric α-Helical Membrane Proteins by Water- and Lipid-Edited Methyl NMR. J Phys Chem B 2023; 127:7518-7530. [PMID: 37606918 PMCID: PMC10893779 DOI: 10.1021/acs.jpcb.3c05295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Single-span oligomeric α-helical transmembrane proteins are common in virus ion channels, which are targets of antiviral drugs. Knowledge about the high-resolution structures of these oligomeric α-helical bundles is so far scarce. Structure determination of these membrane proteins by solid-state NMR traditionally requires resolving and assigning protein chemical shifts and measuring many interhelical distances, which are time-consuming. To accelerate experimental structure determination, here we introduce a simple solid-state NMR approach that uses magnetization transfer from water and lipid protons to the protein. By detecting the water- and lipid-transferred intensities of the high-sensitivity methyl 13C signals of Leu, Val, and Ile residues, which are highly enriched in these membrane proteins, we can derive models of the topology of these homo-oligomeric helical bundles. The topology is specified by the positions of amino acid residues in heptad repeats and the orientations of residues relative to the channel pore, lipids, and the helical interface. We demonstrate this water- and lipid-edited methyl NMR approach on the envelope (E) protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. We show that water-edited and lipid-edited 2D 13C-13C correlation spectra can be measured with sufficient sensitivity. Even without resolving multiple residues of the same type in the NMR spectra, we can obtain the helical bundle topology. We apply these experiments to the structurally unknown E proteins of the MERS coronavirus and the human coronavirus NL63. The resulting structural topologies show interesting differences in the positions of the aromatic residues in these three E proteins, suggesting that these viroporins may have different mechanisms of activation and ion conduction.
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Affiliation(s)
- Iva Sučec
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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17
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El Mammeri N, Duan P, Dregni AJ, Hong M. Amyloid fibril structures of tau: Conformational plasticity of the second microtubule-binding repeat. SCIENCE ADVANCES 2023; 9:eadh4731. [PMID: 37450599 PMCID: PMC10348678 DOI: 10.1126/sciadv.adh4731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
The intrinsically disordered protein tau associates with microtubules in neurons but aggregates into cross-β amyloid fibrils that propagate in neurodegenerative brains. Different tauopathies have different structures for the rigid fibril core. To understand the molecular basis of tau assembly into different polymorphs, here we use solid-state nuclear magnetic resonance (NMR) spectroscopy to determine the structure of a tau protein that includes all microtubule-binding repeats and a proline-rich domain. This P2R tau assembles into well-ordered filaments when induced by heparin. Two- and three-dimensional NMR spectra indicate that R2 and R3 repeats constitute the rigid β-sheet core of the fibril. Unexpectedly, the amino-terminal half of R2 forms a β-arch at ambient temperature (24°C) but a continuous β-strand at 12°C, which dimerizes with the R2 of another protofilament. This temperature-dependent structure indicates that R2 is conformationally more plastic than the R3 domain. The distinct conformational stabilities of different microtubule-binding repeats give insight into the energy landscape of tau fibril formation.
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Affiliation(s)
- Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
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18
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Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Somberg NH, Liu L, Hong M, Voth GA, DeGrado WF. Transient water wires mediate selective proton transport in designed channel proteins. Nat Chem 2023; 15:1012-1021. [PMID: 37308712 PMCID: PMC10475958 DOI: 10.1038/s41557-023-01210-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/19/2023] [Indexed: 06/14/2023]
Abstract
Selective proton transport through proteins is essential for forming and using proton gradients in cells. Protons are conducted along hydrogen-bonded 'wires' of water molecules and polar side chains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways, inferred from static protein structures. Here we hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess protons in the water wire. To test this hypothesis, we performed molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+ over Na+. These studies inform the mechanisms of biological proton conduction and the principles for engineering proton-conductive materials.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Laura C Watkins
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, IL, USA
- Kemper Insurance, Chicago, IL, USA
| | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
- Department of Integrative Structural and Computational Biology Scripps Research Institute, La Jolla, CA, USA
| | - Jessica L Thomaston
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - John M Nicoludis
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
- Genentech, San Francisco, CA, USA
| | - Noah H Somberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, IL, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.
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19
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Sharma R, Malviya R, Singh S, Prajapati B. A Critical Review on Classified Excipient Sodium-Alginate-Based Hydrogels: Modification, Characterization, and Application in Soft Tissue Engineering. Gels 2023; 9:gels9050430. [PMID: 37233021 DOI: 10.3390/gels9050430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Alginates are polysaccharides that are produced naturally and can be isolated from brown sea algae and bacteria. Sodium alginate (SA) is utilized extensively in the field of biological soft tissue repair and regeneration owing to its low cost, high biological compatibility, and quick and moderate crosslinking. In addition to their high printability, SA hydrogels have found growing popularity in tissue engineering, particularly due to the advent of 3D bioprinting. There is a developing curiosity in tissue engineering with SA-based composite hydrogels and their potential for further improvement in terms of material modification, the molding process, and their application. This has resulted in numerous productive outcomes. The use of 3D scaffolds for growing cells and tissues in tissue engineering and 3D cell culture is an innovative technique for developing in vitro culture models that mimic the in vivo environment. Especially compared to in vivo models, in vitro models were more ethical and cost-effective, and they stimulate tissue growth. This article discusses the use of sodium alginate (SA) in tissue engineering, focusing on SA modification techniques and providing a comparative examination of the properties of several SA-based hydrogels. This review also covers hydrogel preparation techniques, and a catalogue of patents covering different hydrogel formulations is also discussed. Finally, SA-based hydrogel applications and future research areas concerning SA-based hydrogels in tissue engineering were examined.
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Affiliation(s)
- Rishav Sharma
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida 203201, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida 203201, India
| | - Sudarshan Singh
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Bhupendra Prajapati
- Shree S. K. Patel College of Pharmaceutical Education and Research, Ganpat University, Kherva 384012, India
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20
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Shcherbakov AA, Brousseau M, Henzler-Wildman KA, Hong M. Microsecond Motion of the Bacterial Transporter EmrE in Lipid Bilayers. J Am Chem Soc 2023; 145:10104-10115. [PMID: 37097985 PMCID: PMC10905379 DOI: 10.1021/jacs.3c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
The bacterial transporter EmrE is a homo-dimeric membrane protein that effluxes cationic polyaromatic substrates against the concentration gradient by coupling to proton transport. As the archetype of the small multidrug resistance family of transporters, EmrE structure and dynamics provide atomic insights into the mechanism of transport by this family of proteins. We recently determined high-resolution structures of EmrE in complex with a cationic substrate, tetra(4-fluorophenyl)phosphonium (F4-TPP+), using solid-state NMR spectroscopy and an S64V-EmrE mutant. The substrate-bound protein exhibits distinct structures at acidic and basic pH, reflecting changes upon binding or release of a proton from residue E14, respectively. To obtain insight into the protein dynamics that mediate substrate transport, here we measure 15N rotating-frame spin-lattice relaxation (R1ρ) rates of F4-TPP+-bound S64V-EmrE in lipid bilayers under magic-angle spinning (MAS). Using perdeuterated and back-exchanged protein and 1H-detected 15N spin-lock experiments under 55 kHz MAS, we measured 15N R1ρ rates site-specifically. Many residues show spin-lock field-dependent 15N R1ρ relaxation rates. This relaxation dispersion indicates the presence of backbone motions at a rate of about 6000 s-1 at 280 K for the protein at both acidic and basic pH. This motional rate is 3 orders of magnitude faster than the alternating access rate but is within the range estimated for substrate binding. We propose that these microsecond motions may allow EmrE to sample different conformations to facilitate substrate binding and release from the transport pore.
