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Zong X, Liu P, Wang Z, Zhu H, Zhong C, Zhong P, Jiang H, Liu J, Ma Z, Liu X, Liu R, Ding Y. Structural insights into the binding of nanobodies to the Staphylococcal enterotoxin B. Int J Biol Macromol 2024; 276:133957. [PMID: 39029852 DOI: 10.1016/j.ijbiomac.2024.133957] [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: 04/16/2024] [Revised: 05/21/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
Staphylococcal Enterotoxin Type B (SEB), produced by Staphylococcus aureus bacteria, is notorious for inducing severe food poisoning and toxic shock syndrome. While nanobody-based treatments hold promises for combating SEB-induced diseases, the lack of structural information between SEB and nanobodies has hindered the development of nanobody-based therapeutics. Here, we present crystal structures of SEB-Nb3, SEB-Nb6, SEB-Nb8, SEB-Nb11, and SEB-Nb20 at resolutions ranging from 1.59 Å to 2.33 Å. Crystallographic analysis revealed that Nb3, Nb8, Nb11, and Nb20 bind to SEB at the T-cell receptor (TCR) interface, while Nb6 binds at the major histocompatibility complex (MHC) interface, suggesting their potential to inhibit SEB function by disrupting interactions with TCR or MHC molecules. Molecular biological analyses confirmed the thermodynamic and kinetic parameters of Nb3, Nb5, Nb6, Nb8, Nb11, Nb15, Nb18, and Nb20 to SEB. The competitive inhibition was further confirmed by cell-based experiments demonstrating nanobody neutralization. These findings elucidate the structural basis for developing specific nanobodies to neutralize SEB threats, providing crucial insights into the underlying mechanisms and offering significant assistance for further optimization towards future therapeutic strategies.
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Affiliation(s)
- Xin Zong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peng Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ziying Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Haoran Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chao Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peiyu Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jiayuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zhiqiang Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xihuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Rui Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; Quzhou Fudan Institute, Quzhou, Zhejiang 324002, China.
| | - Yu Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; Quzhou Fudan Institute, Quzhou, Zhejiang 324002, China.
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2
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Kermani AA. Applications of fluorescent protein tagging in structural studies of membrane proteins. FEBS J 2024; 291:2719-2732. [PMID: 37470714 DOI: 10.1111/febs.16910] [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: 02/23/2023] [Revised: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Generating active, pure, and monodisperse protein remains a major bottleneck for structural studies using X-ray crystallography and cryo-electron microscopy (cryo-EM). The current methodology heavily relies on overexpressing the recombinant protein fused with a histidine tag in conventional expression systems and evaluating the quality and stability of purified protein using size exclusion chromatography (SEC). This requires a large amount of protein and can be highly laborious and time consuming. Therefore, this approach is not suitable for high-throughput screening and low-expressing macromolecules, particularly eukaryotic membrane proteins. Using fluorescent proteins fused to the target protein (applicable to both soluble and membrane proteins) enables rapid and efficient screening of expression level and monodispersity of tens of unpurified constructs using fluorescence-based size exclusion chromatography (FSEC). Moreover, FSEC proves valuable for screening multiple detergents to identify the most stabilizing agent in the case of membrane proteins. Additionally, FSEC can facilitate nanodisc reconstitution by determining the optimal ratio of membrane scaffold protein (MSP), lipids, and target protein. The distinct advantages offered by FSEC indicate that fluorescent proteins can serve as a viable alternative to commonly used affinity tags for both characterization and purification purposes. In this review, I will summarize the advantages of this technique using examples from my own work. It should be noted that this article is not intended to provide an exhaustive review of all available literature, but rather to offer representative examples of FSEC applications.
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Affiliation(s)
- Ali A Kermani
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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3
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Kaneko H, Korenaga R, Nakamura R, Kawai S, Ando T, Shiroishi M. Binding characteristics of the doxepin E/Z-isomers to the histamine H 1 receptor revealed by receptor-bound ligand analysis and molecular dynamics study. J Mol Recognit 2024:e3098. [PMID: 38924170 DOI: 10.1002/jmr.3098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/14/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Doxepin is an antihistamine and tricyclic antidepressant that binds to the histamine H1 receptor (H1R) with high affinity. Doxepin is an 85:15 mixture of the E- and Z-isomers. The Z-isomer is well known to be more effective than the E-isomer, whereas based on the crystal structure of the H1R/doxepin complex, the hydroxyl group of Thr1123.37 is close enough to form a hydrogen bond with the oxygen atom of the E-isomer. The detailed binding characteristics and reasons for the differences remain unclear. In this study, we analyzed doxepin isomers bound to the receptor following extraction from a purified H1R protein complexed with doxepin. The ratio of the E- and Z-isomers bound to wild-type (WT) H1R was 55:45, indicating that the Z-isomer was bound to WT H1R with an approximately 5.2-fold higher affinity than the E-isomer. For the T1123.37V mutant, the E/Z ratio was 89:11, indicating that both isomers have similar affinities. Free energy calculations using molecular dynamics (MD) simulations also reproduced the experimental results of the relative binding free energy differences between the isomers for WT and T1123.37V. Furthermore, MD simulations revealed that the hydroxyl group of T1123.37 did not form hydrogen bonds with the E-isomer, but with the adjacent residues in the binding pocket. Analysis of the receptor-bound doxepin and MD simulations suggested that the hydroxyl group of T1123.37 contributes to the formation of a chemical environment in the binding pocket, which is slightly more favorable for the Z-isomer without hydrogen bonding with doxepin.
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Affiliation(s)
- Hiroto Kaneko
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Ryunosuke Korenaga
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Ryota Nakamura
- Department of Applied Electronics, Tokyo University of Science, Tokyo, Japan
| | - Shinnosuke Kawai
- Department of Applied Electronics, Tokyo University of Science, Tokyo, Japan
| | - Tadashi Ando
- Department of Applied Electronics, Tokyo University of Science, Tokyo, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Mitsunori Shiroishi
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
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4
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Nemecz D, Nowak WA, Nemecz Á. VHH Nanobody Versatility against Pentameric Ligand-Gated Ion Channels. J Med Chem 2024; 67:8502-8518. [PMID: 38829690 PMCID: PMC11181324 DOI: 10.1021/acs.jmedchem.4c00231] [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: 01/26/2024] [Revised: 04/17/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
Pentameric ligand-gated ion channels provide rapid chemical-electrical signal transmission between cells in the central and peripheral nervous system. Their dysfunction is associated with many nervous system disorders. They are composed of five identical (homomeric receptors) or homologous (heteromeric receptors) subunits. VHH nanobodies, or single-chain antibodies, are the variable domain, VHH, of antibodies that are composed of the heavy chain only from camelids. Their unique structure results in many specific biochemical and biophysical properties that make them an excellent alternative to conventional antibodies. This Perspective explores the published VHH nanobodies which have been isolated against pentameric ligand-gated ion channel subfamilies. It outlines the genetic and chemical modifications available to alter nanobody function. An assessment of the available functional and structural data indicate that it is feasible to create therapeutic agents and impart, through their modification, a given desired modulatory effect of its target receptor for current stoichiometric-specific VHH nanobodies.
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Affiliation(s)
- Dorota Nemecz
- Biochemistry
Department, Nicolaus Copernicus University
in Torun, 87-100 Torun, Poland
| | - Weronika A. Nowak
- Biochemistry
Department, Nicolaus Copernicus University
in Torun, 87-100 Torun, Poland
| | - Ákos Nemecz
- Biochemistry
Department, Nicolaus Copernicus University
in Torun, 87-100 Torun, Poland
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5
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Egorkin NA, Dominnik EE, Maksimov EG, Sluchanko NN. Insights into the molecular mechanism of yellow cuticle coloration by a chitin-binding carotenoprotein in gregarious locusts. Commun Biol 2024; 7:448. [PMID: 38605243 PMCID: PMC11009388 DOI: 10.1038/s42003-024-06149-x] [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: 12/21/2023] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Carotenoids are hydrophobic pigments binding to diverse carotenoproteins, many of which remain unexplored. Focusing on yellow gregarious locusts accumulating cuticular carotenoids, here we use engineered Escherichia coli cells to reconstitute a functional water-soluble β-carotene-binding protein, BBP. HPLC and Raman spectroscopy confirmed that recombinant BBP avidly binds β-carotene, inducing the unusual vibronic structure of its absorbance spectrum, just like native BBP extracted from the locust cuticles. Bound to recombinant BBP, β-carotene exhibits pronounced circular dichroism and allows BBP to withstand heating (T0.5 = 68 °C), detergents and pH variations. Using bacteria producing distinct xanthophylls we demonstrate that, while β-carotene is the preferred carotenoid, BBP can also extract from membranes ketocarotenoids and, very poorly, hydroxycarotenoids. We show that BBP-carotenoid complex reversibly binds to chitin, but not to chitosan, implying the role for chitin acetyl groups in cuticular BBP deposition. Reconstructing such locust coloration mechanism in vitro paves the way for structural studies and BBP applications.
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Affiliation(s)
- Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Eva E Dominnik
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- M.V. Lomonosov Moscow State University, Faculty of Chemistry, Moscow, Russia
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
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6
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Kunii K, Yamanaka T, Miyamoto A, Nanatani K, Abe K. Thermostability optimization of the aspartate/alanine exchange transporter from Tetragenococcus halophilus. J Biochem 2024; 175:439-446. [PMID: 38616642 DOI: 10.1093/jb/mvad104] [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: 08/15/2023] [Accepted: 11/20/2023] [Indexed: 12/29/2023] Open
Abstract
Aspartate/alanine exchange transporter (AspT) is a secondary transporter isolated from the lactic acid bacterium Tetragenococcus halophilus D10 strain. This transporter cooperates with aspartate decarboxylase to produce proton-motive force through decarboxylative phosphorylation. A method that successfully analyzes the AspT mechanism could serve as a prototype for elucidating the substrate transport mechanism of other exchange transporters; therefore, the purpose of this study was to search for conditions that improve the thermal stability of AspT for 3D structure analysis. We used the fluorescence size-exclusion chromatography-based thermostability assay to evaluate conditions that contribute to AspT stability. We found that the AspT thermostability was enhanced at pH 5.0 to 6.0 and in the presence of Na+ and Li+. Pyridoxal phosphate, a coenzyme of aspartate decarboxylase, also had a thermostabilizing effect on AspT. Under the conditions obtained from these results, it was possible to increase the temperature at which 50% of dimer AspT remained by 14°C. We expect these conditions to provide useful information for future structural analysis of AspT.
