1
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Langeland J, Lindkvist TT, Kjær C, Nielsen SB. Gas-phase Förster resonance energy transfer in mass-selected and trapped ions. MASS SPECTROMETRY REVIEWS 2024; 43:477-499. [PMID: 36514825 DOI: 10.1002/mas.21828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/21/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Förster Resonance Energy transfer (FRET) is a nonradiative process that may occur from an electronically excited donor to an acceptor when the emission spectrum of the donor overlaps with the absorption spectrum of the acceptor. FRET experiments have been done in the gas phase based on specially designed mass-spectroscopy setups with the goal to obtain structural information on biomolecular ions labeled with a FRET pair (i.e., donor and acceptor dyes) and to shed light on the energy-transfer process itself. Ions are accumulated in a radio-frequency ion trap or a Penning trap where mass selection of those of interest takes place, followed by photoexcitation. Gas-phase FRET is identified from detection of emitted light either from the donor, the acceptor, or both, or from a fragmentation channel that is specific to the acceptor when electronically excited. The challenge associated with the first approach is the collection and detection of photons emitted from a thin ion cloud that is not easily accessible while the second approach relies both on the photophysical and chemical behavior of the acceptor. In this review, we present the different instrumentation used for gas-phase FRET, including a discussion of advantages and disadvantages, and examples on how the technique has provided important structural information that is not easily obtainable otherwise. Furthermore, we describe how the spectroscopic properties of the dyes are affected by nearby electric fields, which is readily discernable from experiments on simple model systems with alkyl or π-conjugated bridges. Such spectral changes can have a significant effect on the FRET efficiency. Ideas for new directions are presented at the end with special focus on cold-ion spectroscopy.
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Affiliation(s)
- Jeppe Langeland
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | | | - Christina Kjær
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
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2
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Li W, Lu L, Du H. Deciphering DOM-metal binding using EEM-PARAFAC: Mechanisms, challenges, and perspectives. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:14388-14405. [PMID: 38289550 DOI: 10.1007/s11356-024-32072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Dissolved organic matter (DOM) is a pivotal component of the biogeochemical cycles and can combine with metal ions through chelation or complexation. Understanding this process is crucial for tracing metal solubility, mobility, and bioavailability. Fluorescence excitation emission matrix (EEM) and parallel factor analysis (PARAFAC) has emerged as a popular tool in deciphering DOM-metal interactions. In this review, we primarily discuss the advantages of EEM-PARAFAC compared with other algorithms and its main limitations in studying DOM-metal binding, including restrictions in spectral considerations, mathematical assumptions, and experimental procedures, as well as how to overcome these constraints and shortcomings. We summarize the principles of EEM to uncover DOM-metal association, including why fluorescence gets quenched and some potential mechanisms that affect the accuracy of fluorescence quenching. Lastly, we review some significant and innovative research, including the application of 2D-COS in DOM-metal binding analysis, hoping to provide a fresh perspective for possible future hotspots of study. We argue the expansion of EEM applications to a broader range of areas related to natural organic matter. This extension would facilitate our exploration of the mobility and fate of metals in the environment.
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Affiliation(s)
- Weijun Li
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410127, China
- Yuelu Mountain Laboratory, Hunan Agricultural University Area, Changsha, 410000, China
| | - Lei Lu
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410127, China
- Yuelu Mountain Laboratory, Hunan Agricultural University Area, Changsha, 410000, China
| | - Huihui Du
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410127, China.
- Yuelu Mountain Laboratory, Hunan Agricultural University Area, Changsha, 410000, China.