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Affiliation(s)
- Alexander A. Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Merissa Brousseau
- Department of Biochemistry, University of Wisconsin at Madison, Madison, WI 53706, United States
| | | | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
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21
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El Mammeri N, Gampp O, Duan P, Hong M. Membrane-induced tau amyloid fibrils. Commun Biol 2023; 6:467. [PMID: 37117483 PMCID: PMC10147698 DOI: 10.1038/s42003-023-04847-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/17/2023] [Indexed: 04/30/2023] Open
Abstract
The intrinsically disordered protein tau aggregates into β-sheet amyloid fibrils that spread in human brains afflicted with Alzheimer's disease and other neurodegenerative diseases. Tau interaction with lipid membranes might play a role in the formation and spreading of these pathological aggregates. Here we investigate the conformation and assembly of membrane-induced tau aggregates using solid-state NMR and transmission electron microscopy. A tau construct that encompasses the microtubule-binding repeats and a proline-rich domain is reconstituted into cholesterol-containing phospholipid membranes. 2D 13C-13C correlation spectra indicate that tau converted from a random coil to a β-sheet conformation over weeks. Small unilamellar vesicles (SUVs) cause different equilibrium conformations from large unilamellar vesicles (LUVs) and multilamellar vesicles (MLVs). Importantly, SUV-bound tau developed long fibrils that exhibit the characteristic β-sheet chemical shifts of Tyr310 in heparin-fibrillized tau. In comparison, LUVs and MLVs do not induce fibrils but cause different β-sheet aggregates. Lipid-protein correlation spectra indicate that these tau aggregates reside at the membrane-water interface, without inserting into the middle of the lipid bilayer. Removal of cholesterol from the SUVs abolished the fibrils, indicating that both membrane curvature and cholesterol are required for tau fibril formation. These results have implications for how lipid membranes might nucleate tau aggregates.
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Affiliation(s)
- Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Olivia Gampp
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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22
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Pfister S, Rabl J, Wiegand T, Mattei S, Malär AA, Lecoq L, Seitz S, Bartenschlager R, Böckmann A, Nassal M, Boehringer D, Meier BH. Structural conservation of HBV-like capsid proteins over hundreds of millions of years despite the shift from non-enveloped to enveloped life-style. Nat Commun 2023; 14:1574. [PMID: 36949039 PMCID: PMC10033635 DOI: 10.1038/s41467-023-37068-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/02/2023] [Indexed: 03/24/2023] Open
Abstract
The discovery of nackednaviruses provided new insight into the evolutionary history of the hepatitis B virus (HBV): The common ancestor of HBV and nackednaviruses was non-enveloped and while HBV acquired an envelope during evolution, nackednaviruses remained non-enveloped. We report the capsid structure of the African cichlid nackednavirus (ACNDV), determined by cryo-EM at 3.7 Å resolution. This enables direct comparison with the known capsid structures of HBV and duck HBV, prototypic representatives of the mammalian and avian lineages of the enveloped Hepadnaviridae, respectively. The sequence identity with HBV is 24% and both the ACNDV capsid protein fold and the capsid architecture are very similar to those of the Hepadnaviridae and HBV in particular. Acquisition of the hepadnaviral envelope was thus not accompanied by a major change in capsid structure. Dynamic residues at the spike tip are tentatively assigned by solid-state NMR, while the C-terminal domain is invisible due to dynamics. Solid-state NMR characterization of the capsid structure reveals few conformational differences between the quasi-equivalent subunits of the ACNDV capsid and an overall higher capsid structural disorder compared to HBV. Despite these differences, the capsids of ACNDV and HBV are structurally highly similar despite the 400 million years since their separation.
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Affiliation(s)
- Sara Pfister
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Julius Rabl
- Cryo-EM Knowledge hub, ETH Zurich, 8093, Zurich, Switzerland
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Simone Mattei
- EMBL Imaging Centre, European Molecular Biology Laboratory, EMBL Heidelberg, 69117, Heidelberg, Germany
| | | | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 69367, Lyon, France
| | - Stefan Seitz
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Ralf Bartenschlager
- Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon, 69367, Lyon, France.
| | - Michael Nassal
- Department of Medicine II / Molecular Biology, University of Freiburg, Freiburg im Breisgau, Germany.
| | | | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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23
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Dregni AJ, McKay MJ, Surya W, Queralt-Martin M, Medeiros-Silva J, Wang HK, Aguilella V, Torres J, Hong M. The Cytoplasmic Domain of the SARS-CoV-2 Envelope Protein Assembles into a β-Sheet Bundle in Lipid Bilayers. J Mol Biol 2023; 435:167966. [PMID: 36682677 PMCID: PMC9851921 DOI: 10.1016/j.jmb.2023.167966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/23/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein forms a pentameric ion channel in the lipid membrane of the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of the infected cell. The cytoplasmic domain of E interacts with host proteins to cause virus pathogenicity and may also mediate virus assembly and budding. To understand the structural basis of these functions, here we investigate the conformation and dynamics of an E protein construct (residues 8-65) that encompasses the transmembrane domain and the majority of the cytoplasmic domain using solid-state NMR. 13C and 15N chemical shifts indicate that the cytoplasmic domain adopts a β-sheet-rich conformation that contains three β-strands separated by turns. The five subunits associate into an umbrella-shaped bundle that is attached to the transmembrane helices by a disordered loop. Water-edited NMR spectra indicate that the third β-strand at the C terminus of the protein is well hydrated, indicating that it is at the surface of the β-bundle. The structure of the cytoplasmic domain cannot be uniquely determined from the inter-residue correlations obtained here due to ambiguities in distinguishing intermolecular and intramolecular contacts for a compact pentameric assembly of this small domain. Instead, we present four structural topologies that are consistent with the measured inter-residue contacts. These data indicate that the cytoplasmic domain of the SARS-CoV-2 E protein has a strong propensity to adopt β-sheet conformations when the protein is present at high concentrations in lipid bilayers. The equilibrium between the β-strand conformation and the previously reported α-helical conformation may underlie the multiple functions of E in the host cell and in the virion.