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Affiliation(s)
- Kota Kunii
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Takashi Yamanaka
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Akari Miyamoto
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Kei Nanatani
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
- Structural Biology Group, Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Keietsu Abe
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
- Microbial Genomics Laboratory, New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 6-6-10, Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
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7
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Abstract
The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson's disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2's importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here, we report a 3.1 Å resolution cryo-electron microscopy (cryo-EM) structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington's chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics.
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Affiliation(s)
- Michael P Dalton
- Department of Structural Biology, University of PittsburghPittsburghUnited States
| | - Mary Hongying Cheng
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook UniversityStony BrookUnited States
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook UniversityStony BrookUnited States
| | - Jonathan A Coleman
- Department of Structural Biology, University of PittsburghPittsburghUnited States
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8
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Sinclair M, Stein RA, Sheehan JH, Hawes EM, O’Brien RM, Tajkhorshid E, Claxton DP. Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model. PNAS NEXUS 2024; 3:pgae036. [PMID: 38328777 PMCID: PMC10849595 DOI: 10.1093/pnasnexus/pgae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
Mediating the terminal reaction of gluconeogenesis and glycogenolysis, the integral membrane protein glucose-6-phosphate catalytic subunit 1 (G6PC1) regulates hepatic glucose production by catalyzing hydrolysis of glucose-6-phosphate (G6P) within the lumen of the endoplasmic reticulum. Consistent with its vital contribution to glucose homeostasis, inactivating mutations in G6PC1 causes glycogen storage disease (GSD) type 1a characterized by hepatomegaly and severe hypoglycemia. Despite its physiological importance, the structural basis of G6P binding to G6PC1 and the molecular disruptions induced by missense mutations within the active site that give rise to GSD type 1a are unknown. In this study, we determine the atomic interactions governing G6P binding as well as explore the perturbations imposed by disease-linked missense variants by subjecting an AlphaFold2 G6PC1 structural model to molecular dynamics simulations and in silico predictions of thermodynamic stability validated with robust in vitro and in situ biochemical assays. We identify a collection of side chains, including conserved residues from the signature phosphatidic acid phosphatase motif, that contribute to a hydrogen bonding and van der Waals network stabilizing G6P in the active site. The introduction of GSD type 1a mutations modified the thermodynamic landscape, altered side chain packing and substrate-binding interactions, and induced trapping of catalytic intermediates. Our results, which corroborate the high quality of the AF2 model as a guide for experimental design and to interpret outcomes, not only confirm the active-site structural organization but also identify previously unobserved mechanistic contributions of catalytic and noncatalytic side chains.
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Affiliation(s)
- Matt Sinclair
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
- Center for Applied Artificial Intelligence in Protein Dynamics, Vanderbilt University, Nashville, TN 37240, USA
| | - Jonathan H Sheehan
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Emily M Hawes
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Richard M O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
- Center for Applied Artificial Intelligence in Protein Dynamics, Vanderbilt University, Nashville, TN 37240, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
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9
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Dalton MP, Cheng MH, Bahar I, Coleman JA. Structural mechanisms for VMAT2 inhibition by tetrabenazine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.05.556211. [PMID: 37732203 PMCID: PMC10508774 DOI: 10.1101/2023.09.05.556211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson's disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2's importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here we report a 3.1 Å resolution cryo-EM structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington's chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics.
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Affiliation(s)
- Michael P Dalton
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Mary Hongying Cheng
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jonathan A Coleman
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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10
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Hoare BL, Tippett DN, Kaur A, Cullum SA, Miljuš T, Koers EJ, Harwood CR, Dijon N, Holliday ND, Sykes DA, Veprintsev DB. ThermoBRET: A Ligand-Engagement Nanoscale Thermostability Assay Applied to GPCRs. Chembiochem 2024; 25:e202300459. [PMID: 37872746 DOI: 10.1002/cbic.202300459] [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: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Measurements of membrane protein thermostability reflect ligand binding. Current thermostability assays often require protein purification or rely on pre-existing radiolabelled or fluorescent ligands, limiting their application to established targets. Alternative methods, such as fluorescence-detection size exclusion chromatography thermal shift, detect protein aggregation but are not amenable to high-throughput screening. Here, we present a ThermoBRET method to quantify the relative thermostability of G protein coupled receptors (GPCRs), using cannabinoid receptors (CB1 and CB2 ) and the β2 -adrenoceptor (β2 AR) as model systems. ThermoBRET reports receptor unfolding, does not need labelled ligands and can be used with non-purified proteins. It uses Bioluminescence Resonance Energy Transfer (BRET) between Nanoluciferase (Nluc) and a thiol-reactive fluorescent dye that binds cysteines exposed by unfolding. We demonstrate that the melting point (Tm ) of Nluc-fused GPCRs can be determined in non-purified detergent solubilised membrane preparations or solubilised whole cells, revealing differences in thermostability for different solubilising conditions and in the presence of stabilising ligands. We extended the range of the assay by developing the thermostable tsNLuc by incorporating mutations from the fragments of split-Nluc (Tm of 87 °C versus 59 °C). ThermoBRET allows the determination of GPCR thermostability, which is useful for protein purification optimisation and drug discovery screening.
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Affiliation(s)
- Bradley L Hoare
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - David N Tippett
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Amandeep Kaur
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Sean A Cullum
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Tamara Miljuš
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Eline J Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicola Dijon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicholas D Holliday
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
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11
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Hiraizumi M, Akashi T, Murasaki K, Kishida H, Kumanomidou T, Torimoto N, Nureki O, Miyaguchi I. Transport and inhibition mechanism of the human SGLT2-MAP17 glucose transporter. Nat Struct Mol Biol 2024; 31:159-169. [PMID: 38057552 PMCID: PMC10803289 DOI: 10.1038/s41594-023-01134-0] [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: 01/10/2023] [Accepted: 09/22/2023] [Indexed: 12/08/2023]
Abstract
Sodium-glucose cotransporter 2 (SGLT2) is imporant in glucose reabsorption. SGLT2 inhibitors suppress renal glucose reabsorption, therefore reducing blood glucose levels in patients with type 2 diabetes. We and others have developed several SGLT2 inhibitors starting from phlorizin, a natural product. Using cryo-electron microscopy, we present the structures of human (h)SGLT2-MAP17 complexed with five natural or synthetic inhibitors. The four synthetic inhibitors (including canagliflozin) bind the transporter in the outward conformations, while phlorizin binds it in the inward conformation. The phlorizin-hSGLT2 interaction exhibits biphasic kinetics, suggesting that phlorizin alternately binds to the extracellular and intracellular sides. The Na+-bound outward-facing and unbound inward-open structures of hSGLT2-MAP17 suggest that the MAP17-associated bundle domain functions as a scaffold, with the hash domain rotating around the Na+-binding site. Thus, Na+ binding stabilizes the outward-facing conformation, and its release promotes state transition to inward-open conformation, exhibiting a role of Na+ in symport mechanism. These results provide structural evidence for the Na+-coupled alternating-access mechanism proposed for the transporter family.
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Affiliation(s)
- Masahiro Hiraizumi
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan.
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Tomoya Akashi
- DMPK Research Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Kouta Murasaki
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Hiroyuki Kishida
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Taichi Kumanomidou
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Nao Torimoto
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Ikuko Miyaguchi
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan.
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12
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Dey D, Hasan SS. Strategies for rapid production of crystallization quality coatomer WD40 domains. Protein Expr Purif 2023; 212:106358. [PMID: 37625737 PMCID: PMC10529451 DOI: 10.1016/j.pep.2023.106358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
The vesicular secretion of soluble cargo proteins from the endoplasmic reticulum (ER) is accompanied by the export of ER-resident membrane proteins that are co-packaged in secretory vesicles. The cytosolic coatomer protein complex I (COPI) utilizes the N-terminal WD40 domains of α-COPI and β'-COPI subunits to bind these membrane protein "clients" for ER retrieval. These "αWD40" and "β'WD40" domains are structural homologs that demonstrate distinct selectivity for client proteins. However, elucidation of the atomic-level principles of coatomer-client interactions has been challenging due to the tendency of αWD40 domain to undergo aggregation during expression and purification. Here we describe a rapid recombinant production strategy from E. coli, which substantially enhances the quality of the purified αWD40 domain. The αWD40 purification and crystallization are completed within one day, which minimizes aggregation losses and yields a 1.9 Å resolution crystal structure. We demonstrate the versatility of this strategy by applying it to purify the β'WD40 domain, which yields crystal structures in the 1.2-1.3 Å resolution range. As an alternate recombinant production system, we develop a cost-effective strategy for αWD40 production in human Expi293 cells. Finally, we suggest a roadmap to simplify these protocols further, which is of significance for the production of WD40 mutants prone to rapid aggregation. The WD40 production strategies presented here are likely to have broad applications because the WD40 domain represents one of the largest families of biomolecular interaction modules in the eukaryotic proteome and is critical for trafficking of host as well as viral proteins such as the SARS-CoV-2 spike protein.
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Affiliation(s)
- Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - S Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD, 21201, USA; Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Rockville, MD, 20850, USA.
