1
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Abdullin D, Rauh Corro P, Hett T, Schiemann O. PDSFit: PDS data analysis in the presence of orientation selectivity, g-anisotropy, and exchange coupling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:37-60. [PMID: 38130168 DOI: 10.1002/mrc.5415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS), encompassing techniques such as pulsed electron-electron double resonance (PELDOR or DEER) and relaxation-induced dipolar modulation enhancement (RIDME), is a valuable method in structural biology and materials science for obtaining nanometer-scale distance distributions between electron spin centers. An important aspect of PDS is the extraction of distance distributions from the measured time traces. Most software used for this PDS data analysis relies on simplifying assumptions, such as assuming isotropic g-factors of ~2 and neglecting orientation selectivity and exchange coupling. Here, the program PDSFit is introduced, which enables the analysis of PELDOR and RIDME time traces with or without orientation selectivity. It can be applied to spin systems consisting of up to two spin centers with anisotropic g-factors and to spin systems with exchange coupling. It employs a model-based fitting of the time traces using parametrized distance and angular distributions, and parametrized PDS background functions. The fitting procedure is followed by an error analysis for the optimized parameters of the distributions and backgrounds. Using five different experimental data sets published previously, the performance of PDSFit is tested and found to provide reliable solutions.
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Affiliation(s)
- Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Pablo Rauh Corro
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Tobias Hett
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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2
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Scheyer MW, Campbell C, William PL, Hussain M, Begum A, Fonseca SE, Asare IK, Dabney P, Dabney-Smith C, Lorigan GA, Sahu ID. Electron paramagnetic resonance spectroscopic characterization of the human KCNE3 protein in lipodisq nanoparticles for structural dynamics of membrane proteins. Biophys Chem 2023; 301:107080. [PMID: 37531799 DOI: 10.1016/j.bpc.2023.107080] [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: 05/25/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
One of the major challenges in solubilization of membrane proteins is to find the optimal physiological environment for their biophysical studies. EPR spectroscopy is a powerful biophysical technique for studying the structural and dynamic properties of macromolecules. However, the challenges in the membrane protein sample preparation and flexible motion of the spin label limit the utilization of EPR spectroscopy to a majority of membrane protein systems in a physiological membrane-bound state. Recently, lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have emerged as a membrane mimetic system for investigating the structural studies of membrane proteins. However, its detail characterization for membrane protein studies is still poorly understood. Recently, we characterized the potassium channel membrane protein KCNQ1 voltage sensing domain (KCNQ1-VSD) and KCNE1 reconstituted into lipodisq nanoparticles using EPR spectroscopy. In this study, the potassium channel accessory protein KCNE3 containing flexible N- and C-termini was encapsulated into proteoliposomes and lipodisq nanoparticles and characterized for studying its structural and dynamic properties using nitroxide based site-directed spin labeling EPR spectroscopy. CW-EPR lineshape analysis data indicated an increase in spectral line broadenings with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated an enhanced quality of distance measurements with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles, when compared to proteoliposomes. These results agree with the solution NMR structural structure of the KCNE3 and EPR studies of other membrane proteins in lipodisq nanoparticles. This study along with our earlier studies will provide the reference characterization data that will provide benefit to the membrane protein researchers for studying structural dynamics of challenging membrane proteins.
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Affiliation(s)
- Matthew W Scheyer
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Conner Campbell
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Patrick L William
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Mustakim Hussain
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Afsana Begum
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | | | - Isaac K Asare
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Peyton Dabney
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
| | - Carole Dabney-Smith
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Indra D Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
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3
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Casto J, Bogetti X, Hunter HR, Hasanbasri Z, Saxena S. "Store-bought is fine": Sensitivity considerations using shaped pulses for DEER measurements on Cu(II) labels. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 349:107413. [PMID: 36867974 DOI: 10.1016/j.jmr.2023.107413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/27/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
The narrow excitation bandwidth of monochromic pulses is a sensitivity limitation for pulsed dipolar spectroscopy on Cu(II)-based measurements. In response, frequency-swept pulses with large excitation bandwidths have been adopted to probe a greater range of the EPR spectrum. However, much of the work utilizing frequency-swept pulses in Cu(II) distance measurements has been carried out on home-built spectrometers and equipment. Herein, we carry out systematic Cu(II) based distance measurements to demonstrate the capability of chirp pulses on commercial instrumentation. More importantly we delineate sensitivity considerations under acquisition schemes that are necessary for robust distance measurements using Cu(II) labels for proteins. We show that a 200 MHz sweeping bandwidth chirp pulse can improve the sensitivity of long-range distance measurements by factors of three to four. The sensitivity of short-range distances only increases slightly due to special considerations for the chirp pulse duration relative to the period length of the modulated dipolar signal. Enhancements in sensitivity also dramatically reduce measurement collection times enabling rapid collection of orientationally averaged Cu(II) distance measurements in under two hours.