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Affiliation(s)
- Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Matthew J McKay
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Maria Queralt-Martin
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Harrison K Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Vicente Aguilella
- Laboratory of Molecular Biophysics. Department of Physics. Universitat Jaume I. 12080 Castellón, Spain
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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24
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Duma L, Senicourt L, Rigaud B, Papadopoulos V, Lacapère JJ. Solid-state NMR study of structural heterogeneity of the apo WT mouse TSPO reconstituted in liposomes. Biochimie 2023; 205:73-85. [PMID: 36029902 DOI: 10.1016/j.biochi.2022.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/08/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
In the last decades, ligand binding to human TSPO has been largely used in clinical neuroimaging, but little is known about the interaction mechanism. Protein conformational mobility plays a key role in the ligand recognition and both, ligand-free and ligand-bound structures, are mandatory for characterizing the molecular binding mechanism. In the absence of crystals for mammalian TSPO, we have exploited solid-state nuclear magnetic resonance (ssNMR) spectroscopy under magic-angle spinning (MAS) to study the apo form of recombinant mouse TSPO (mTSPO) reconstituted in lipids. This environment has been previously described to permit binding of its high-affinity drug ligand PK11195 and appears therefore favourable for the study of molecular dynamics. We have optimized the physical conditions to get the best resolution for MAS ssNMR spectra of the ligand-free mTSPO. We have compared and combined various ssNMR spectra to get dynamical information either for the lipids or for the mTSPO. Partial assignment of residue types suggests few agreements with the published solution NMR assignment of the PK11195-bound mTSPO in DPC detergent. Moreover, we were able to observe some lateral chains of aromatic residues that were not assigned in solution. 13C double-quantum NMR spectroscopy shows remarkable dynamics for ligand-free mTSPO in lipids which may have significant implications on the recognition of the ligand and/or other protein partners.
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Affiliation(s)
- Luminita Duma
- Champagne-Ardenne University, CNRS, ICMR UMR, 7312, Reims, France.
| | - Lucile Senicourt
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 4 Place Jussieu, F-75005, Paris, France
| | - Baptiste Rigaud
- CNRS Institut des Matériaux de Paris Centre (FR2482), 4 Place Jussieu, 75005, Paris, France
| | - Vassilios Papadopoulos
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jean-Jacques Lacapère
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 4 Place Jussieu, F-75005, Paris, France
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25
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Molecular elucidation of drug-induced abnormal assemblies of the hepatitis B virus capsid protein by solid-state NMR. Nat Commun 2023; 14:471. [PMID: 36709212 PMCID: PMC9884277 DOI: 10.1038/s41467-023-36219-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
Hepatitis B virus (HBV) capsid assembly modulators (CAMs) represent a recent class of anti-HBV antivirals. CAMs disturb proper nucleocapsid assembly, by inducing formation of either aberrant assemblies (CAM-A) or of apparently normal but genome-less empty capsids (CAM-E). Classical structural approaches have revealed the CAM binding sites on the capsid protein (Cp), but conformational information on the CAM-induced off-path aberrant assemblies is lacking. Here we show that solid-state NMR can provide such information, including for wild-type full-length Cp183, and we find that in these assemblies, the asymmetric unit comprises a single Cp molecule rather than the four quasi-equivalent conformers typical for the icosahedral T = 4 symmetry of the normal HBV capsids. Furthermore, while in contrast to truncated Cp149, full-length Cp183 assemblies appear, on the mesoscopic level, unaffected by CAM-A, NMR reveals that on the molecular level, Cp183 assemblies are equally aberrant. Finally, we use a eukaryotic cell-free system to reveal how CAMs modulate capsid-RNA interactions and capsid phosphorylation. Our results establish a structural view on assembly modulation of the HBV capsid, and they provide a rationale for recently observed differences between in-cell versus in vitro capsid assembly modulation.
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26
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Bousset L, Alik A, Arteni A, Böckmann A, Meier BH, Melki R. α-Synuclein Fibril, Ribbon and Fibril-91 Amyloid Polymorphs Generation for Structural Studies. Methods Mol Biol 2023; 2551:345-355. [PMID: 36310214 DOI: 10.1007/978-1-0716-2597-2_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The human α-synuclein protein, identified as one of the main markers of Parkinson's disease, is a 140-amino acid thermostable protein that can easily be overexpressed in E. coli. The purification protocol determines the ability of the protein to assemble into amyloid fibrils of well-defined structures. Here, we describe the purification and assembly protocols to obtain three well-characterized amyloid forms (ribbon, fibrils, and fibril-91) used to assess their activity in biochemical and cellular assays or to investigate their atomic structure by cryo-electron microscopy and solid-state NMR.
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Affiliation(s)
- Luc Bousset
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France.
| | - Ania Alik
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Ana Arteni
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Ronald Melki
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
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27
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Al-Hilaly YK, Hurt C, Rickard JE, Harrington CR, Storey JMD, Wischik CM, Serpell LC, Siemer AB. Solid-state NMR of paired helical filaments formed by the core tau fragment tau(297-391). Front Neurosci 2022; 16:988074. [PMID: 36570831 PMCID: PMC9774000 DOI: 10.3389/fnins.2022.988074] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Aggregation of the tau protein into fibrillar cross-β aggregates is a hallmark of Alzheimer's diseases (AD) and many other neurodegenerative tauopathies. Recently, several core structures of patient-derived tau paired helical filaments (PHFs) have been solved revealing a structural variability that often correlates with a specific tauopathy. To further characterize the dynamics of these fibril cores, to screen for strain-specific small molecules as potential biomarkers and therapeutics, and to develop strain-specific antibodies, recombinant in-vitro models of tau filaments are needed. We recently showed that a 95-residue fragment of tau (from residue 297 to 391), termed dGAE, forms filaments in vitro in the absence of polyanionic co-factors often used for in vitro aggregation of full-length tau. Tau(297-391) was identified as the proteolytic resistant core of tau PHFs and overlaps with the structures characterized by cryo-electron microscopy in ex vivo PHFs, making it a promising model for the study of AD tau filaments in vitro. In the present study, we used solid-state NMR to characterize tau(297-391) filaments and show that such filaments assembled under non-reducing conditions are more dynamic and less ordered than those made in the presence of the reducing agent DTT. We further report the resonance assignment of tau(297-391)+DTT filaments and compare it to existing core structures of tau.