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13
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Yeo H, Mehta V, Gulati A, Drew D. Structure and electromechanical coupling of a voltage-gated Na +/H + exchanger. Nature 2023; 623:193-201. [PMID: 37880360 PMCID: PMC10620092 DOI: 10.1038/s41586-023-06518-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/04/2023] [Indexed: 10/27/2023]
Abstract
Voltage-sensing domains control the activation of voltage-gated ion channels, with a few exceptions1. One such exception is the sperm-specific Na+/H+ exchanger SLC9C1, which is the only known transporter to be regulated by voltage-sensing domains2-5. After hyperpolarization of sperm flagella, SLC9C1 becomes active, causing pH alkalinization and CatSper Ca2+ channel activation, which drives chemotaxis2,6. SLC9C1 activation is further regulated by cAMP2,7, which is produced by soluble adenyl cyclase (sAC). SLC9C1 is therefore an essential component of the pH-sAC-cAMP signalling pathway in metazoa8,9, required for sperm motility and fertilization4. Despite its importance, the molecular basis of SLC9C1 voltage activation is unclear. Here we report cryo-electron microscopy (cryo-EM) structures of sea urchin SLC9C1 in detergent and nanodiscs. We show that the voltage-sensing domains are positioned in an unusual configuration, sandwiching each side of the SLC9C1 homodimer. The S4 segment is very long, 90 Å in length, and connects the voltage-sensing domains to the cytoplasmic cyclic-nucleotide-binding domains. The S4 segment is in the up configuration-the inactive state of SLC9C1. Consistently, although a negatively charged cavity is accessible for Na+ to bind to the ion-transporting domains of SLC9C1, an intracellular helix connected to S4 restricts their movement. On the basis of the differences in the cryo-EM structure of SLC9C1 in the presence of cAMP, we propose that, upon hyperpolarization, the S4 segment moves down, removing this constriction and enabling Na+/H+ exchange.
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Affiliation(s)
- Hyunku Yeo
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ved Mehta
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ashutosh Gulati
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
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14
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Chowdhury S, Pal K. Architecture and rearrangements of a sperm-specific Na +/H + exchanger. RESEARCH SQUARE 2023:rs.3.rs-3396005. [PMID: 37886505 PMCID: PMC10602139 DOI: 10.21203/rs.3.rs-3396005/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The sperm-specific sodium hydrogen exchanger, SLC9C1, underlies hyperpolarization and cyclic nucleotide stimulated proton fluxes across sperm membranes and regulates their hyperactivated motility. SLC9C1 is the first known instance of an ion transporter that uses a canonical voltage-sensing domain (VSD) and an evolutionarily conserved cyclic nucleotide binding domain (CNBD) to influence the dynamics of its ion-exchange domain (ED). The structural organization of this 'tripartite transporter' and the mechanisms whereby it integrates physical (membrane voltage) and chemical (cyclic nucleotide) cues are unknown. In this study, we use single particle cryo-electron microscopy to determine structures of a metazoan SLC9C1 in different conformational states. We find that the three structural domains are uniquely organized around a distinct ring-shaped scaffold that we call the 'allosteric ring domain' or ARD. The ARD undergoes coupled proton-dependent rearrangements with the ED and acts as a 'signaling hub' enabling allosteric communication between the key functional modules of sp9C1. We demonstrate that binding of cAMP causes large conformational changes in the cytoplasmic domains and disrupts key ARD-linked interfaces. We propose that these structural changes rescue the transmembrane domains from an auto-inhibited state and facilitate their functional dynamics. Our study provides a structural framework to understand and further probe electrochemical linkage in SLC9C1.
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15
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Tajima S, Kim YS, Fukuda M, Jo Y, Wang PY, Paggi JM, Inoue M, Byrne EFX, Kishi KE, Nakamura S, Ramakrishnan C, Takaramoto S, Nagata T, Konno M, Sugiura M, Katayama K, Matsui TE, Yamashita K, Kim S, Ikeda H, Kim J, Kandori H, Dror RO, Inoue K, Deisseroth K, Kato HE. Structural basis for ion selectivity in potassium-selective channelrhodopsins. Cell 2023; 186:4325-4344.e26. [PMID: 37652010 PMCID: PMC7615185 DOI: 10.1016/j.cell.2023.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/11/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
KCR channelrhodopsins (K+-selective light-gated ion channels) have received attention as potential inhibitory optogenetic tools but more broadly pose a fundamental mystery regarding how their K+ selectivity is achieved. Here, we present 2.5-2.7 Å cryo-electron microscopy structures of HcKCR1 and HcKCR2 and of a structure-guided mutant with enhanced K+ selectivity. Structural, electrophysiological, computational, spectroscopic, and biochemical analyses reveal a distinctive mechanism for K+ selectivity; rather than forming the symmetrical filter of canonical K+ channels achieving both selectivity and dehydration, instead, three extracellular-vestibule residues within each monomer form a flexible asymmetric selectivity gate, while a distinct dehydration pathway extends intracellularly. Structural comparisons reveal a retinal-binding pocket that induces retinal rotation (accounting for HcKCR1/HcKCR2 spectral differences), and design of corresponding KCR variants with increased K+ selectivity (KALI-1/KALI-2) provides key advantages for optogenetic inhibition in vitro and in vivo. Thus, discovery of a mechanism for ion-channel K+ selectivity also provides a framework for next-generation optogenetics.
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Affiliation(s)
- Seiya Tajima
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Masahiro Fukuda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - YoungJu Jo
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Peter Y Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Eamon F X Byrne
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Koichiro E Kishi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Seiwa Nakamura
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | | | - Shunki Takaramoto
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Toshiki E Matsui
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Suhyang Kim
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Hisako Ikeda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Jaeah Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; CNC Program, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
| | - Hideaki E Kato
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
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16
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Sinclair M, Stein RA, Sheehan JH, Hawes EM, O'Brien RM, Tajkhorshid E, Claxton DP. Molecular mechanisms of catalytic inhibition for active site mutations in glucose-6-phosphatase catalytic subunit 1 linked to glycogen storage disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532485. [PMID: 36993754 PMCID: PMC10054992 DOI: 10.1101/2023.03.13.532485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Mediating the terminal reaction of gluconeogenesis and glycogenolysis, the integral membrane protein G6PC1 regulates hepatic glucose production by catalyzing hydrolysis of glucose-6-phosphate (G6P) within the lumen of the endoplasmic reticulum. Consistent with its vital contribution to glucose homeostasis, inactivating mutations in G6PC1 cause glycogen storage disease (GSD) type 1a characterized by hepatomegaly and severe hypoglycemia. Despite its physiological importance, the structural basis of G6P binding to G6PC1 and the molecular disruptions induced by missense mutations within the active site that give rise to GSD type 1a are unknown. Exploiting a computational model of G6PC1 derived from the groundbreaking structure prediction algorithm AlphaFold2 (AF2), we combine molecular dynamics (MD) simulations and computational predictions of thermodynamic stability with a robust in vitro screening platform to define the atomic interactions governing G6P binding as well as explore the energetic perturbations imposed by disease-linked variants. We identify a collection of side chains, including conserved residues from the signature phosphatidic acid phosphatase motif, that contribute to a hydrogen bonding and van der Waals network stabilizing G6P in the active site. Introduction of GSD type 1a mutations into the G6PC1 sequence elicits changes in G6P binding energy, thermostability and structural properties, suggesting multiple pathways of catalytic impairment. Our results, which corroborate the high quality of the AF2 model as a guide for experimental design and to interpret outcomes, not only confirm active site structural organization but also suggest novel mechanistic contributions of catalytic and non-catalytic side chains.
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17
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Rump A, Ratas K, Lepasepp TK, Suurväli J, Smolander OP, Gross-Paju K, Toomsoo T, Kanellopoulos J, Rüütel Boudinot S. Sex-dependent expression levels of VAV1 and P2X7 in PBMC of multiple sclerosis patients. Scand J Immunol 2023; 98:e13283. [PMID: 38441379 DOI: 10.1111/sji.13283] [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: 10/15/2022] [Revised: 01/21/2023] [Accepted: 05/01/2023] [Indexed: 03/07/2024]
Abstract
Multiple sclerosis (MS) is an inflammatory autoimmune disorder of the central nervous system and the leading cause of progressive neurological disability in young adults. It decreases the patient's lifespan by about 10 years and affects women more than men. No medication entirely restricts or reverses neurological degradation. However, early diagnosis and treatment increase the possibility of a better outcome. To identify new MS biomarkers, we tested the expression of six potential markers (P2X4, P2X7, CXCR4, RGS1, RGS16 and VAV1) using qPCR in peripheral blood mononuclear cells (PBMC) of MS patients treated with interferon β (IFNβ), with glatiramer acetate (GA) or untreated. We showed that P2X7 and VAV1 are significantly induced in MS patients. In contrast, the expression of P2X4, CXCR4, RGS1 and RGS16 was not significantly modified by MS in PBMC. P2X7 and VAV1 are essentially induced in female patients, suggesting these markers are connected to sex-specific mechanisms. Strikingly, VAV1 expression is higher in healthy women than healthy men and IFNβ treatment of MS reduced VAV1 expression in female MS patients while it up-regulated VAV1 in male MS patients. Our data point to the differential, sex-dependent value of MS markers and treatment effects. Although rgs16 expression in PBMC was not a valid MS marker in patients, the strong upregulation of P2X4 and P2X7 induced in the spinal cord of WT mice by EAE was abrogated in rgs16KO mice suggesting that rgs16 is required for P2X4 and P2X7 induction by neurological diseases.
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Affiliation(s)
- Airi Rump
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kristel Ratas
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- Synlab, Tallinn, Estonia
| | - Tuuli Katarina Lepasepp
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Jaanus Suurväli
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Olli-Pekka Smolander
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Katrin Gross-Paju
- Department of Health Technologies, School of Information Technologies, Tallinn University of Technology, Tallinn, Estonia
- West-Tallinn Central Hospital, Tallinn, Estonia
| | - Toomas Toomsoo
- School of Natural Sciences and Health, Tallinn University, Tallinn, Estonia
- Confido Medical Center, Tallinn, Estonia
| | - Jean Kanellopoulos
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, France
| | - Sirje Rüütel Boudinot
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
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18
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Ma C, Gong C. Considerations in production of the prokaryotic ZIP family transporters for structural and functional studies. Methods Enzymol 2023; 687:1-30. [PMID: 37666628 DOI: 10.1016/bs.mie.2023.04.018] [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: 09/06/2023]
Abstract
Zinc ions play essential roles as components of enzymes and many other important biomolecules, and are associated with numerous diseases. The uptake of Zn2+ and other metal ions require a widely distributed transporter protein family called Zrt/Irt-like Proteins (ZIP family), the majority members of which tend to have eight transmembrane helices with both N- and C- termini located on the extracellular or periplasmic side. Their small sizes and dynamic conformations bring many difficulties in their production for structural studies either by crystallography or Cryo-EM. Here, we summarize the problems that may encounter at the various steps of processing the ZIP proteins from gene to structural and functional studies, and provide some solutions and examples from our and other labs for the cloning, expression, purification, stability screening, metal ion transport assays and structural studies of prokaryotic ZIP family transporters using Escherichia coli as a heterologous host.