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3
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultrafast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. J Am Chem Soc 2023; 145:14608-14620. [PMID: 37364003 PMCID: PMC10440187 DOI: 10.1021/jacs.3c00967] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Site-directed spin-labeling (SDSL)─in combination with double electron-electron resonance (DEER) spectroscopy─has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. DEER combined with in situ SDSL in live cells is challenging since current bioorthogonal labeling approaches are too slow to allow for complete labeling with low concentrations of spin label prior to loss of signal from cellular reduction. Here, we overcome this limitation by genetically encoding a novel family of small, tetrazine-bearing noncanonical amino acids (Tet-v4.0) at multiple sites in proteins expressed in Escherichia coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans-cyclooctene (sTCO)-functionalized nitroxides─including a gem-diethyl-substituted nitroxide with enhanced stability in cells─with rate constants that can exceed 106 M-1 s-1. The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro. Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and support assignment of the conformational state of an MBP mutant within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification.
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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4
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultra-Fast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525763. [PMID: 36747808 PMCID: PMC9901033 DOI: 10.1101/2023.01.26.525763] [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] [Indexed: 06/18/2023]
Abstract
Studying protein structures and dynamics directly in the cellular environments in which they function is essential to fully understand the molecular mechanisms underlying cellular processes. Site-directed spin-labeling (SDSL)-in combination with double electron-electron resonance (DEER) spectroscopy-has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. In-cell DEER spectroscopy on proteins in mammalian cells has thus far not been possible due to the notable challenges of spin-labeling in live cells. In-cell SDSL requires exquisite biorthogonality, high labeling reaction rates and low background signal from unreacted residual spin label. While the bioorthogonal reaction must be highly specific and proceed under physiological conditions, many spin labels display time-dependent instability in the reducing cellular environment. Additionally, high concentrations of spin label can be toxic. Thus, an exceptionally fast bioorthogonal reaction is required that can allow for complete labeling with low concentrations of spin-label prior to loss of signal. Here we utilized genetic code expansion to site-specifically encode a novel family of small, tetrazine-bearing non-canonical amino acids (Tet-v4.0) at multiple sites in green fluorescent protein (GFP) and maltose binding protein (MBP) expressed both in E. coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans -cyclooctene (sTCO)-functionalized nitroxides-including a gem -diethyl-substituted nitroxide with enhanced stability in cells-with rate constants that can exceed 10 6 M -1 s -1 . The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live HEK293T cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide added directly to the culture medium. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro . Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and successfully discerned the conformational state of MBP within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification. TOC
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
- Equal contributors
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
- Equal contributors
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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5
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Billet B, Chovelon B, Fiore E, Faure P, Ravelet C, Peyrin E. Detection of small molecules by fluorescence intensity using single dye labeled aptamers and quencher transition metal ions. Biosens Bioelectron 2022; 205:114091. [PMID: 35217256 DOI: 10.1016/j.bios.2022.114091] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022]
Abstract
We describe herein an aptamer-based sensing approach that signal the presence of small-molecule targets when fluorescent DNA probes are challenged with the Ni2+ or Co2+ quencher metal ions. Functional oligonucleotides targeting L-tyrosinamide (L-Tym), adenosine (Ade) or cocaine (Coc) were end-labeled by the Texas-Red fluorophore. A fluorescence quenching occurred upon association of these transition metal ions with the free conjugates. The formation of the target-probe complex, by the way of variations in the overall binding of quencher metal ions along the DNA strands, led to a partial restoration (for the Ade and Coc systems) or a further attenuation (for the L-Tym system) of the fluorescence intensity. The absolute signal gain varied from 40 to 180% depending on the target-probe pair investigated. The approach was also used to detect the compound Ade in a spiked biological matrix in 1 min or less. The transition metal ion-based quenching strategy is characterized by its very simple implementation, low cost, and rapid signaling.
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Affiliation(s)
- Blandine Billet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Patrice Faure
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
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6
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Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. eLife 2021; 10:e70236. [PMID: 34623258 PMCID: PMC8500717 DOI: 10.7554/elife.70236] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022] Open
Abstract
With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose-binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.