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Affiliation(s)
- Youssra K. Al-Hilaly
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, United Kingdom,Chemistry Department, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Connor Hurt
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Janet E. Rickard
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Charles R. Harrington
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom,TauRx Therapeutics Ltd., Aberdeen, United Kingdom
| | - John M. D. Storey
- TauRx Therapeutics Ltd., Aberdeen, United Kingdom,Department of Chemistry, University of Aberdeen, Aberdeen, United Kingdom
| | - Claude M. Wischik
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom,TauRx Therapeutics Ltd., Aberdeen, United Kingdom
| | - Louise C. Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Ansgar B. Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States,*Correspondence: Ansgar B. Siemer,
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28
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Abstract
α-synuclein misfolding and aggregation into fibrils is a common feature of α-synucleinopathies, such as Parkinson's disease, in which α-synuclein fibrils are a characteristic hallmark of neuronal inclusions called Lewy bodies. Studies on the composition of Lewy bodies extracted postmortem from brain tissue of Parkinson's patients revealed that lipids and membranous organelles are also a significant component. Interactions between α-synuclein and lipids have been previously identified as relevant for Parkinson's disease pathology, however molecular insights into their interactions have remained elusive. Here we present cryo-electron microscopy structures of six α-synuclein fibrils in complex with lipids, revealing specific lipid-fibril interactions. We observe that phospholipids promote an alternative protofilament fold, mediate an unusual arrangement of protofilaments, and fill the central cavities of the fibrils. Together with our previous studies, these structures also indicate a mechanism for fibril-induced lipid extraction, which is likely to be involved in the development of α-synucleinopathies. Specifically, one potential mechanism for the cellular toxicity is the disruption of intracellular vesicles mediated by fibrils and oligomers, and therefore the modulation of these interactions may provide a promising strategy for future therapeutic interventions.
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29
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Matlahov I, Boatz JC, C.A. van der Wel P. Selective observation of semi-rigid non-core residues in dynamically complex mutant huntingtin protein fibrils. J Struct Biol X 2022; 6:100077. [PMID: 36419510 PMCID: PMC9677204 DOI: 10.1016/j.yjsbx.2022.100077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/20/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
Abstract
Mutant huntingtin exon 1 fibrils feature a broad range of molecular dynamics. Molecular motion is coupled to water dynamics outside the fiber core. Dynamics-based spectral editing ssNMR reveals mobile non-core residues. Intermediate-motion selection via dipolar dephasing of rigid sites. Semi-mobile glutamines outside the fiber core observed and identified.
Many amyloid-forming proteins, which are normally intrinsically disordered, undergo a disorder-to-order transition to form fibrils with a rigid β-sheet core flanked by disordered domains. Solid-state NMR (ssNMR) and cryogenic electron microscopy (cryoEM) excel at resolving the rigid structures within amyloid cores but studying the dynamically disordered domains remains challenging. This challenge is exemplified by mutant huntingtin exon 1 (HttEx1), which self-assembles into pathogenic neuronal inclusions in Huntington disease (HD). The mutant protein’s expanded polyglutamine (polyQ) segment forms a fibril core that is rigid and sequestered from the solvent. Beyond the core, solvent-exposed surface residues mediate biological interactions and other properties of fibril polymorphs. Here we deploy magic angle spinning ssNMR experiments to probe for semi-rigid residues proximal to the fibril core and examine how solvent dynamics impact the fibrils’ segmental dynamics. Dynamic spectral editing (DYSE) 2D ssNMR based on a combination of cross-polarization (CP) ssNMR with selective dipolar dephasing reveals the weak signals of solvent-mobilized glutamine residues, while suppressing the normally strong background of rigid core signals. This type of ‘intermediate motion selection’ (IMS) experiment based on cross-polarization (CP) ssNMR, is complementary to INEPT- and CP-based measurements that highlight highly flexible or highly rigid protein segments, respectively. Integration of the IMS-DYSE element in standard CP-based ssNMR experiments permits the observation of semi-rigid residues in a variety of contexts, including in membrane proteins and protein complexes. We discuss the relevance of semi-rigid solvent-facing residues outside the fibril core to the latter’s detection with specific dyes and positron emission tomography tracers.
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30
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Duan P, Dregni AJ, Hong M. Solid-State NMR 19F- 1H- 15N Correlation Experiments for Resonance Assignment and Distance Measurements of Multifluorinated Proteins. J Phys Chem A 2022; 126:7021-7032. [PMID: 36150071 PMCID: PMC10867861 DOI: 10.1021/acs.jpca.2c05154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several solid-state NMR techniques have been introduced recently to measure nanometer distances involving 19F, whose high gyromagnetic ratio makes it a potent nuclear spin for structural investigation. These solid-state NMR techniques either use 19F correlation with 1H or 13C to obtain qualitative interatomic contacts or use the rotational-echo double-resonance (REDOR) pulse sequence to measure quantitative distances. However, no NMR technique is yet available for disambiguating 1H-19F distances in multiply fluorinated proteins and protein-ligand complexes. Here, we introduce a three-dimensional (3D) 19F-15N-1H correlation experiment that resolves the distances of multiple fluorines to their adjacent amide protons. We show that optimal polarization transfer between 1H and 19F spins is achieved using an out-and-back 1H-19F REDOR sequence. We demonstrate this 3D correlation experiment on the model protein GB1 and apply it to the multidrug-resistance transporter, EmrE, complexed to a tetrafluorinated substrate. This technique should be useful for resolving and assigning distance constraints in multiply fluorinated proteins, leading to significant savings of time and precious samples compared to producing several singly fluorinated samples. Moreover, the method enables structural determination of protein-ligand complexes for ligands that contain multiple fluorines.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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31
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The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils. Nat Commun 2022; 13:5385. [PMID: 36104315 PMCID: PMC9474542 DOI: 10.1038/s41467-022-32797-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/12/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractAggregation of amyloidogenic proteins is a characteristic of multiple neurodegenerative diseases. Atomic resolution of small molecule binding to such pathological protein aggregates is of interest for the development of therapeutics and diagnostics. Here we investigate the interaction between α-synuclein fibrils and anle138b, a clinical drug candidate for disease modifying therapy in neurodegeneration and a promising scaffold for positron emission tomography tracer design. We used nuclear magnetic resonance spectroscopy and the cryogenic electron microscopy structure of α-synuclein fibrils grown in the presence of lipids to locate anle138b within a cavity formed between two β-strands. We explored and quantified multiple binding modes of the compound in detail using molecular dynamics simulations. Our results reveal stable polar interactions between anle138b and backbone moieties inside the tubular cavity of the fibrils. Such cavities are common in other fibril structures as well.