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Affiliation(s)
- Cheng Ma
- Protein Facility, Zhejiang University School of Medicine, Hangzhou, P.R. China; The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, P.R. China.
| | - Caixia Gong
- The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, P.R. China; Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-chemical Injury Diseases, Hangzhou, P.R. China.
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19
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Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP. Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase. Nat Chem Biol 2023; 19:575-584. [PMID: 36604564 PMCID: PMC10154233 DOI: 10.1038/s41589-022-01219-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/28/2022] [Indexed: 01/07/2023]
Abstract
C-linked glycosylation is essential for the trafficking, folding and function of secretory and transmembrane proteins involved in cellular communication processes. The tryptophan C-mannosyltransferase (CMT) enzymes that install the modification attach a mannose to the first tryptophan of WxxW/C sequons in nascent polypeptide chains by an unknown mechanism. Here, we report cryogenic-electron microscopy structures of Caenorhabditis elegans CMT in four key states: apo, acceptor peptide-bound, donor-substrate analog-bound and as a trapped ternary complex with both peptide and a donor-substrate mimic bound. The structures indicate how the C-mannosylation sequon is recognized by this CMT and its paralogs, and how sequon binding triggers conformational activation of the donor substrate: a process relevant to all glycosyltransferase C superfamily enzymes. Our structural data further indicate that the CMTs adopt an unprecedented electrophilic aromatic substitution mechanism to enable the C-glycosylation of proteins. These results afford opportunities for understanding human disease and therapeutic targeting of specific CMT paralogs.
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Affiliation(s)
- Joël S Bloch
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
- Laboratory of Molecular Neurobiology and Biophysics and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Alan John
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Runyu Mao
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Jérémy Boilevin
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | | | - Tamis Darbre
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
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20
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Sano FK, Akasaka H, Shihoya W, Nureki O. Cryo-EM structure of the endothelin-1-ET B-G i complex. eLife 2023; 12:85821. [PMID: 37096326 PMCID: PMC10129325 DOI: 10.7554/elife.85821] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/23/2023] [Indexed: 04/26/2023] Open
Abstract
The endothelin ETB receptor is a promiscuous G-protein coupled receptor that is activated by vasoactive peptide endothelins. ETB signaling induces reactive astrocytes in the brain and vasorelaxation in vascular smooth muscle. Consequently, ETB agonists are expected to be drugs for neuroprotection and improved anti-tumor drug delivery. Here, we report the cryo-electron microscopy structure of the endothelin-1-ETB-Gi complex at 2.8 Å resolution, with complex assembly stabilized by a newly established method. Comparisons with the inactive ETB receptor structures revealed how endothelin-1 activates the ETB receptor. The NPxxY motif, essential for G-protein activation, is not conserved in ETB, resulting in a unique structural change upon G-protein activation. Compared with other GPCR-G-protein complexes, ETB binds Gi in the shallowest position, further expanding the diversity of G-protein binding modes. This structural information will facilitate the elucidation of G-protein activation and the rational design of ETB agonists.
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Affiliation(s)
- Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Akasaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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21
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Liang H, Ma Z, Wang Z, Zhong P, Li R, Jiang H, Zong X, Zhong C, Liu X, Liu P, Liu J, Zhu H, Liu R, Ding Y. Structural Insights into the Binding of Red Fluorescent Protein mCherry-Specific Nanobodies. Int J Mol Sci 2023; 24:ijms24086952. [PMID: 37108116 PMCID: PMC10138814 DOI: 10.3390/ijms24086952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Red fluorescent proteins (RFPs) have broad applications in life science research, and the manipulation of RFPs using nanobodies can expand their potential uses. However, the structural information available for nanobodies that bind with RFPs is still insufficient. In this study, we cloned, expressed, purified, and crystallized complexes formed by mCherry with LaM1, LaM3, and LaM8. Then, we analyzed the biochemical properties of the complexes using mass spectrometry (MS), fluorescence-detected size exclusion chromatography (FSEC), isothermal titration calorimetry (ITC), and bio-layer interferometry (BLI) technology. We determined the crystal structure of mCherry-LaM1, mCherry-LaM3, and mCherry-LaM8, with resolutions of 2.05 Å, 3.29 Å, and 1.31 Å, respectively. In this study, we systematically compared various parameters of several LaM series nanobodies, including LaM1, LaM3, and LaM8, with previously reported data on LaM2, LaM4, and LaM6, specifically examining their structural information. After designing multivalent tandem LaM1-LaM8 and LaM8-LaM4 nanobodies based on structural information, we characterized their properties, revealing their higher affinity and specificity to mCherry. Our research provides novel structural insights that could aid in understanding nanobodies targeting a specific target protein. This could provide a starting point for developing enhanced mCherry manipulation tools.
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Affiliation(s)
- Hui Liang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhiqiang Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ziying Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Peiyu Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ran Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin Zong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chao Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xihuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Peng Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiayuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haoran Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Rui Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
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22
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Lehmann EF, Liziczai M, Drożdżyk K, Altermatt P, Langini C, Manolova V, Sundstrom H, Dürrenberger F, Dutzler R, Manatschal C. Structures of ferroportin in complex with its specific inhibitor vamifeport. eLife 2023; 12:83053. [PMID: 36943194 PMCID: PMC10030120 DOI: 10.7554/elife.83053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
A central regulatory mechanism of iron homeostasis in humans involves ferroportin (FPN), the sole cellular iron exporter, and the peptide hormone hepcidin, which inhibits Fe2+ transport and induces internalization and degradation of FPN. Dysregulation of the FPN/hepcidin axis leads to diverse pathological conditions, and consequently, pharmacological compounds that inhibit FPN-mediated iron transport are of high clinical interest. Here, we describe the cryo-electron microscopy structures of human FPN in complex with synthetic nanobodies and vamifeport (VIT-2763), the first clinical-stage oral FPN inhibitor. Vamifeport competes with hepcidin for FPN binding and is currently in clinical development for β-thalassemia and sickle cell disease. The structures display two distinct conformations of FPN, representing outward-facing and occluded states of the transporter. The vamifeport site is located in the center of the protein, where the overlap with hepcidin interactions underlies the competitive relationship between the two molecules. The introduction of point mutations in the binding pocket of vamifeport reduces its affinity to FPN, emphasizing the relevance of the structural data. Together, our study reveals conformational rearrangements of FPN that are of potential relevance for transport, and it provides initial insight into the pharmacological targeting of this unique iron efflux transporter.
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Affiliation(s)
| | - Márton Liziczai
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | | | | | - Cassiano Langini
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | | | | | | | - Raimund Dutzler
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
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23
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Kozai D, Numoto N, Nishikawa K, Kamegawa A, Kawasaki S, Hiroaki Y, Irie K, Oshima A, Hanzawa H, Shimada K, Kitano Y, Fujiyoshi Y. Recognition mechanism of a novel gabapentinoid drug, mirogabalin, for recombinant human α 2δ1, a voltage-gated calcium channel subunit. J Mol Biol 2023; 435:168049. [PMID: 36933823 DOI: 10.1016/j.jmb.2023.168049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/22/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023]
Abstract
Mirogabalin is a novel gabapentinoid drug with a hydrophobic bicyclo substituent on the γ-aminobutyric acid moiety that targets the voltage-gated calcium channel subunit α2δ1. Here, to reveal the mirogabalin recognition mechanisms of α2δ1, we present structures of recombinant human α2δ1 with and without mirogabalin analyzed by cryo-electron microscopy. These structures show the binding of mirogabalin to the previously reported gabapentinoid binding site, which is the extracellular dCache_1 domain containing a conserved amino acid binding motif. A slight conformational change occurs around the residues positioned close to the hydrophobic group of mirogabalin. Mutagenesis binding assays identified that residues in the hydrophobic interaction region, in addition to several amino acid binding motif residues around the amino and carboxyl groups of mirogabalin, are critical for mirogabalin binding. The A215L mutation introduced to decrease the hydrophobic pocket volume predictably suppressed mirogabalin binding and promoted the binding of another ligand, L-Leu, with a smaller hydrophobic substituent than mirogabalin. Alterations of residues in the hydrophobic interaction region of α2δ1 to those of the α2δ2, α2δ3, and α2δ4 isoforms, of which α2δ3 and α2δ4 are gabapentin-insensitive, suppressed the binding of mirogabalin. These results support the importance of hydrophobic interactions in α2δ1 ligand recognition.
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Affiliation(s)
- Daisuke Kozai
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Japan Biological Informatics Consortium, 2-4-32 Aomi, Koto-ku, Tokyo 135-0063, Japan; Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8501, Japan.
| | - Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8501, Japan.
| | - Kouki Nishikawa
- CeSPIA Inc., 2-1-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan; Joint Research Course for Advanced Biomolecular Characterization, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
| | - Akiko Kamegawa
- Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8501, Japan; CeSPIA Inc., 2-1-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.
| | - Shohei Kawasaki
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan.
| | - Yoko Hiroaki
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Japan Biological Informatics Consortium, 2-4-32 Aomi, Koto-ku, Tokyo 135-0063, Japan.
| | - Katsumasa Irie
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan; Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Hiroyuki Hanzawa
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan.
| | - Kousei Shimada
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.
| | - Yutaka Kitano
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.
| | - Yoshinori Fujiyoshi
- Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8501, Japan; CeSPIA Inc., 2-1-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.