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Affiliation(s)
- William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Brandon S Sim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Anthony K Nhim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Marium M Raza
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Eric Gb Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Chloe M Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
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7
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Tiwari P, Wu R, Metternich JB, Zenobi R. Transition Metal Ion FRET in the Gas Phase: A 10-40 Å Range Molecular Ruler for Mass-Selected Biomolecular Ions. J Am Chem Soc 2021; 143:11291-11295. [PMID: 34291949 DOI: 10.1021/jacs.1c01915] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Structural studies of mass-selected biomolecules in the gas phase can reveal their intrinsic properties and provide useful benchmarks for biomolecular modeling. Here, we report the first evidence of transition metal ion FRET (tmFRET) in the gas phase and its application to measure short (10-40 Å) biomolecular backbone distances. The measured FRET efficiencies in rhodamine dye (donor) labeled helical peptides complexed with Cu2+ ions (acceptor) decreased with increasing donor - acceptor distances, confirming the occurrence of tmFRET. The distances estimated for similar peptide sequences from the FRET efficiencies were consistently longer in the gas phase compared to those reported in solution, indicating an expanded structure and a possible loss of helicity.
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Affiliation(s)
- Prince Tiwari
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Ri Wu
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Jonas B Metternich
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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8
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Abstract
Measurement of atomic-scale conformational dynamics in proteins has proved a challenging endeavor, although these movements are pivotal for understanding the mechanisms behind protein function. Herein we describe a fluorescence-based method that enables the measurement of distances between specific domains within a protein and how it might change during protein function. The method is transition metal ion Förster resonance energy transfer (tmFRET) and builds on the principle that the fluorescence emission from a fluorophore can be quenched in a distance-dependent manner by a colored transition metal such as nickel (Ni2+), copper (Cu2+), or cobalt (Co2+). It can be applied to literally any protein where it is possible to perform site-specific incorporation of a fluorescent molecule. This chapter will explain the use and applications of tmFRET in detail using incorporation of the dye with cysteine chemistry on a purified protein sample.
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Affiliation(s)
- Jonas S Mortensen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, The Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, The Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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9
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Fischer J, Renn D, Quitterer F, Radhakrishnan A, Liu M, Makki A, Ghorpade S, Rueping M, Arold ST, Groll M, Eppinger J. Robust and Versatile Host Protein for the Design and Evaluation of Artificial Metal Centers. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Johannes Fischer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Dominik Renn
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Felix Quitterer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | | | | | | | | | | | - Stefan T. Arold
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Michael Groll
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
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10
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Raghuraman H, Chatterjee S, Das A. Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins. Front Mol Biosci 2019; 6:96. [PMID: 31608290 PMCID: PMC6774292 DOI: 10.3389/fmolb.2019.00096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.
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Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
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11
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Gordon SE, Munari M, Zagotta WN. Visualizing conformational dynamics of proteins in solution and at the cell membrane. eLife 2018; 7:37248. [PMID: 29923827 PMCID: PMC6056233 DOI: 10.7554/elife.37248] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/05/2018] [Indexed: 01/03/2023] Open
Abstract
Conformational dynamics underlie enzyme function, yet are generally inaccessible via traditional structural approaches. FRET has the potential to measure conformational dynamics in vitro and in intact cells, but technical barriers have thus far limited its accuracy, particularly in membrane proteins. Here, we combine amber codon suppression to introduce a donor fluorescent noncanonical amino acid with a new, biocompatible approach for labeling proteins with acceptor transition metals in a method called ACCuRET (Anap Cyclen-Cu2+ resonance energy transfer). We show that ACCuRET measures absolute distances and distance changes with high precision and accuracy using maltose binding protein as a benchmark. Using cell unroofing, we show that ACCuRET can accurately measure rearrangements of proteins in native membranes. Finally, we implement a computational method for correcting the measured distances for the distance distributions observed in proteins. ACCuRET thus provides a flexible, powerful method for measuring conformational dynamics in both soluble proteins and membrane proteins.