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32
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El Mammeri N, Dregni AJ, Duan P, Wang HK, Hong M. Microtubule-binding core of the tau protein. SCIENCE ADVANCES 2022; 8:eabo4459. [PMID: 35857846 PMCID: PMC9299549 DOI: 10.1126/sciadv.abo4459] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/07/2022] [Indexed: 05/15/2023]
Abstract
The protein tau associates with microtubules to maintain neuronal health. Posttranslational modifications of tau interfere with this binding, leading to tau aggregation in neurodegenerative disorders. Here, we use solid-state nuclear magnetic resonance (NMR) to investigate the structure of the microtubule-binding domain of tau. Wild-type tau that contains four microtubule-binding repeats and a pseudorepeat R' is studied. Complexed with taxol-stabilized microtubules, the immobilized residues exhibit well-resolved two-dimensional spectra that can be assigned to the amino-terminal region of R4 and the R' domain. When tau coassembles with tubulin to form unstable microtubules, the R' signals remain, whereas the R4 signals disappear, indicating that R' remains immobilized, whereas R4 becomes more mobile. Therefore, R' outcompetes the other four repeats to associate with microtubules. These NMR data, together with previous cryo-electron microscopy densities, indicate an extended conformation for microtubule-bound R'. R' contains the largest number of charged residues among all repeats, suggesting that charge-charge interaction drives tau-microtubule association.
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Affiliation(s)
- Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | | | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Harrison K. Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
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33
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Sutherland M, Tran N, Hong M. Clustering of tetrameric influenza M2 peptides in lipid bilayers investigated by 19F solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183909. [PMID: 35276226 DOI: 10.1016/j.bbamem.2022.183909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/08/2022] [Accepted: 03/05/2022] [Indexed: 11/19/2022]
Abstract
The influenza M2 protein forms a drug-targeted tetrameric proton channel to mediate virus uncoating, and carries out membrane scission to enable virus release. While the proton channel function of M2 has been extensively studied, the mechanism by which M2 catalyzes membrane scission is still not well understood. Previous fluorescence and electron microscopy studies indicated that M2 tetramers concentrate at the neck of the budding virus in the host plasma membrane. However, molecular evidence for this clustering is scarce. Here, we use 19F solid-state NMR to investigate M2 clustering in phospholipid bilayers. By mixing equimolar amounts of 4F-Phe47 labeled M2 peptide and CF3-Phe47 labeled M2 peptide and measuring F-CF3 cross peaks in 2D 19F19F correlation spectra, we show that M2 tetramers form nanometer-scale clusters in lipid bilayers. This clustering is stronger in cholesterol-containing membranes and phosphatidylethanolamine (PE) membranes than in cholesterol-free phosphatidylcholine and phosphatidylglycerol membranes. The observed correlation peaks indicate that Phe47 sidechains from different tetramers are less than ~2 nm apart. 1H19F correlation peaks between lipid chain protons and fluorinated Phe47 indicate that Phe47 is more deeply inserted into the lipid bilayer in the presence of cholesterol than in its absence, suggesting that Phe47 preferentially interacts with cholesterol. Static 31P NMR spectra indicate that M2 induces negative Gaussian curvature in the PE membrane. These results suggest that M2 tetramers cluster at cholesterol- and PE-rich regions of cell membranes to cause membrane curvature, which in turn can facilitate membrane scission in the last step of virus budding and release.
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Affiliation(s)
- Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America.
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34
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El Hariri El Nokab M, Lasorsa A, Sebakhy KO, Picchioni F, van der Wel PC. Solid-state NMR spectroscopy insights for resolving different water pools in alginate hydrogels. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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35
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Xue K, Sarkar R, Tošner Z, Reif B. Field and magic angle spinning frequency dependence of proton resonances in rotating solids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:47-61. [PMID: 36113917 DOI: 10.1016/j.pnmrs.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Proton detection in solid state NMR is continuously developing and allows one to gain new insights in structural biology. Overall, this progress is a result of the synergy between hardware development, new NMR methodology and new isotope labeling strategies, to name a few factors. Even though current developments are rapid, it is worthwhile to summarize what can currently be achieved employing proton detection in biological solids. We illustrate this by analysing the signal-to-noise ratio (SNR) for spectra obtained for a microcrystalline α-spectrin SH3 domain protein sample by (i) employing different degrees of chemical dilution to replace protons by incorporating deuterons in different sites, by (ii) variation of the magic angle spinning (MAS) frequencies between 20 and 110 kHz, and by (iii) variation of the static magnetic field B0. The experimental SNR values are validated with numerical simulations employing up to 9 proton spins. Although in reality a protein would contain far more than 9 protons, in a deuterated environment this is a sufficient number to achieve satisfactory simulations consistent with the experimental data. The key results of this analysis are (i) with current hardware, deuteration is still necessary to record spectra of optimum quality; (ii) 13CH3 isotopomers for methyl groups yield the best SNR when MAS frequencies above 100 kHz are available; and (iii) sensitivity increases with a factor beyond B0 3/2 with the static magnetic field due to a transition of proton-proton dipolar interactions from a strong to a weak coupling limit.
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Affiliation(s)
- Kai Xue
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology, Am Fassberg. 11, Goettingen, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany
| | - Zdeněk Tošner
- Department of Chemistry, Faculty of Science, Charles University, Hlavova 8, 12842 Praha 2, Czech Republic
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.
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36
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Dregni AJ, Duan P, Xu H, Changolkar L, El Mammeri N, Lee VMY, Hong M. Fluent molecular mixing of Tau isoforms in Alzheimer's disease neurofibrillary tangles. Nat Commun 2022; 13:2967. [PMID: 35624093 PMCID: PMC9142584 DOI: 10.1038/s41467-022-30585-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/04/2022] [Indexed: 12/28/2022] Open
Abstract
Alzheimer's disease (AD) is defined by intracellular neurofibrillary tangles formed by the microtubule-associated protein tau and extracellular plaques formed by the β-amyloid peptide. AD tau tangles contain a mixture of tau isoforms with either four (4R) or three (3R) microtubule-binding repeats. Here we use solid-state NMR to determine how 4R and 3R tau isoforms mix at the molecular level in AD tau aggregates. By seeding differentially isotopically labeled 4R and 3R tau monomers with AD brain-derived tau, we measured intermolecular contacts of the two isoforms. The NMR data indicate that 4R and 3R tau are well mixed in the AD-tau seeded fibrils, with a 60:40 incorporation ratio of 4R to 3R tau and a small homotypic preference. The AD-tau templated 4R tau, 3R tau, and mixed 4R and 3R tau fibrils exhibit no structural differences in the rigid β-sheet core or the mobile domains. Therefore, 4R and 3R tau are fluently recruited into the pathological fold of AD tau aggregates, which may explain the predominance of AD among neurodegenerative disorders.
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Affiliation(s)
- Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Hong Xu
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Lakshmi Changolkar
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Virginia M-Y Lee
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA.