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24
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Plummer-Medeiros AM, Culbertson AT, Morales-Perez CL, Liao M. Activity and Structural Dynamics of Human ABCA1 in a Lipid Membrane. J Mol Biol 2023; 435:168038. [PMID: 36889459 DOI: 10.1016/j.jmb.2023.168038] [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: 01/19/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023]
Abstract
The human ATP-binding cassette (ABC) transporter ABCA1 plays a critical role in lipid homeostasis as it extracts sterols and phospholipids from the plasma membrane for excretion to the extracellular apolipoprotein A-I and subsequent formation of high-density lipoprotein (HDL) particles. Deleterious mutations of ABCA1 lead to sterol accumulation and are associated with atherosclerosis, poor cardiovascular outcomes, cancer, and Alzheimer's disease. The mechanism by which ABCA1 drives lipid movement is poorly understood, and a unified platform to produce active ABCA1 protein for both functional and structural studies has been missing. In this work, we established a stable expression system for both a human cell-based sterol export assay and protein purification for in vitro biochemical and structural studies. ABCA1 produced in this system was active in sterol export and displayed enhanced ATPase activity after reconstitution into a lipid bilayer. Our single-particle cryo-EM study of ABCA1 in nanodiscs showed protein induced membrane curvature, revealed multiple distinct conformations, and generated a structure of nanodisc-embedded ABCA1 at 4.0-Å resolution representing a previously unknown conformation. Comparison of different ABCA1 structures and molecular dynamics simulations demonstrates both concerted domain movements and conformational variations within each domain. Taken together, our platform for producing and characterizing ABCA1 in a lipid membrane enabled us to gain important mechanistic and structural insights and paves the way for investigating modulators that target the functions of ABCA1.
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Affiliation(s)
- Ashlee M Plummer-Medeiros
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Bryn Mawr College Chemistry Department, 101 N Merion Avenue, Bryn Mawr, PA 19010, USA
| | - Alan T Culbertson
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Roivant Sciences, Inc., 451 D Street, Boston, MA 02210, USA
| | - Claudio L Morales-Perez
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Generate Biomedicines, 4 Corporate Drive Andover, MA, 01810, USA
| | - Maofu Liao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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25
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Atsumi N, Yasumatsu K, Takashina Y, Ito C, Yasui N, Margolskee RF, Yamashita A. Chloride ions evoke taste sensations by binding to the extracellular ligand-binding domain of sweet/umami taste receptors. eLife 2023; 12:84291. [PMID: 36852482 PMCID: PMC9977269 DOI: 10.7554/elife.84291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/31/2023] [Indexed: 03/01/2023] Open
Abstract
Salt taste sensation is multifaceted: NaCl at low or high concentrations is preferably or aversively perceived through distinct pathways. Cl- is thought to participate in taste sensation through an unknown mechanism. Here, we describe Cl- ion binding and the response of taste receptor type 1 (T1r), a receptor family composing sweet/umami receptors. The T1r2a/T1r3 heterodimer from the medaka fish, currently the sole T1r amenable to structural analyses, exhibited a specific Cl- binding in the vicinity of the amino-acid-binding site in the ligand-binding domain (LBD) of T1r3, which is likely conserved across species, including human T1r3. The Cl- binding induced a conformational change in T1r2a/T1r3LBD at sub- to low-mM concentrations, similar to canonical taste substances. Furthermore, oral Cl- application to mice increased impulse frequencies of taste nerves connected to T1r-expressing taste cells and promoted their behavioral preferences attenuated by a T1r-specific blocker or T1r3 knock-out. These results suggest that the Cl- evokes taste sensations by binding to T1r, thereby serving as another preferred salt taste pathway at a low concentration.
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Affiliation(s)
- Nanako Atsumi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayamaJapan
| | - Keiko Yasumatsu
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayamaJapan
- Tokyo Dental Junior CollegeTokyoJapan
- Monell Chemical Senses CenterPhiladelphiaUnited States
| | - Yuriko Takashina
- School of Pharmaceutical Sciences, Okayama UniversityOkayamaJapan
| | - Chiaki Ito
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayamaJapan
| | - Norihisa Yasui
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayamaJapan
- School of Pharmaceutical Sciences, Okayama UniversityOkayamaJapan
| | | | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama UniversityOkayamaJapan
- School of Pharmaceutical Sciences, Okayama UniversityOkayamaJapan
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26
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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27
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Zhu C, Liang X, Chen X, Liang M, Zheng J, Wan B, Luo S. Characterizing the Specific Recognition of Xanthurenic Acid by GEP1 and GEP1-GCα Interactions in cGMP Signaling Pathway in Gametogenesis of Malaria Parasites. Int J Mol Sci 2023; 24:ijms24032561. [PMID: 36768882 PMCID: PMC9916804 DOI: 10.3390/ijms24032561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Gametogenesis is an essential step for malaria parasite transmission and is activated in mosquito by signals including temperature drop, pH change, and mosquito-derived xanthurenic acid (XA). Recently, a membrane protein gametogenesis essential protein 1 (GEP1) was found to be responsible for sensing these signals and interacting with a giant guanylate cyclase α (GCα) to activate the cGMP-PKG-Ca2+ signaling pathway for malaria parasite gametogenesis. However, the molecular mechanisms for this process remain unclear. In this study, we used AlphaFold2 to predict the structure of GEP1 and found that it consists of a conserved N-terminal helical domain and a transmembrane domain that adopts a structure similar to that of cationic amino acid transporters. Molecular docking results showed that XA binds to GEP1 via a pocket similar to the ligand binding sites of known amino acid transporters. In addition, truncations of this N-terminal sequence significantly enhanced the expression, solubility, and stability of GEP1. In addition, we found that GEP1 interacts with GCα via its C-terminal region, which is interrupted by mutations of a few conserved residues. These findings provide further insights into the molecular mechanism for the XA recognition by GEP1 and the activation of the gametogenesis of malaria parasites through GEP1-GCα interaction.
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Affiliation(s)
- Cheng Zhu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Xiaoge Liang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Xu Chen
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Miaomiao Liang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Jianting Zheng
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Bingbing Wan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Shukun Luo
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
- Correspondence:
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28
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Niebling S, Burastero O, García-Alai M. Biophysical Characterization of Membrane Proteins. Methods Mol Biol 2023; 2652:215-230. [PMID: 37093478 DOI: 10.1007/978-1-0716-3147-8_12] [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] [Indexed: 04/25/2023]
Abstract
Membrane proteins are responsible for a large variety of tasks in organisms and of particular interesting as drug targets. At the same time, they are notoriously difficult to work with and require a thorough characterization before proceeding with structural studies. Here, we present a biophysical pipeline to characterize membrane proteins focusing on the optimization of stability, aggregation behavior, and homogeneity. The pipeline shown here is built on three biophysical techniques: differential scanning fluorimetry using native protein fluorescence (nano differential scanning fluorimetry), dynamic light scattering, and mass photometry. For each of these techniques, we provide detailed protocols for performing experiments and data analysis.
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Affiliation(s)
- Stephan Niebling
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Osvaldo Burastero
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - María García-Alai
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany.
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany.
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29
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Yao H, Cai H, Li D. Fluorescence-Detection Size-Exclusion Chromatography-Based Thermostability Assay for Membrane Proteins. Methods Mol Biol 2023; 2564:299-315. [PMID: 36107350 DOI: 10.1007/978-1-0716-2667-2_16] [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
Green fluorescent proteins (GFPs) have lightened up almost every aspect of biological research including protein sciences. In the field of membrane protein structural biology, GFPs have been used widely to monitor membrane protein localization, expression level, the purification process and yield, and the stability inside the cells and in the test tube. Of particular interest is the fluorescence-detector size-exclusion chromatography-based thermostability assay (FSEC-TS). By simple heating and FSEC, the generally applicable method allows rapid assessment of the thermostability of GFP-fused membrane proteins without purification. Here we describe the experimental details and some typical results for the FSEC-TS method.
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Affiliation(s)
| | | | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
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30
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Futamata H, Fukuda M, Umeda R, Yamashita K, Tomita A, Takahashi S, Shikakura T, Hayashi S, Kusakizako T, Nishizawa T, Homma K, Nureki O. Cryo-EM structures of thermostabilized prestin provide mechanistic insights underlying outer hair cell electromotility. Nat Commun 2022; 13:6208. [PMID: 36266333 PMCID: PMC9584906 DOI: 10.1038/s41467-022-34017-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/11/2022] [Indexed: 01/11/2023] Open
Abstract
Outer hair cell elecromotility, driven by prestin, is essential for mammalian cochlear amplification. Here, we report the cryo-EM structures of thermostabilized prestin (PresTS), complexed with chloride, sulfate, or salicylate at 3.52-3.63 Å resolutions. The central positively-charged cavity allows flexible binding of various anion species, which likely accounts for the known distinct modulations of nonlinear capacitance (NLC) by different anions. Comparisons of these PresTS structures with recent prestin structures suggest rigid-body movement between the core and gate domains, and provide mechanistic insights into prestin inhibition by salicylate. Mutations at the dimeric interface severely diminished NLC, suggesting that stabilization of the gate domain facilitates core domain movement, thereby contributing to the expression of NLC. These findings advance our understanding of the molecular mechanism underlying mammalian cochlear amplification.