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Affiliation(s)
- Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Mika Munari
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
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12
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Wong ZC, Fan WY, Chwee TS. Computational modelling of singlet excitation energy transfer: a DFT/TD-DFT study of the ground and excited state properties of a syn bimane dimer system using non-empirically tuned range-separated functionals. NEW J CHEM 2018. [DOI: 10.1039/c8nj02920b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Range-tuned DFT/TD-DFT improves predicted properties for the sequence of events leading to excitation energy transfer (EET) in bimanes.
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Affiliation(s)
- Z. C. Wong
- Institute of High Performance Computing
- Agency for Science, Technology and Research (A*STAR)
- Singapore
- NUS Graduate School for Integrative Sciences and Engineering
- National University of Singapore
| | - W. Y. Fan
- Department of Chemistry
- National University of Singapore
- Singapore
| | - T. S. Chwee
- Institute of High Performance Computing
- Agency for Science, Technology and Research (A*STAR)
- Singapore
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13
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Skjold-Jørgensen J, Vind J, Svendsen A, Bjerrum MJ. Understanding the activation mechanism ofThermomyces lanuginosuslipase using rational design and tryptophan-induced fluorescence quenching. EUR J LIPID SCI TECH 2016. [DOI: 10.1002/ejlt.201600059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
| | | | | | - Morten J. Bjerrum
- Department of Chemistry; University of Copenhagen; Copenhagen Denmark
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14
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Transition metal ion FRET uncovers K + regulation of a neurotransmitter/sodium symporter. Nat Commun 2016; 7:12755. [PMID: 27678200 PMCID: PMC5052704 DOI: 10.1038/ncomms12755] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/29/2016] [Indexed: 01/14/2023] Open
Abstract
Neurotransmitter/sodium symporters (NSSs) are responsible for Na+-dependent reuptake of neurotransmitters and represent key targets for antidepressants and psychostimulants. LeuT, a prokaryotic NSS protein, constitutes a primary structural model for these transporters. Here we show that K+ inhibits Na+-dependent binding of substrate to LeuT, promotes an outward-closed/inward-facing conformation of the transporter and increases uptake. To assess K+-induced conformational dynamics we measured fluorescence resonance energy transfer (FRET) between fluorescein site-specifically attached to inserted cysteines and Ni2+ bound to engineered di-histidine motifs (transition metal ion FRET). The measurements supported K+-induced closure of the transporter to the outside, which was counteracted by Na+ and substrate. Promoting an outward-open conformation of LeuT by mutation abolished the K+-effect. The K+-effect depended on an intact Na1 site and mutating the Na2 site potentiated K+ binding by facilitating transition to the inward-facing state. The data reveal an unrecognized ability of K+ to regulate the LeuT transport cycle. The neurotransmitter transporter SERT counter transport K+ to transport serotonin. Here the authors show that the activity of the prokaryotic orthologue LeuT is also modulated by this cation, suggesting a general regulatory role for K+ on neutrotrasmitter:sodium symporters function.
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15
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Aman TK, Gordon SE, Zagotta WN. Regulation of CNGA1 Channel Gating by Interactions with the Membrane. J Biol Chem 2016; 291:9939-47. [PMID: 26969165 DOI: 10.1074/jbc.m116.723932] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 11/06/2022] Open
Abstract
Cyclic nucleotide-gated (CNG) channels are expressed in rod photoreceptors and open in response to direct binding of cyclic nucleotides. We have previously shown that potentiation of CNGA1 channels by transition metals requires a histidine in the A' helix following the S6 transmembrane segment. Here, we used transition metal ion FRET and patch clamp fluorometry with a fluorescent, noncanonical amino acid (3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap)) to show that the potentiating transition metal Co(2+) binds in or near the A' helix. Adding high-affinity metal-binding sites to the membrane (stearoyl-nitrilotriacetic acid (C18-NTA)) increased potentiation for low Co(2+) concentrations, indicating that the membrane can coordinate metal ions with the A' helix. These results suggest that restraining the A' helix to the plasma membrane potentiates CNGA1 channel opening. Similar interactions between the A' helix and the plasma membrane may underlie regulation of structurally related hyperpolarization-activated cyclic nucleotide-gated (HCN) and voltage-gated potassium subfamily H (KCNH) channels by plasma membrane components.