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37
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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38
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Medeiros-Silva J, Somberg NH, Wang HK, McKay MJ, Mandala VS, Dregni AJ, Hong M. pH- and Calcium-Dependent Aromatic Network in the SARS-CoV-2 Envelope Protein. J Am Chem Soc 2022; 144:6839-6850. [PMID: 35380805 DOI: 10.1021/jacs.2c00973] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The envelope (E) protein of the SARS-CoV-2 virus is a membrane-bound viroporin that conducts cations across the endoplasmic reticulum Golgi intermediate compartment (ERGIC) membrane of the host cell to cause virus pathogenicity. The structure of the closed state of the E transmembrane (TM) domain, ETM, was recently determined using solid-state NMR spectroscopy. However, how the channel pore opens to mediate cation transport is unclear. Here, we use 13C and 19F solid-state NMR spectroscopy to investigate the conformation and dynamics of ETM at acidic pH and in the presence of calcium ions, which mimic the ERGIC and lysosomal environment experienced by the E protein in the cell. Acidic pH and calcium ions increased the conformational disorder of the N- and C-terminal residues and also increased the water accessibility of the protein, indicating that the pore lumen has become more spacious. ETM contains three regularly spaced phenylalanine (Phe) residues in the center of the peptide. 19F NMR spectra of para-fluorinated Phe20 and Phe26 indicate that both residues exhibit two sidechain conformations, which coexist within each channel. These two Phe conformations differ in their water accessibility, lipid contact, and dynamics. Channel opening by acidic pH and Ca2+ increases the population of the dynamic lipid-facing conformation. These results suggest an intricate aromatic network that regulates the opening of the ETM channel pore. This aromatic network may be a target for E inhibitors against SARS-CoV-2 and related coronaviruses.
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Affiliation(s)
- João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Noah H Somberg
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Harrison K Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Matthew J McKay
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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39
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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40
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Římal V, Callon M, Malär A, Cadalbert R, Torosyan A, Wiegand T, Ernst M, Böckmann A, Meier B. Correction of field instabilities in biomolecular solid-state NMR by simultaneous acquisition of a frequency reference. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:15-26. [PMID: 37905180 PMCID: PMC10539777 DOI: 10.5194/mr-3-15-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/26/2022] [Indexed: 11/02/2023]
Abstract
With the advent of faster magic-angle spinning (MAS) and higher magnetic fields, the resolution of biomolecular solid-state nuclear magnetic resonance (NMR) spectra has been continuously increasing. As a direct consequence, the always narrower spectral lines, especially in proton-detected spectroscopy, are also becoming more sensitive to temporal instabilities of the magnetic field in the sample volume. Field drifts in the order of tenths of parts per million occur after probe insertion or temperature change, during cryogen refill, or are intrinsic to the superconducting high-field magnets, particularly in the months after charging. As an alternative to a field-frequency lock based on deuterium solvent resonance rarely available for solid-state NMR, we present a strategy to compensate non-linear field drifts using simultaneous acquisition of a frequency reference (SAFR). It is based on the acquisition of an auxiliary 1D spectrum in each scan of the experiment. Typically, a small-flip-angle pulse is added at the beginning of the pulse sequence. Based on the frequency of the maximum of the solvent signal, the field evolution in time is reconstructed and used to correct the raw data after acquisition, thereby acting in its principle as a digital lock system. The general applicability of our approach is demonstrated on 2D and 3D protein spectra during various situations with a non-linear field drift. SAFR with small-flip-angle pulses causes no significant loss in sensitivity or increase in experimental time in protein spectroscopy. The correction leads to the possibility of recording high-quality spectra in a typical biomolecular experiment even during non-linear field changes in the order of 0.1 ppm h- 1 without the need for hardware solutions, such as stabilizing the temperature of the magnet bore. The improvement of linewidths and peak shapes turns out to be especially important for 1 H-detected spectra under fast MAS, but the method is suitable for the detection of carbon or other nuclei as well.
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Affiliation(s)
- Václav Římal
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | - Morgane Callon
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | | | | | | | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086,
CNRS/Université de Lyon, 69367 Lyon, France
| | - Beat H. Meier
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
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41
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Duan P, Chen KJ, Wijegunawardena G, Dregni AJ, Wang HK, Wu H, Hong M. Binding Sites of a Positron Emission Tomography Imaging Agent in Alzheimer's β-Amyloid Fibrils Studied Using 19F Solid-State NMR. J Am Chem Soc 2022; 144:1416-1430. [PMID: 35015530 PMCID: PMC8855532 DOI: 10.1021/jacs.1c12056] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amyloid imaging by positron emission tomography (PET) is an important method for diagnosing neurodegenerative disorders such as Alzheimer's disease. Many 11C- and 18F-labeled PET tracers show varying binding capacities, specificities, and affinities for their target proteins. The structural basis of these variations is poorly understood. Here we employ 19F and 13C solid-state NMR to investigate the binding sites of a PET ligand, flutemetamol, to the 40-residue Alzheimer's β-amyloid peptide (Aβ40). Analytical high-performance liquid chromatography and 19F NMR spectra show that flutemetamol binds the current Aβ40 fibril polymorph with a stoichiometry of one ligand per four to five peptides. Half of the ligands are tightly bound while the other half are loosely bound. 13C and 15N chemical shifts indicate that this Aβ40 polymorph has an immobilized N-terminus, a non-β-sheet His14, and a non-β-sheet C-terminus. We measured the proximity of the ligand fluorine to peptide residues using 19F-13C and 19F-1H rotational-echo double-resonance (REDOR) experiments. The spectra show that three segments in the peptide, 12VHH14, 18VFF20, and 39VV40, lie the closest to the ligand. REDOR-constrained docking simulations indicate that these three segments form multiple binding sites, and the ligand orientations and positions at these sites are similar across different Aβ polymorphs. Comparison of the flutemetamol-interacting residues in Aβ40 with the small-molecule binding sites in other amyloid proteins suggest that conjugated aromatic compounds preferentially bind β-sheet surface grooves lined by aromatic, polar, and charged residues. These motifs may explain the specificity of different PET tracers to different amyloid proteins.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Kelly J. Chen
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Gayani Wijegunawardena
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount St, Wichita, KS 67260, United States
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Harrison K. Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount St, Wichita, KS 67260, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
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42
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Malär AA, Callon M, Smith AA, Wang S, Lecoq L, Pérez-Segura C, Hadden-Perilla JA, Böckmann A, Meier BH. Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR. Front Mol Biosci 2022; 8:807577. [PMID: 35047563 PMCID: PMC8762115 DOI: 10.3389/fmolb.2021.807577] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 01/14/2023] Open
Abstract
Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from 240 copies of the Cp149 core protein. We measure both T1 and T1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.
