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Schmidt T, Kubatova N, Clore GM. Deconvoluting Monomer- and Dimer-Specific Distance Distributions between Spin Labels in a Monomer/Dimer Mixture Using T1-Edited DEER EPR Spectroscopy. J Am Chem Soc 2024. [PMID: 38888555 DOI: 10.1021/jacs.4c03916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Double electron-electron resonance (DEER) EPR is a powerful tool in structural biology, providing distances between pairs of spin labels. When the sample consists of a mixture of oligomeric species (e.g., monomer and dimer), the question arises as to how to assign the peaks in the DEER-derived probability distance distribution to the individual species. Here, we propose incorporating an EPR longitudinal electron relaxation (T1) inversion recovery experiment within a DEER pulse sequence to resolve this problem. The apparent T1 between dipolar coupled electron spins measured from the inversion recovery time (τinv) dependence of the peak intensities in the T1-edited DEER-derived probability P(r) distance distribution will be affected by the number of nitroxide labels attached to the biomolecule of interest, for example, two for a monomer and four for a dimer. We show that global fitting of all the T1-edited DEER echo curves, recorded over a range of τinv values, permits the deconvolution of distances between spin labels originating from monomeric (longer T1) and dimeric (shorter T1) species. This is especially useful when the trapping of spin labels in different conformational states during freezing gives rise to complex P(r) distance distributions. The utility of this approach is demonstrated for two systems, the β1 adrenergic receptor and a construct of the huntingtin exon-1 protein fused to the immunoglobulin domain of protein G, both of which exist in a monomer-dimer equilibrium.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Nina Kubatova
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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Lane BJ, Ma Y, Yan N, Wang B, Ackermann K, Karamanos TK, Bode BE, Pliotas C. Monitoring the conformational ensemble and lipid environment of a mechanosensitive channel under cyclodextrin-induced membrane tension. Structure 2024; 32:739-750.e4. [PMID: 38521071 DOI: 10.1016/j.str.2024.02.020] [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: 09/14/2023] [Revised: 12/29/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Membrane forces shift the equilibria of mechanosensitive channels enabling them to convert mechanical cues into electrical signals. Molecular tools to stabilize and methods to capture their highly dynamic states are lacking. Cyclodextrins can mimic tension through the sequestering of lipids from membranes. Here we probe the conformational ensemble of MscS by EPR spectroscopy, the lipid environment with NMR, and function with electrophysiology under cyclodextrin-induced tension. We show the extent of MscS activation depends on the cyclodextrin-to-lipid ratio, and that lipids are depleted slower when MscS is present. This has implications in MscS' activation kinetics when distinct membrane scaffolds such as nanodiscs or liposomes are used. We find MscS transits from closed to sub-conducting state(s) before it desensitizes, due to the lack of lipid availability in its vicinity required for closure. Our approach allows for monitoring tension-sensitive states in membrane proteins and screening molecules capable of inducing molecular tension in bilayers.
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Affiliation(s)
- Benjamin J Lane
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yue Ma
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Nana Yan
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Bolin Wang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Theodoros K Karamanos
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK; Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
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Bermejo GA, Tjandra N, Clore GM, Schwieters CD. Xplor-NIH: Better parameters and protocols for NMR protein structure determination. Protein Sci 2024; 33:e4922. [PMID: 38501482 PMCID: PMC10962493 DOI: 10.1002/pro.4922] [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: 10/28/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 03/20/2024]
Abstract
The present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor-NIH biomolecular structure determination package. In combination with an improved treatment of selected non-bonded interactions between atoms three bonds apart, such as those involving methyl hydrogens, and a previously developed term that affects the system's gyration volume, the new parameters are tested using structure calculations on 30 proteins with restraints derived from nuclear magnetic resonance data. Using modern structure validation criteria, including several formally adopted by the Protein Data Bank, and a clear measure of structural accuracy, the results show superior performance relative to previous Xplor-NIH implementations. Additionally, the Xplor-NIH structures compare favorably against originally determined NMR models.
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Affiliation(s)
- Guillermo A. Bermejo
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMarylandUSA
| | - G. Marius Clore
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Charles D. Schwieters
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
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Mao Q, Wang L, Xue D, Lin X, Sun F, Xu P, Chen J, Li W, Li X, Yan F, Hu C. Imaging GPCR Dimerization in Living Cells with Cucurbit[7]uril and Hemicyanine as a "Turn-On" Fluorescence Probe. Anal Chem 2024; 96:2022-2031. [PMID: 38259189 DOI: 10.1021/acs.analchem.3c04493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Although multiple forms of dimers have been described for GPCR, their dynamics and function are still controversially discussed field. Fluorescence microscopy allows GPCR to be imaged within their native context; however, a key challenge is to site-specifically incorporate reporter moieties that can produce high-quality signals upon formation of GPCR dimers. To this end, we propose a supramolecular sensor approach to detect agonist-induced dimer formation of μ-opioid receptors (μORs) at the surface of intact cells. With the macrocyclic host cucurbit[7]uril and its guest hemicyanine dye tethered to aptamer strands directed against the histidine residues, the sensing module is assembled by host-guest complexation once the histidine-tagged μORs dimerize and bring the discrete supramolecular units into close proximity. With the enhanced sensitivity attributed by the "turn-on" fluorescence emission and high specificity afforded by the intermolecular recognition, in situ visualization of dynamic GPCR dimerization was realized with high precision, thereby validating the supramolecular sensing entity as a sophisticated and versatile strategy to investigate GPCR dimers, which represent an obvious therapeutic target.
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Affiliation(s)
- Qiuxiang Mao
- Department of Pharmaceutical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Lancheng Wang
- Department of Pharmaceutical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Dandan Xue
- Department of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Xiaoxuan Lin
- Department of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Fang Sun
- Department of Pharmaceutical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Pengcheng Xu
- Department of Pharmaceutical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Jieru Chen
- Department of Pharmaceutical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Wenying Li
- Department of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Xiuchen Li
- Department of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Fang Yan
- Department of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Chi Hu
- Department of Pharmaceutical Engineering, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing 210009, China
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