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Affiliation(s)
- Teresa K Aman
- From the Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - Sharona E Gordon
- From the Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
| | - William N Zagotta
- From the Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195
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16
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Hershey DM, Ren X, Melnyk RA, Browne PJ, Ozyamak E, Jones SR, Chang MCY, Hurley JH, Komeili A. MamO Is a Repurposed Serine Protease that Promotes Magnetite Biomineralization through Direct Transition Metal Binding in Magnetotactic Bacteria. PLoS Biol 2016; 14:e1002402. [PMID: 26981620 PMCID: PMC4794232 DOI: 10.1371/journal.pbio.1002402] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/10/2016] [Indexed: 11/19/2022] Open
Abstract
Many living organisms transform inorganic atoms into highly ordered crystalline materials. An elegant example of such biomineralization processes is the production of nano-scale magnetic crystals in magnetotactic bacteria. Previous studies implicated the involvement of two putative serine proteases, MamE and MamO, during the early stages of magnetite formation in Magnetospirillum magneticum AMB-1. Here, using genetic analysis and X-ray crystallography, we show that MamO has a degenerate active site, rendering it incapable of protease activity. Instead, MamO promotes magnetosome formation through two genetically distinct, noncatalytic activities: activation of MamE-dependent proteolysis of biomineralization factors and direct binding to transition metal ions. By solving the structure of the protease domain bound to a metal ion, we identify a surface-exposed di-histidine motif in MamO that contributes to metal binding and show that it is required to initiate biomineralization in vivo. Finally, we find that pseudoproteases are widespread in magnetotactic bacteria and that they have evolved independently in three separate taxa. Our results highlight the versatility of protein scaffolds in accommodating new biochemical activities and provide unprecedented insight into the earliest stages of biomineralization.
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Affiliation(s)
- David M. Hershey
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Xuefeng Ren
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
| | - Ryan A. Melnyk
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Patrick J. Browne
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Ertan Ozyamak
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Stephanie R. Jones
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - Michelle C. Y. Chang
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemistry, University of California, Berkeley, California, United States of America
| | - James H. Hurley
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Department of Molecular and Cellular Biology, University of California, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, United States of America
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17
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Trappl K, Joseph S. Ribosome Induces a Closed to Open Conformational Change in Release Factor 1. J Mol Biol 2016; 428:1333-1344. [PMID: 26827724 DOI: 10.1016/j.jmb.2016.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 01/15/2016] [Accepted: 01/22/2016] [Indexed: 11/19/2022]
Abstract
Bacterial translation termination is triggered when a stop codon arrives at the ribosomal A site. Stop codons are recognized by class I release factors (RF1 and RF2 in Escherichia coli), which bind to the ribosome and catalyze the release of the newly synthesized protein. Crystal structures showed that RF1 and RF2 are in an open conformation when bound to the ribosome but are in a closed conformation when not bound to the ribosome. It is not clear whether only the open form of RF1 and RF2 binds to the ribosome. Alternatively, the closed form of RF1 and RF2 may bind to the ribosome and undergo a conformational change to the open state upon binding. We used transition metal ion fluorescence resonance energy transfer experiments to monitor precisely the conformation of RF1 in the absence and presence of the ribosome. Our results indicate that RF1 undergoes a large conformational change from a closed to an open form upon binding to the ribosome. Our results are consistent with the mechanism, in which high termination fidelity is achieved by linking stop codon recognition by RF1 to the change in conformation from closed to open state.
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Affiliation(s)
- Krista Trappl
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA.