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Affiliation(s)
- Joshua Casto
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Hannah R Hunter
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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4
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Ackermann K, Khazaipoul S, Wort JL, Sobczak AIS, Mkami HE, Stewart AJ, Bode BE. Investigating Native Metal Ion Binding Sites in Mammalian Histidine-Rich Glycoprotein. J Am Chem Soc 2023; 145:8064-8072. [PMID: 37001144 PMCID: PMC10103162 DOI: 10.1021/jacs.3c00587] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Mammalian histidine-rich glycoprotein (HRG) is a highly versatile and abundant blood plasma glycoprotein with a diverse range of ligands that is involved in regulating many essential biological processes, including coagulation, cell adhesion, and angiogenesis. Despite its biomedical importance, structural information on the multi-domain protein is sparse, not least due to intrinsically disordered regions that elude high-resolution structural characterization. Binding of divalent metal ions, particularly ZnII, to multiple sites within the HRG protein is of critical functional importance and exerts a regulatory role. However, characterization of the ZnII binding sites of HRG is a challenge; their number and composition as well as their affinities and stoichiometries of binding are currently not fully understood. In this study, we explored modern electron paramagnetic resonance (EPR) spectroscopy methods supported by protein secondary and tertiary structure prediction to assemble a holistic picture of native HRG and its interaction with metal ions. To the best of our knowledge, this is the first time that this suite of EPR techniques has been applied to count and characterize endogenous metal ion binding sites in a native mammalian protein of unknown structure.
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Affiliation(s)
- Katrin Ackermann
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
| | - Siavash Khazaipoul
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, Scotland
| | - Joshua L. Wort
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
| | - Amélie I. S. Sobczak
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, Scotland
| | - Hassane El Mkami
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, Scotland
| | - Alan J. Stewart
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, Scotland
| | - Bela E. Bode
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland
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5
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Fábregas-Ibáñez L, Mertens V, Ritsch I, von Hagens T, Stoll S, Jeschke G. Dipolar pathways in multi-spin and multi-dimensional dipolar EPR spectroscopy. Phys Chem Chem Phys 2022; 24:22645-22660. [PMID: 36106486 PMCID: PMC9516884 DOI: 10.1039/d2cp03048a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022]
Abstract
Dipolar electron paramagnetic resonance (EPR) experiments, such as double electron-electron resonance (DEER), measure distributions of nanometer-scale distances between unpaired electrons, which provide valuable information for structural characterization of proteins and other macromolecular systems. We present an extension to our previously published general model based on dipolar pathways valid for multi-dimensional dipolar EPR experiments with more than two spin-1/2 labels. We examine the 4-pulse DEER and TRIER experiments in terms of dipolar pathways and show experimental results confirming the theoretical predictions. This extension to the dipolar pathways model allows the analysis of previously challenging datasets and the extraction of multivariate distance distributions.
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Affiliation(s)
- Luis Fábregas-Ibáñez
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
| | - Valerie Mertens
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
| | - Irina Ritsch
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
| | - Tona von Hagens
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, Washington, USA
| | - Gunnar Jeschke
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
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6
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Peter MF, Gebhardt C, Mächtel R, Muñoz GGM, Glaenzer J, Narducci A, Thomas GH, Cordes T, Hagelueken G. Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET. Nat Commun 2022; 13:4396. [PMID: 35906222 PMCID: PMC9338047 DOI: 10.1038/s41467-022-31945-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are frequently used to determine conformational changes, structural heterogeneity, and inter probe distances in biological macromolecules. They provide qualitative information that facilitates mechanistic understanding of biochemical processes and quantitative data for structural modelling. To provide a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET, we use a library of double cysteine variants of four proteins that undergo large-scale conformational changes upon ligand binding. With either method, we use established standard experimental protocols and data analysis routines to determine inter-probe distances in the presence and absence of ligands. The results are compared to distance predictions from structural models. Despite an overall satisfying and similar distance accuracy, some inconsistencies are identified, which we attribute to the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. This large-scale cross-validation of PELDOR/DEER and smFRET highlights the strengths, weaknesses, and synergies of these two important and complementary tools in integrative structural biology.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gabriel G Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Janin Glaenzer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, UK
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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7
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Hett T, Schiemann O. PELDOR Measurements on Nitroxide-Labeled Oligonucleotides. Methods Mol Biol 2022; 2439:241-274. [PMID: 35226326 DOI: 10.1007/978-1-0716-2047-2_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: 06/14/2023]
Abstract
In the past decades, pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) has emerged as a powerful tool in biophysical chemistry to study the structure, dynamics, and function of biomolecules like oligonucleotides and proteins. Structural information is obtained from PDS methods in form of a distribution of distances between spin centers. Such spin centers can either be intrinsically present paramagnetic metal ions and organic radicals or may be attached to the biomolecule by means of site-directed spin labeling. The most common PDS experiment for probing interspin distances in the nanometer range is pulsed electron-electron double resonance (PELDOR or DEER). In the protocol presented here, we provide a step-by-step workflow on how to set up a PELDOR experiment on a commercially available pulsed EPR spectrometer, outline the data analysis, and highlight potential pitfalls. We suggest PELDOR measurements on nitroxide-labeled oligonucleotides to study the structure of either RNA-cleaving DNAzymes in complex with their RNA targets or modified DNAzymes with different functions and targets, in which deoxynucleotides are substituted by nitroxide-labeled nucleotides.