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Affiliation(s)
| | | | - Albert A Smith
- Institute of Medical Physics and Biophysics, Universität Leipzig, Leipzig, Germany
| | - Shishan Wang
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
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43
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1H detection and dynamic nuclear polarization-enhanced NMR of Aβ 1-42 fibrils. Proc Natl Acad Sci U S A 2022; 119:2114413119. [PMID: 34969859 PMCID: PMC8740738 DOI: 10.1073/pnas.2114413119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2021] [Indexed: 12/25/2022] Open
Abstract
Amyloid-β (Aβ) is the subject of intense scrutiny because of its close association with Alzheimer’s disease (AD), which currently afflicts about 50 million people worldwide. The results reported in this manuscript focus on the new possibilities provided by ultrafast magic-angle spinning (MAS) 1H detection and fast-MAS dynamic nuclear polarization (DNP), which have ushered in a new era for NMR-based structural biology, but whose potential has not yet been fully exploited for the structural investigation of complex amyloid assemblies. This work demonstrates the expeditious structural analysis of amyloid fibrils, without requiring preparation of large sample amounts, and sets the stage for future studies of unlabeled AD peptides derived from tissue samples available in limited quantities. Several publications describing high-resolution structures of amyloid-β (Aβ) and other fibrils have demonstrated that magic-angle spinning (MAS) NMR spectroscopy is an ideal tool for studying amyloids at atomic resolution. Nonetheless, MAS NMR suffers from low sensitivity, requiring relatively large amounts of samples and extensive signal acquisition periods, which in turn limits the questions that can be addressed by atomic-level spectroscopic studies. Here, we show that these drawbacks are removed by utilizing two relatively recent additions to the repertoire of MAS NMR experiments—namely, 1H detection and dynamic nuclear polarization (DNP). We show resolved and sensitive two-dimensional (2D) and three-dimensional (3D) correlations obtained on 13C,15N-enriched, and fully protonated samples of M0Aβ1-42 fibrils by high-field 1H-detected NMR at 23.4 T and 18.8 T, and 13C-detected DNP MAS NMR at 18.8 T. These spectra enable nearly complete resonance assignment of the core of M0Aβ1-42 (K16-A42) using submilligram sample quantities, as well as the detection of numerous unambiguous internuclear proximities defining both the structure of the core and the arrangement of the different monomers. An estimate of the sensitivity of the two approaches indicates that the DNP experiments are currently ∼6.5 times more sensitive than 1H detection. These results suggest that 1H detection and DNP may be the spectroscopic approaches of choice for future studies of Aβ and other amyloid systems.
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44
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Barret L, Schubeis T, Kugler V, Guyot L, Pintacuda G, Wagner R. Production and Preparation of Isotopically Labeled Human Membrane Proteins in Pichia pastoris for Fast-MAS-NMR Analyses. Methods Mol Biol 2022; 2507:201-221. [PMID: 35773584 DOI: 10.1007/978-1-0716-2368-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Membrane proteins (MPs) comprise about one-third of the human proteome, playing critical roles in many physiological processes and associated disorders. Consistently, they represent one of the largest classes of targets for the pharmaceutical industry. Their study at the molecular level is however particularly challenging, resulting in a severe lack of structural and dynamic information that is hindering their detailed functional characterization and the identification of novel potent drug candidates.Magic Angle Spinning (MAS) NMR is a reliable and efficient method for the determination of protein structures and dynamics and for the identification of ligand binding sites and equilibria. MAS-NMR is particularly well suited for MPs since they can be directly analysed in a native-like lipid bilayer environment but used to require aggravating large amounts of isotope enriched material. The frequent toxicity of human MP overexpression in bacterial cultures poses an additional hurdle, resulting in the need for alternative (and often more costly) expression systems. The recent development of very fast (up to 150 kHz) MAS probes has revolutionized the field of biomolecular solid-state NMR enabling higher spectral resolution with significant reduction of the required sample, rendering eukaryotic expression systems cost-effective.Here is presented a set of accessible procedures validated for the production and preparation of eukaryotic MPs for Fast-MAS 1H-detected NMR analysis. The methodology is illustrated with the human copper uptake protein hCTR1 recombinantly produced and 13C-15N uniformly labeled with the versatile and affordable Pichia pastoris system. Subsequent purification procedures allow the recovery of mg amounts that are then reconstituted into liposome formulations compatible with solid-state NMR handling and analysis.
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Affiliation(s)
- Lina Barret
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs de Lyon (UMR 5082-CNRS, Université Claude Bernard Lyon 1, École Normale Supérieure Lyon), Université de Lyon, Villeurbanne, France
| | - Tobias Schubeis
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs de Lyon (UMR 5082-CNRS, Université Claude Bernard Lyon 1, École Normale Supérieure Lyon), Université de Lyon, Villeurbanne, France
| | - Valérie Kugler
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France
| | - Lucile Guyot
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France
- NovAliX, Illkirch, France
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs de Lyon (UMR 5082-CNRS, Université Claude Bernard Lyon 1, École Normale Supérieure Lyon), Université de Lyon, Villeurbanne, France
| | - Renaud Wagner
- Biotechnology and Cell Signalling, IMPReSs Protein Facility, UMR7242 CNRS-University of Strasbourg, Illkirch, France.
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45
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Reif B. Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR. Chem Rev 2021; 122:10019-10035. [PMID: 34870415 DOI: 10.1021/acs.chemrev.1c00681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B0 field in a perdeuterated environment are compiled.
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Affiliation(s)
- Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at the Department of Chemistry, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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46
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Zehnder J, Cadalbert R, Yulikov M, Künze G, Wiegand T. Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 332:107075. [PMID: 34597956 DOI: 10.1016/j.jmr.2021.107075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Labeling of biomolecules with a paramagnetic probe for nuclear magnetic resonance (NMR) spectroscopy enables determining long-range distance restraints, which are otherwise not accessible by classically used dipolar coupling-based NMR approaches. Distance restraints derived from paramagnetic relaxation enhancements (PREs) can facilitate the structure determination of large proteins and protein complexes. We herein present the site-directed labeling of the large oligomeric bacterial DnaB helicase from Helicobacter pylori with cysteine-reactive maleimide tags carrying either a nitroxide radical or a lanthanide ion. The success of the labeling reaction was followed by quantitative continuous-wave electron paramagnetic resonance (EPR) experiments performed on the nitroxide-labeled protein. PREs were extracted site-specifically from 2D and 3D solid-state NMR spectra. A good agreement with predicted PRE values, derived by computational modeling of nitroxide and Gd3+ tags in the low-resolution DnaB crystal structure, was found. Comparison of experimental PREs and model-predicted spin label-nucleus distances indicated that the size of the "blind sphere" around the paramagnetic center, in which NMR resonances are not detected, is slightly larger for Gd3+ (∼14 Å) than for nitroxide (∼11 Å) in 13C-detected 2D spectra of DnaB. We also present Gd3+-Gd3+ dipolar electron-electron resonance EPR experiments on DnaB supporting the conclusion that DnaB was present as a hexameric assembly.