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18
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Gordon SE, Senning EN, Aman TK, Zagotta WN. Transition metal ion FRET to measure short-range distances at the intracellular surface of the plasma membrane. ACTA ACUST UNITED AC 2016; 147:189-200. [PMID: 26755772 PMCID: PMC4727948 DOI: 10.1085/jgp.201511530] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/21/2015] [Indexed: 11/20/2022]
Abstract
A novel method is presented to measure short distances in cell plasma membranes using transition metal ion FRET with metal ions bound to introduced sites in the membrane. Biological membranes are complex assemblies of lipids and proteins that serve as platforms for cell signaling. We have developed a novel method for measuring the structure and dynamics of the membrane based on fluorescence resonance energy transfer (FRET). The method marries four technologies: (1) unroofing cells to isolate and access the cytoplasmic leaflet of the plasma membrane; (2) patch-clamp fluorometry (PCF) to measure currents and fluorescence simultaneously from a membrane patch; (3) a synthetic lipid with a metal-chelating head group to decorate the membrane with metal-binding sites; and (4) transition metal ion FRET (tmFRET) to measure short distances between a fluorescent probe and a transition metal ion on the membrane. We applied this method to measure the density and affinity of native and introduced metal-binding sites in the membrane. These experiments pave the way for measuring structural rearrangements of membrane proteins relative to the membrane.
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Affiliation(s)
- Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Eric N Senning
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Teresa K Aman
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
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19
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Zagotta WN, Gordon MT, Senning EN, Munari MA, Gordon SE. Measuring distances between TRPV1 and the plasma membrane using a noncanonical amino acid and transition metal ion FRET. ACTA ACUST UNITED AC 2016; 147:201-16. [PMID: 26755770 PMCID: PMC4727949 DOI: 10.1085/jgp.201511531] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/17/2015] [Indexed: 12/14/2022]
Abstract
Transition metal ion FRET between a noncanonical fluorescent amino acid incorporated into TRPV1 and metal ions bound to the cell plasma can be used to measure distances and dynamics between cytosolic domains of proteins and the membrane. Despite recent advances, the structure and dynamics of membrane proteins in cell membranes remain elusive. We implemented transition metal ion fluorescence resonance energy transfer (tmFRET) to measure distances between sites on the N-terminal ankyrin repeat domains (ARDs) of the pain-transducing ion channel TRPV1 and the intracellular surface of the plasma membrane. To preserve the native context, we used unroofed cells, and to specifically label sites in TRPV1, we incorporated a fluorescent, noncanonical amino acid, L-ANAP. A metal chelating lipid was used to decorate the plasma membrane with high-density/high-affinity metal-binding sites. The fluorescence resonance energy transfer (FRET) efficiencies between L-ANAP in TRPV1 and Co2+ bound to the plasma membrane were consistent with the arrangement of the ARDs in recent cryoelectron microscopy structures of TRPV1. No change in tmFRET was observed with the TRPV1 agonist capsaicin. These results demonstrate the power of tmFRET for measuring structure and rearrangements of membrane proteins relative to the cell membrane.
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Affiliation(s)
- William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Moshe T Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Eric N Senning
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Mika A Munari
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
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20
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Wong ZC, Fan WY, Chwee TS, Sullivan MB. Modelling fluorescence lifetimes with TD-DFT: a case study with syn-bimanes. RSC Adv 2016. [DOI: 10.1039/c6ra11495d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Syn-bimanes are a class of fluorophores that are widely used for labelling thiol containing biological systems. We used TD-DFT to study their absorption, emission, solvatochromism, and fluorescence lifetimes.