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Affiliation(s)
- Haon Futamata
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo; Meguro-ku, Tokyo, 153-8503, Japan
| | - Rie Umeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Satoe Takahashi
- Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Takafumi Shikakura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
| | - Kazuaki Homma
- Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, IL, 60608, USA.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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31
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Conformational transition induced in the aspartate:alanine antiporter by L-Ala binding. Sci Rep 2022; 12:15871. [PMID: 36151227 PMCID: PMC9508256 DOI: 10.1038/s41598-022-19974-z] [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: 05/02/2022] [Accepted: 09/07/2022] [Indexed: 12/14/2022] Open
Abstract
An aspartate:alanine antiporter (AspT) from the lactic acid bacterium Tetragenococcus halophilus catalyzes the electrogenic aspartate<sup>1-</sup>:alanine<sup>0</sup> exchange reaction. Our previous kinetic analyses of transport reactions mediated by AspT in reconstituted liposomes suggested that, although the substrate transport reactions are physiologically coupled, the putative binding sites of L-aspartate (-Asp) and L-alanine (-Ala) are independently located on AspT. By using the fluorescent probe Oregon Green maleimide (OGM), which reacts specifically with cysteine, we also found that the presence of L-Asp changes the conformation of AspT. In this study, we conducted an OGM labeling assay in the presence of L-Ala. The labeling efficiency of single cysteine mutants (G62C and P79C) in transmembrane helix 3 of the AspT showed novel patterns depending on the presence of L-Ala or analogs. A concentration-dependent shift of AspT from the conformation in the presence of one substrate to that specific to the substrate added subsequently (L-Ala or L-Asp) was observed. Moreover, size-exclusion-chromatography-based thermostability assays indicated that the thermal stability of AspT in the presence of L-Ala differed from that in the presence of L-Asp. From these results, we concluded that L-Ala binding yields a conformation different from the apo or L-Asp binding conformations.
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32
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Xia H, Hong Y, Li X, Fan R, Li Q, Ouyang Z, Yao X, Lu S, Guo L, Tang S. BnaNTT2 regulates ATP homeostasis in plastid to sustain lipid metabolism and plant growth in Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:54. [PMID: 37313423 PMCID: PMC10248631 DOI: 10.1007/s11032-022-01322-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The plastid inner envelope membrane-bond nucleotide triphosphate transporter (NTT) transports cytosolic adenosine triphosphate (ATP) into plastid, which is necessary for the biochemical activities in plastid. We identified a chloroplast-localized BnaC08.NTT2 and obtained the overexpressed lines of BnaC08.NTT2 and CRISPR/Cas9 edited double mutant lines of BnaC08.NTT2 and BnaA08.NTT2 in B. napus. Further studies certified that overexpression (OE) of BnaC08.NTT2 could help transport ATP into chloroplast and exchange adenosine diphosphate (ADP) and this process was inhibited in BnaNTT2 mutants. Additional results showed that the thylakoid was abnormal in a8 c8 double mutants, which also had lower photosynthetic efficiency, leading to retarded plant growth. The BnaC08.NTT2 OE plants had higher photosynthetic efficiency and better growth compared to WT. OE of BnaC08.NTT2 could improve carbon flowing into protein and oil synthesis from glycolysis both in leaves and seeds. Lipid profile analysis showed that the contents of main chloroplast membrane lipids, including monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), and phosphatidylglycerol (PG), were significantly reduced in mutants, while there were no differences in OE lines compared to WT. These results suggest that BnaNTT2 is involved in the regulation of ATP/ADP homeostasis in plastid to impact plant growth and seed oil accumulation in B. napus. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01322-8.
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Affiliation(s)
- Hui Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Yue Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Xiao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Ruyi Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Zhewen Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Shan Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Hongshan Laboratory, Wuhan, 430070 China
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33
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Sugaya K, Yasuda S, Sato S, Sisi C, Yamamoto T, Umeno D, Matsuura T, Hayashi T, Ogasawara S, Kinoshita M, Murata T. A methodology for creating thermostabilized mutants of G‐protein coupled receptors by combining statistical thermodynamics and evolutionary molecular engineering. Protein Sci 2022. [DOI: 10.1002/pro.4404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kanna Sugaya
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
| | - Shingo Sato
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Chen Sisi
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
| | - Taisei Yamamoto
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Daisuke Umeno
- Department of Applied Chemistry Waseda University Tokyo Japan
| | - Tomoaki Matsuura
- Earth‐Life Science Institute Tokyo Institute of Technology Tokyo Japan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering Niigata University Niigata Japan
- Institute of Advanced Energy Kyoto University Kyoto Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
- Institute for Advanced Academic Research Chiba University Chiba Japan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Institute of Advanced Energy Kyoto University Kyoto Japan
- Center for the Promotion of Interdisciplinary Education and Research Kyoto University Kyoto‐shi Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
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34
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TTYH family members form tetrameric complexes at the cell membrane. Commun Biol 2022; 5:886. [PMID: 36042377 PMCID: PMC9427776 DOI: 10.1038/s42003-022-03862-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 08/18/2022] [Indexed: 11/08/2022] Open
Abstract
The conserved Tweety homolog (TTYH) family consists of three paralogs in vertebrates, displaying a ubiquitous expression pattern. Although considered as ion channels for almost two decades, recent structural and functional analyses refuted this role. Intriguingly, while all paralogs shared a dimeric stoichiometry following detergent solubilization, their structures revealed divergence in their relative subunit orientation. Here, we determined the stoichiometry of intact mouse TTYH (mTTYH) complexes in cells. Using cross-linking and single-molecule fluorescence microscopy, we demonstrate that mTTYH1 and mTTYH3 form tetramers at the plasma membrane, stabilized by interactions between their extracellular domains. Using blue-native PAGE, fluorescence-detection size-exclusion chromatography, and hydrogen/deuterium exchange mass spectrometry (HDX-MS), we reveal that detergent solubilization results in tetramers destabilization, leading to their dissolution into dimers. Moreover, HDX-MS demonstrates that the extracellular domains are stabilized in the context of the tetrameric mTTYH complex. Together, our results expose the innate tetrameric organization of TTYH complexes at the cell membrane. Future structural analyses of these assemblies in native membranes are required to illuminate their long-sought cellular function.
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35
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Protein Fusion Strategies for Membrane Protein Stabilization and Crystal Structure Determination. CRYSTALS 2022. [DOI: 10.3390/cryst12081041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Crystal structures of membrane proteins are highly desired for their use in the mechanistic understanding of their functions and the designing of new drugs. However, obtaining the membrane protein structures is difficult. One way to overcome this challenge is with protein fusion methods, which have been successfully used to determine the structures of many membrane proteins, including receptors, enzymes and adhesion molecules. Existing fusion strategies can be categorized into the N or C terminal fusion, the insertion fusion and the termini restraining. The fusions facilitate protein expression, purification, crystallization and phase determination. Successful applications often require further optimization of protein fusion linkers and interactions, whose design can be facilitated by a shared helix strategy and by AlphaFold prediction in the future.
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36
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Goutam K, Ielasi FS, Pardon E, Steyaert J, Reyes N. Structural basis of sodium-dependent bile salt uptake into the liver. Nature 2022; 606:1015-1020. [PMID: 35545671 PMCID: PMC9242856 DOI: 10.1038/s41586-022-04723-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 04/04/2022] [Indexed: 02/08/2023]
Abstract
The liver takes up bile salts from blood to generate bile, enabling absorption of lipophilic nutrients and excretion of metabolites and drugs1. Human Na+–taurocholate co-transporting polypeptide (NTCP) is the main bile salt uptake system in liver. NTCP is also the cellular entry receptor of human hepatitis B and D viruses2,3 (HBV/HDV), and has emerged as an important target for antiviral drugs4. However, the molecular mechanisms underlying NTCP transport and viral receptor functions remain incompletely understood. Here we present cryo-electron microscopy structures of human NTCP in complexes with nanobodies, revealing key conformations of its transport cycle. NTCP undergoes a conformational transition opening a wide transmembrane pore that serves as the transport pathway for bile salts, and exposes key determinant residues for HBV/HDV binding to the outside of the cell. A nanobody that stabilizes pore closure and inward-facing states impairs recognition of the HBV/HDV receptor-binding domain preS1, demonstrating binding selectivity of the viruses for open-to-outside over inward-facing conformations of the NTCP transport cycle. These results provide molecular insights into NTCP ‘gated-pore’ transport and HBV/HDV receptor recognition mechanisms, and are expected to help with development of liver disease therapies targeting NTCP. Structural studies of human Na+–taurocholate co-transporting polypeptide in complex with nanobodies reveal mechanisms for bile salts transport and HBV recognition involving an open-pore intermediate state.
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Affiliation(s)
- Kapil Goutam
- Membrane Protein Mechanisms Group, European Institute of Chemistry and Biology, University of Bordeaux, CNRS-UMR5234, Pessac, France.,Membrane Protein Mechanisms Unit, Institut Pasteur, Paris, France
| | | | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Nicolas Reyes
- Membrane Protein Mechanisms Group, European Institute of Chemistry and Biology, University of Bordeaux, CNRS-UMR5234, Pessac, France. .,Membrane Protein Mechanisms Unit, Institut Pasteur, Paris, France.
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37
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Matsuoka R, Fudim R, Jung S, Zhang C, Bazzone A, Chatzikyriakidou Y, Robinson CV, Nomura N, Iwata S, Landreh M, Orellana L, Beckstein O, Drew D. Structure, mechanism and lipid-mediated remodeling of the mammalian Na +/H + exchanger NHA2. Nat Struct Mol Biol 2022; 29:108-120. [PMID: 35173351 PMCID: PMC8850199 DOI: 10.1038/s41594-022-00738-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
The Na+/H+ exchanger SLC9B2, also known as NHA2, correlates with the long-sought-after Na+/Li+ exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite the functional importance of NHA2, structural information and the molecular basis for its ion-exchange mechanism have been lacking. Here we report the cryo-EM structures of bison NHA2 in detergent and in nanodiscs, at 3.0 and 3.5 Å resolution, respectively. The bison NHA2 structure, together with solid-state membrane-based electrophysiology, establishes the molecular basis for electroneutral ion exchange. NHA2 consists of 14 transmembrane (TM) segments, rather than the 13 TMs previously observed in mammalian Na+/H+ exchangers (NHEs) and related bacterial antiporters. The additional N-terminal helix in NHA2 forms a unique homodimer interface with a large intracellular gap between the protomers, which closes in the presence of phosphoinositol lipids. We propose that the additional N-terminal helix has evolved as a lipid-mediated remodeling switch for the regulation of NHA2 activity.