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Affiliation(s)
| | | | - Maxim Yulikov
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Georg Künze
- Institute for Drug Discovery, Medical School, Leipzig University, 04103 Leipzig, Germany.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland; Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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47
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Bohg C, Öster C, Utesch T, Bischoff S, Lange S, Shi C, Sun H, Lange A. A combination of solid-state NMR and MD simulations reveals the binding mode of a rhomboid protease inhibitor. Chem Sci 2021; 12:12754-12762. [PMID: 34703562 PMCID: PMC8494044 DOI: 10.1039/d1sc02146j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022] Open
Abstract
Intramembrane proteolysis plays a fundamental role in many biological and pathological processes. Intramembrane proteases thus represent promising pharmacological targets, but few selective inhibitors have been identified. This is in contrast to their soluble counterparts, which are inhibited by many common drugs, and is in part explained by the inherent difficulty to characterize the binding of drug-like molecules to membrane proteins at atomic resolution. Here, we investigated the binding of two different inhibitors to the bacterial rhomboid protease GlpG, an intramembrane protease characterized by a Ser–His catalytic dyad, using solid-state NMR spectroscopy. H/D exchange of deuterated GlpG can reveal the binding position while chemical shift perturbations additionally indicate the allosteric effects of ligand binding. Finally, we determined the exact binding mode of a rhomboid protease-inhibitor using a combination of solid-state NMR and molecular dynamics simulations. We believe this approach can be widely adopted to study the structure and binding of other poorly characterized membrane protein–ligand complexes in a native-like environment and under physiological conditions. Proton-detected solid-state NMR in combination with molecular docking and molecular dynamics (MD) simulations allow the study of rhomboid protease inhibition under native-like conditions.![]()
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Affiliation(s)
- Claudia Bohg
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Tillmann Utesch
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Susanne Bischoff
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany .,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China Huangshan Road 443 Hefei 230027 People's Republic of China
| | - Han Sun
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Straße 10 13125 Berlin Germany .,Institut für Biologie, Humboldt-Universität zu Berlin Invalidenstraße 42 10115 Berlin Germany
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48
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Malär AA, Wili N, Völker LA, Kozlova MI, Cadalbert R, Däpp A, Weber ME, Zehnder J, Jeschke G, Eckert H, Böckmann A, Klose D, Mulkidjanian AY, Meier BH, Wiegand T. Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase. Nat Commun 2021; 12:5293. [PMID: 34489448 PMCID: PMC8421360 DOI: 10.1038/s41467-021-25599-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.
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Affiliation(s)
| | - Nino Wili
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | | | - Maria I Kozlova
- Department of Physics, Osnabrück University, Osnabrück, Germany
| | | | | | | | | | | | - Hellmut Eckert
- Institut für Physikalische Chemie, WWU Münster, Münster, Germany
- Instituto de Física de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, SP, Brazil
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Daniel Klose
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Armen Y Mulkidjanian
- Department of Physics, Osnabrück University, Osnabrück, Germany.
- School of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany.
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen, Aachen, Germany.
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49
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Dong XQ, Lin JY, Wang PF, Li Y, Wang J, Li B, Liao J, Lu JX. Solid-State NMR Studies of the Succinate-Acetate Permease from Citrobacter Koseri in Liposomes and Native Nanodiscs. Life (Basel) 2021; 11:life11090908. [PMID: 34575058 PMCID: PMC8471396 DOI: 10.3390/life11090908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022] Open
Abstract
The succinate-acetate permease (SatP) is an anion channel with six transmembrane domains. It forms different oligomers, especially hexamers in the detergent as well as in the membrane. Solid-state NMR studies of SatP were carried out successfully on SatP complexes by reconstructing the protein into liposomes or retaining the protein in the native membrane of E. coli., where it was expressed. The comparison of 13C-13C 2D correlation spectra between the two samples showed great similarity, opening the possibility to further study the acetate transport mechanism of SatP in its native membrane environment. Solid-state NMR studies also revealed small chemical shift differences of SatP in the two different membrane systems, indicating the importance of the lipid environment in determining the membrane protein structures and dynamics. Combining different 2D SSNMR spectra, chemical shift assignments were made on some sites, consistent with the helical structures in the transmembrane domains. In the end, we pointed out the limitation in the sensitivity for membrane proteins with such a size, and also indicated possible ways to overcome it.
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Affiliation(s)
- Xing-Qi Dong
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing-Yu Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Fei Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
| | - Bing Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
| | - Jun Liao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
| | - Jun-Xia Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; (X.-Q.D.); (J.-Y.L.); (P.-F.W.); (Y.L.); (J.W.); (B.L.); (J.L.)
- Correspondence:
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50
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Sutherland M, Kwon B, Hong M. Interactions of HIV gp41's membrane-proximal external region and transmembrane domain with phospholipid membranes from 31P NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183723. [PMID: 34352242 DOI: 10.1016/j.bbamem.2021.183723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/30/2021] [Indexed: 11/30/2022]
Abstract
HIV-1 entry into cells requires coordinated changes of the conformation and dynamics of both the fusion protein, gp41, and the lipids in the cell membrane and virus envelope. Commonly proposed features of membrane deformation during fusion include high membrane curvature, lipid disorder, and membrane surface dehydration. The virus envelope and target cell membrane contain a diverse set of phospholipids and cholesterol. To dissect how different lipids interact with gp41 to contribute to membrane fusion, here we use 31P solid-state NMR spectroscopy to investigate the curvature, dynamics, and hydration of POPE, POPC and POPS membranes, with and without cholesterol, in the presence of a peptide comprising the membrane proximal external region (MPER) and transmembrane domain (TMD) of gp41. Static 31P NMR spectra indicate that the MPER-TMD induces strong negative Gaussian curvature (NGC) to the POPE membrane but little curvature to POPC and POPC:POPS membranes. The NGC manifests as an isotropic peak in the static NMR spectra, whose intensity increases with the peptide concentration. Cholesterol inhibits the NGC formation and stabilizes the lamellar phase. Relative intensities of magic-angle spinning 31P cross-polarization and direct-polarization spectra indicate that all three phospholipids become more mobile upon peptide binding. Finally, 2D 1H-31P correlation spectra show that the MPER-TMD enhances water 1H polarization transfer to the lipids, indicating that the membrane surfaces become more hydrated. These results suggest that POPE is an essential component of the high-curvature fusion site, and lipid dynamic disorder is a general feature of membrane restructuring during fusion.
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Affiliation(s)
- Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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