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Affiliation(s)
- Z. C. Wong
- Institute of High Performance Computing
- Agency for Science
- Technology and Research (A*STAR)
- Singapore
- NUS Graduate School for Integrative Sciences and Engineering
| | - W. Y. Fan
- Department of Chemistry
- National University of Singapore
- Singapore
| | - T. S. Chwee
- Institute of High Performance Computing
- Agency for Science
- Technology and Research (A*STAR)
- Singapore
| | - M. B. Sullivan
- Institute of High Performance Computing
- Agency for Science
- Technology and Research (A*STAR)
- Singapore
- Department of Chemistry
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21
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Yu X, Strub MP, Barnard TJ, Noinaj N, Piszczek G, Buchanan SK, Taraska JW. An engineered palette of metal ion quenchable fluorescent proteins. PLoS One 2014; 9:e95808. [PMID: 24752441 PMCID: PMC3994163 DOI: 10.1371/journal.pone.0095808] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/31/2014] [Indexed: 12/17/2022] Open
Abstract
Many fluorescent proteins have been created to act as genetically encoded biosensors. With these sensors, changes in fluorescence report on chemical states in living cells. Transition metal ions such as copper, nickel, and zinc are crucial in many physiological and pathophysiological pathways. Here, we engineered a spectral series of optimized transition metal ion-binding fluorescent proteins that respond to metals with large changes in fluorescence intensity. These proteins can act as metal biosensors or imaging probes whose fluorescence can be tuned by metals. Each protein is uniquely modulated by four different metals (Cu2+, Ni2+, Co2+, and Zn2+). Crystallography revealed the geometry and location of metal binding to the engineered sites. When attached to the extracellular terminal of a membrane protein VAMP2, dimeric pairs of the sensors could be used in cells as ratiometric probes for transition metal ions. Thus, these engineered fluorescent proteins act as sensitive transition metal ion-responsive genetically encoded probes that span the visible spectrum.
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Affiliation(s)
- Xiaozhen Yu
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marie-Paule Strub
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Travis J. Barnard
- Laboratory of Molecular Biology, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicholas Noinaj
- Laboratory of Molecular Biology, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Grzegorz Piszczek
- Laboratory of Biochemistry, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Justin W. Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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22
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Wu X, Subramaniam S, Case DA, Wu KW, Brooks BR. Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps. J Struct Biol 2013; 183:429-440. [PMID: 23876978 DOI: 10.1016/j.jsb.2013.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 07/11/2013] [Accepted: 07/12/2013] [Indexed: 11/30/2022]
Abstract
We present a map-restrained self-guided Langevin dynamics (MapSGLD) simulation method for efficient targeted conformational search. The targeted conformational search represents simulations under restraints defined by experimental observations and/or by user specified structural requirements. Through map-restraints, this method provides an efficient way to maintain substructures and to set structure targets during conformational searching. With an enhanced conformational searching ability of self-guided Langevin dynamics, this approach is suitable for simulating large-scale conformational changes, such as the formation of macromolecular assemblies and transitions between different conformational states. Using several examples, we illustrate the application of this method in flexible fitting of atomic structures into density maps derived from cryo-electron microscopy.
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Affiliation(s)
- Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
| | - Sriram Subramaniam
- Laboratory of Cell Biology, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - David A Case
- BioMaPS Institute and Dept. of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Katherine W Wu
- Thomas Jefferson High School for Science and Technology, Alexandria, VA 22312, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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23
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Puljung MC, Zagotta WN. A secondary structural transition in the C-helix promotes gating of cyclic nucleotide-regulated ion channels. J Biol Chem 2013; 288:12944-56. [PMID: 23525108 DOI: 10.1074/jbc.m113.464123] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cyclic nucleotide-regulated ion channels bind second messengers like cAMP to a C-terminal domain, consisting of a β-roll, followed by two α-helices (B- and C-helices). We monitored the cAMP-dependent changes in the structure of the C-helix of a C-terminal fragment of HCN2 channels using transition metal ion FRET between fluorophores on the C-helix and metal ions bound between histidine pairs on the same helix. cAMP induced a change in the dimensions of the C-helix and an increase in the metal binding affinity of the histidine pair. cAMP also caused an increase in the distance between a fluorophore on the C-helix and metal ions bound to the B-helix. Stabilizing the C-helix of intact CNGA1 channels by metal binding to a pair of histidines promoted channel opening. These data suggest that ordering of the C-helix is part of the gating conformational change in cyclic nucleotide-regulated channels.
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Affiliation(s)
- Michael C Puljung
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195-7290, USA
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