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Affiliation(s)
- Rei Matsuoka
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Roman Fudim
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Sukkyeong Jung
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Chenou Zhang
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA
| | | | | | | | - Norimichi Nomura
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - So Iwata
- Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Orellana
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Beckstein
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ, USA.
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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38
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Structural mechanism of human TRPC3 and TRPC6 channel regulation by their intracellular calcium-binding sites. Neuron 2022; 110:1023-1035.e5. [PMID: 35051376 DOI: 10.1016/j.neuron.2021.12.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/09/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022]
Abstract
TRPC3 and TRPC6 channels are calcium-permeable non-selective cation channels that are involved in many physiological processes. The gain-of-function (GOF) mutations of TRPC6 lead to familial focal segmental glomerulosclerosis (FSGS) in humans, but their pathogenic mechanism remains elusive. Here, we report the cryo-EM structures of human TRPC3 in both high-calcium and low-calcium conditions. Based on these structures and accompanying electrophysiological studies, we identified both inhibitory and activating calcium-binding sites in TRPC3 that couple intracellular calcium concentrations to the basal channel activity. These calcium sensors are also structurally and functionally conserved in TRPC6. We uncovered that the GOF mutations of TRPC6 activate the channel by allosterically abolishing the inhibitory effects of intracellular calcium. Furthermore, structures of human TRPC6 in complex with two chemically distinct inhibitors bound at different ligand-binding pockets reveal different conformations of the transmembrane domain, providing templates for further structure-based drug design targeting TRPC6-related diseases such as FSGS.
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39
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Ramanadane K, Straub MS, Dutzler R, Manatschal C. Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family. eLife 2022; 11:74589. [PMID: 35001872 PMCID: PMC8806188 DOI: 10.7554/elife.74589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca2+ and Mg2+, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H+ serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg2+. The protein transports Mg2+ and Mn2+ but not Ca2+ by a mechanism that is not coupled to H+. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell.
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Affiliation(s)
| | - Monique S Straub
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Raimund Dutzler
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
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40
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Ortega C, Oppezzo P, Correa A. Overcoming the Solubility Problem in E. coli: Available Approaches for Recombinant Protein Production. Methods Mol Biol 2022; 2406:35-64. [PMID: 35089549 DOI: 10.1007/978-1-0716-1859-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Despite the importance of recombinant protein production in the academy and industrial fields, many issues concerning the expression of soluble and homogeneous products are still unsolved. Several strategies were developed to overcome these obstacles; however, at present, there is no magic bullet that can be applied for all cases. Indeed, several key expression parameters need to be evaluated for each protein. Among the different hosts for protein expression, Escherichia coli is by far the most widely used. In this chapter, we review many of the different tools employed to circumvent protein insolubility problems.
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Affiliation(s)
- Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Oppezzo
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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41
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Claxton DP, Overway EM, Oeser JK, O'Brien RM, Mchaourab HS. Biophysical and functional properties of purified glucose-6-phosphatase catalytic subunit 1. J Biol Chem 2021; 298:101520. [PMID: 34952005 PMCID: PMC8753184 DOI: 10.1016/j.jbc.2021.101520] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 11/18/2022] Open
Abstract
Glucose-6-phosphatase catalytic subunit 1 (G6PC1) plays a critical role in hepatic glucose production during fasting by mediating the terminal step of the gluconeogenesis and glycogenolysis pathways. In concert with accessory transport proteins, this membrane-integrated enzyme catalyzes glucose production from glucose-6-phosphate (G6P) to support blood glucose homeostasis. Consistent with its metabolic function, dysregulation of G6PC1 gene expression contributes to diabetes, and mutations that impair phosphohydrolase activity form the clinical basis of glycogen storage disease type 1a. Despite its relevance to health and disease, a comprehensive view of G6PC1 structure and mechanism has been limited by the absence of expression and purification strategies that isolate the enzyme in a functional form. In this report, we apply a suite of biophysical and biochemical tools to fingerprint the in vitro attributes of catalytically active G6PC1 solubilized in lauryl maltose neopentyl glycol (LMNG) detergent micelles. When purified from Sf9 insect cell membranes, the glycosylated mouse ortholog (mG6PC1) recapitulated functional properties observed previously in intact hepatic microsomes and displayed the highest specific activity reported to date. Additionally, our results establish a direct correlation between the catalytic and structural stability of mG6PC1, which is underscored by the enhanced thermostability conferred by phosphatidylcholine and the cholesterol analog cholesteryl hemisuccinate. In contrast, the N96A variant, which blocks N-linked glycosylation, reduced thermostability. The methodologies described here overcome long-standing obstacles in the field and lay the necessary groundwork for a detailed analysis of the mechanistic structural biology of G6PC1 and its role in complex metabolic disorders.
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Affiliation(s)
- Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA.
| | - Emily M Overway
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - James K Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard M O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
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42
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Chatzikyriakidou Y, Ahn DH, Nji E, Drew D. The GFP thermal shift assay for screening ligand and lipid interactions to solute carrier transporters. Nat Protoc 2021; 16:5357-5376. [PMID: 34707255 DOI: 10.1038/s41596-021-00619-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/19/2021] [Indexed: 02/03/2023]
Abstract
Solute carrier (SLC) transporters represent the second-largest fraction of the membrane proteome after G-protein-coupled receptors, but have been underutilized as drug targets and the function of many members of this family is still unknown. They are technically challenging to work with as they are difficult to express and highly dynamic, making them unstable in detergent solution. Many SLCs lack known inhibitors that could be utilized for stabilization. Furthermore, as they bind their physiological substrates with high micromolar to low millimolar affinities, binding and transport assays have proven to be particularly challenging to implement. Previously, we reported a GFP-based method for the overexpression and purification of membrane proteins in Saccharomyces cerevisiae. Here, we extend this expression platform with the GFP thermal shift (GFP-TS) assay, which is a simplified version of fluorescence-detection size-exclusion chromatography that combines the sample versatility of fluorescence-detection size-exclusion chromatography with the high-throughput capability of dye-based thermal shift assays. We demonstrate how GFP-TS can be used for detecting specific ligand interactions of SLC transporter fusions and measuring their affinities in crude detergent-solubilized membranes. We further show how GFP-TS can be employed on purified SLC transporter fusions to screen for specific lipid-protein interactions, which is an important complement to native mass spectrometry approaches that cannot cope easily with crude lipid-mixture preparations. This protocol is simple to perform and can be followed by researchers with a basic background in protein chemistry. Starting with an SLC transporter construct that can be expressed and purified from S. cerevisiae in a well-folded state, this protocol extension can be completed in ~4-5 d.
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Affiliation(s)
| | - Do-Hwan Ahn
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Emmanuel Nji
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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43
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Wang Z, Li L, Hu R, Zhong P, Zhang Y, Cheng S, Jiang H, Liu R, Ding Y. Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry. Protein Sci 2021; 30:2298-2309. [PMID: 34562299 PMCID: PMC8521304 DOI: 10.1002/pro.4194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 01/20/2023]
Abstract
Red fluorescent proteins (RFPs) are powerful tools used in molecular biology research. Although RFP can be easily monitored in vivo, manipulation of RFP by suitable nanobodies binding to different epitopes of RFP is still desired. Thus, it is crucial to obtain structural information on how the different nanobodies interact with RFP. Here, we determined the crystal structures of the LaM2-mCherry and LaM4-mCherry complexes at 1.4 and 1.9 Å resolution. Our results showed that LaM2 binds to the side of the mCherry β-barrel, while LaM4 binds to the bottom of the β-barrel. The distinct binding sites of LaM2 and LaM4 were further verified by isothermal titration calorimetry, fluorescence-based size exclusion chromatography, and dynamic light scattering assays. Mutation of the residues at the LaM2 or LaM4 binding interface to mCherry significantly decreased the binding affinity of the nanobody to mCherry. Our results also showed that LaM2 and LaM4 can bind to mCherry simultaneously, which is crucial for recruiting multiple operation elements to the RFP. The binding of LaM2 or LaM4 did not significantly change the chromophore environment of mCherry, which is important for fluorescence quantification assays, while several GFP nanobodies significantly altered the fluorescence. Our results provide atomic resolution interaction information on the binding of nanobodies LaM2 and LaM4 with mCherry, which is important for developing detection and manipulation methods for RFP-based biotechnology.
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Affiliation(s)
- Ziying Wang
- School of Life SciencesFudan UniversityShanghaiChina
| | - Long Li
- Department of MacromoleculesFudan UniversityShanghaiChina
| | - Rongting Hu
- Department of MacromoleculesFudan UniversityShanghaiChina
| | - Peiyu Zhong
- School of Life SciencesFudan UniversityShanghaiChina
| | - Yiran Zhang
- School of Life SciencesFudan UniversityShanghaiChina
| | - Shihao Cheng
- School of Life SciencesFudan UniversityShanghaiChina
| | - He Jiang
- School of Life SciencesFudan UniversityShanghaiChina
| | - Rui Liu
- School of Life SciencesFudan UniversityShanghaiChina
| | - Yu Ding
- School of Life SciencesFudan UniversityShanghaiChina
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44
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Zhu H, Gouaux E. Architecture and assembly mechanism of native glycine receptors. Nature 2021; 599:513-517. [PMID: 34555840 PMCID: PMC8647860 DOI: 10.1038/s41586-021-04022-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/15/2021] [Indexed: 02/08/2023]
Abstract
Glycine receptors (GlyRs) are pentameric, 'Cys-loop' receptors that form chloride-permeable channels and mediate fast inhibitory signalling throughout the central nervous system1,2. In the spinal cord and brainstem, GlyRs regulate locomotion and cause movement disorders when mutated2,3. However, the stoichiometry of native GlyRs and the mechanism by which they are assembled remain unclear, despite extensive investigation4-8. Here we report cryo-electron microscopy structures of native GlyRs from pig spinal cord and brainstem, revealing structural insights into heteromeric receptors and their predominant subunit stoichiometry of 4α:1β. Within the heteromeric pentamer, the β(+)-α(-) interface adopts a structure that is distinct from the α(+)-α(-) and α(+)-β(-) interfaces. Furthermore, the β-subunit contains a unique phenylalanine residue that resides within the pore and disrupts the canonical picrotoxin site. These results explain why inclusion of the β-subunit breaks receptor symmetry and alters ion channel pharmacology. We also find incomplete receptor complexes and, by elucidating their structures, reveal the architectures of partially assembled α-trimers and α-tetramers.
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Affiliation(s)
- Hongtao Zhu
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA.
- Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR, USA.
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45
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Abe K, Yamamoto K, Irie K, Nishizawa T, Oshima A. Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations. Nat Commun 2021; 12:5709. [PMID: 34588453 PMCID: PMC8481561 DOI: 10.1038/s41467-021-26024-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
The gastric H+,K+-ATPase mediates electroneutral exchange of 1H+/1K+ per ATP hydrolysed across the membrane. Previous structural analysis of the K+-occluded E2-P transition state of H+,K+-ATPase showed a single bound K+ at cation-binding site II, in marked contrast to the two K+ ions occluded at sites I and II of the closely-related Na+,K+-ATPase which mediates electrogenic 3Na+/2K+ translocation across the membrane. The molecular basis of the different K+ stoichiometry between these K+-counter-transporting pumps is elusive. We show a series of crystal structures and a cryo-EM structure of H+,K+-ATPase mutants with changes in the vicinity of site I, based on the structure of the sodium pump. Our step-wise and tailored construction of the mutants finally gave a two-K+ bound H+,K+-ATPase, achieved by five mutations, including amino acids directly coordinating K+ (Lys791Ser, Glu820Asp), indirectly contributing to cation-binding site formation (Tyr340Asn, Glu936Val), and allosterically stabilizing K+-occluded conformation (Tyr799Trp). This quintuple mutant in the K+-occluded E2-P state unambiguously shows two separate densities at the cation-binding site in its 2.6 Å resolution cryo-EM structure. These results offer new insights into how two closely-related cation pumps specify the number of K+ accommodated at their cation-binding site. The gastric H+,K+-ATPase is a proton pump that creates the acidic environment of the stomach lumen, maintaining high proton gradient across the gastric mucosa cell membrane. Here, structural analysis of rationally designed H+,K+-ATPase mutants provides insight into this and other P-type ATPases cation binding stoichiometry and mechanisms.
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Affiliation(s)
- Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan. .,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan.
| | - Kenta Yamamoto
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Katsumasa Irie
- Department of Biophysical Chemistry, Faculty of Pharmaceutical Sciences, Wakayama Medical University, 25-1 Shichibancho, Wakayama, 640-8156, Japan
| | - Tomohiro Nishizawa
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, 464-8601, Japan
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46
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Luo Y, Wan G, Zhou X, Wang Q, Zhang Y, Bao J, Cong Y, Zhao Y, Li D. Architecture of Dispatched, a Transmembrane Protein Responsible for Hedgehog Release. Front Mol Biosci 2021; 8:701826. [PMID: 34557519 PMCID: PMC8453165 DOI: 10.3389/fmolb.2021.701826] [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: 05/06/2021] [Accepted: 08/11/2021] [Indexed: 11/30/2022] Open
Abstract
The evolutionarily conserved Hedgehog (Hh) signaling pathway is crucial for programmed cell differentiation and proliferation. Dispatched (Disp) is a 12-transmembrane protein that plays a critical role in the Hedgehog (Hh) signaling pathway by releasing the dually lipidated ligand HhN from the membrane, a prerequisite step to the downstream signaling cascade. In this study, we focus on the Disp from water bear, a primitive animal known as the most indestructible on Earth. Using a zebrafish model, we show that the water bear homolog possesses the function of Disp. We have solved its structure to a 6.5-Å resolution using single-particle cryogenic electron microscopy. Consistent with the evolutional conservation of the pathway, the water bear Disp structure is overall similar to the previously reported structures of the fruit fly and human homologs. Although not revealing much detail at this resolution, the water bear Disp shows a different conformation compared to published structures, suggesting that they represent different functional snapshots.
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Affiliation(s)
- Yitian Luo
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guoyue Wan
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xuan Zhou
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiuwen Wang
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yunbin Zhang
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan Bao
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yao Cong
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yun Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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47
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Functional Analysis of the GPI Transamidase Complex by Screening for Amino Acid Mutations in Each Subunit. Molecules 2021; 26:molecules26185462. [PMID: 34576938 PMCID: PMC8465894 DOI: 10.3390/molecules26185462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/20/2022] Open
Abstract
Glycosylphosphatidylinositol (GPI) anchor modification is a posttranslational modification of proteins that has been conserved in eukaryotes. The biosynthesis and transfer of GPI to proteins are carried out in the endoplasmic reticulum. Attachment of GPI to proteins is mediated by the GPI-transamidase (GPI-TA) complex, which recognizes and cleaves the C-terminal GPI attachment signal of precursor proteins. Then, GPI is transferred to the newly exposed C-terminus of the proteins. GPI-TA consists of five subunits: PIGK, GPAA1, PIGT, PIGS, and PIGU, and the absence of any subunit leads to the loss of activity. Here, we analyzed functionally important residues of the five subunits of GPI-TA by comparing conserved sequences among homologous proteins. In addition, we optimized the purification method for analyzing the structure of GPI-TA. Using purified GPI-TA, preliminary single particle images were obtained. Our results provide guidance for the structural and functional analysis of GPI-TA.
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48
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Cation-π Interactions and their Functional Roles in Membrane Proteins. J Mol Biol 2021; 433:167035. [PMID: 33957146 PMCID: PMC8338773 DOI: 10.1016/j.jmb.2021.167035] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 01/25/2023]
Abstract
Cation-π interactions arise as a result of strong attractive forces between positively charged entities and the π-electron cloud of aromatic groups. The physicochemical characteristics of cation-π interactions are particularly well-suited to the dual hydrophobic/hydrophilic environment of membrane proteins. As high-resolution structural data of membrane proteins bring molecular features into increasingly sharper view, cation-π interactions are gaining traction as essential contributors to membrane protein chemistry, function, and pharmacology. Here we review the physicochemical properties of cation-π interactions and present several prominent examples which demonstrate significant roles for this specialized biological chemistry.
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49
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Cecchetti C, Strauss J, Stohrer C, Naylor C, Pryor E, Hobbs J, Tanley S, Goldman A, Byrne B. A novel high-throughput screen for identifying lipids that stabilise membrane proteins in detergent based solution. PLoS One 2021; 16:e0254118. [PMID: 34252116 PMCID: PMC8274869 DOI: 10.1371/journal.pone.0254118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/20/2021] [Indexed: 12/29/2022] Open
Abstract
Membrane proteins have a range of crucial biological functions and are the target of about 60% of all prescribed drugs. For most studies, they need to be extracted out of the lipid-bilayer, e.g. by detergent solubilisation, leading to the loss of native lipids, which may disturb important protein-lipid/bilayer interactions and thus functional and structural integrity. Relipidation of membrane proteins has proven extremely successful for studying challenging targets, but the identification of suitable lipids can be expensive and laborious. Therefore, we developed a screen to aid the high-throughput identification of beneficial lipids. The screen covers a large lipid space and was designed to be suitable for a range of stability assessment methods. Here, we demonstrate its use as a tool for identifying stabilising lipids for three membrane proteins: a bacterial pyrophosphatase (Tm-PPase), a fungal purine transporter (UapA) and a human GPCR (A2AR). A2AR is stabilised by cholesteryl hemisuccinate, a lipid well known to stabilise GPCRs, validating the approach. Additionally, our screen also identified a range of new lipids which stabilised our test proteins, providing a starting point for further investigation and demonstrating its value as a novel tool for membrane protein research. The pre-dispensed screen will be made commercially available to the scientific community in future and has a number of potential applications in the field.
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Affiliation(s)
- Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jannik Strauss
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Claudia Stohrer
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Edward Pryor
- Anatrace, Maumee, Ohio, United States of America
| | | | | | - Adrian Goldman
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- MIBS, Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- * E-mail: (AG); (BB)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (AG); (BB)
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50
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Nadezhdin KD, Neuberger A, Trofimov YA, Krylov NA, Sinica V, Kupko N, Vlachova V, Zakharian E, Efremov RG, Sobolevsky AI. Structural mechanism of heat-induced opening of a temperature-sensitive TRP channel. Nat Struct Mol Biol 2021; 28:564-572. [PMID: 34239124 PMCID: PMC8283911 DOI: 10.1038/s41594-021-00615-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023]
Abstract
Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been studied extensively, structural determination of their heat- and cold-activated states has remained a challenge. Here, we present cryo-EM structures of the nanodisc-reconstituted wild-type mouse TRPV3 in three distinct conformations: closed, heat-activated sensitized and open states. The heat-induced transformations of TRPV3 are accompanied by changes in the secondary structure of the S2-S3 linker and the N and C termini and represent a conformational wave that links these parts of the protein to a lipid occupying the vanilloid binding site. State-dependent differences in the behavior of bound lipids suggest their active role in thermo-TRP temperature-dependent gating. Our structural data, supported by physiological recordings and molecular dynamics simulations, provide an insight for understanding the molecular mechanism of temperature sensing.
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Affiliation(s)
- Kirill D. Nadezhdin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
| | - Arthur Neuberger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
| | - Yuri A. Trofimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,National Research Nuclear University Moscow Engineering Physics Institute, Moscow, Russia,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Nikolay A. Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,National Research University Higher School of Economics, Moscow, Russia
| | - Viktor Sinica
- Department of Cellular Neurophysiology, Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic
| | - Nikita Kupko
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
| | - Viktorie Vlachova
- Department of Cellular Neurophysiology, Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic
| | - Eleonora Zakharian
- Department of Cancer Biology & Pharmacology, University of Illinois College of Medicine, Peoria, Illinois, USA
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia,National Research University Higher School of Economics, Moscow, Russia
| | - Alexander I. Sobolevsky
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA,Correspondence and requests for materials should be addressed to A.I.S. (; Tel: 212-305-4249)
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