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Affiliation(s)
- Tobias Hett
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany.
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8
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Schiemann O, Heubach CA, Abdullin D, Ackermann K, Azarkh M, Bagryanskaya EG, Drescher M, Endeward B, Freed JH, Galazzo L, Goldfarb D, Hett T, Esteban Hofer L, Fábregas Ibáñez L, Hustedt EJ, Kucher S, Kuprov I, Lovett JE, Meyer A, Ruthstein S, Saxena S, Stoll S, Timmel CR, Di Valentin M, Mchaourab HS, Prisner TF, Bode BE, Bordignon E, Bennati M, Jeschke G. Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules. J Am Chem Soc 2021; 143:17875-17890. [PMID: 34664948 PMCID: PMC11253894 DOI: 10.1021/jacs.1c07371] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Distance distribution information obtained by pulsed dipolar EPR spectroscopy provides an important contribution to many studies in structural biology. Increasingly, such information is used in integrative structural modeling, where it delivers unique restraints on the width of conformational ensembles. In order to ensure reliability of the structural models and of biological conclusions, we herein define quality standards for sample preparation and characterization, for measurements of distributed dipole-dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results. These guidelines are substantiated by a multi-laboratory benchmark study and by analysis of data sets with known distance distribution ground truth. The study and the guidelines focus on proteins labeled with nitroxides and on double electron-electron resonance (DEER aka PELDOR) measurements and provide suggestions on how to proceed analogously in other cases.
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Affiliation(s)
- Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Caspar A Heubach
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, U.K
| | - Mykhailo Azarkh
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Lavrentieva aven 9, 630090 Novosibirsk, Russia
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, and ACERT, National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tobias Hett
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Laura Esteban Hofer
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Luis Fábregas Ibáñez
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Eric J Hustedt
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Svetlana Kucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, U.K
| | - Janet Eleanor Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K
| | - Andreas Meyer
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sharon Ruthstein
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Christiane R Timmel
- Department of Chemistry, Centre for Advanced Electron Spin Resonance, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany
| | - Bela Ernest Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, U.K
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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9
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Probing Structural Dynamics of Membrane Proteins Using Electron Paramagnetic Resonance Spectroscopic Techniques. BIOPHYSICA 2021. [DOI: 10.3390/biophysica1020009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Membrane proteins are essential for the survival of living organisms. They are involved in important biological functions including transportation of ions and molecules across the cell membrane and triggering the signaling pathways. They are targets of more than half of the modern medical drugs. Despite their biological significance, information about the structural dynamics of membrane proteins is lagging when compared to that of globular proteins. The major challenges with these systems are low expression yields and lack of appropriate solubilizing medium required for biophysical techniques. Electron paramagnetic resonance (EPR) spectroscopy coupled with site directed spin labeling (SDSL) is a rapidly growing powerful biophysical technique that can be used to obtain pertinent structural and dynamic information on membrane proteins. In this brief review, we will focus on the overview of the widely used EPR approaches and their emerging applications to answer structural and conformational dynamics related questions on important membrane protein systems.
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10
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Russell H, Stewart R, Prior C, Oganesyan VS, Gaule TG, Lovett JE. DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis. APPLIED MAGNETIC RESONANCE 2021; 52:995-1015. [PMID: 34720439 PMCID: PMC8550341 DOI: 10.1007/s00723-021-01321-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 03/10/2021] [Indexed: 06/13/2023]
Abstract
In the study of biological structures, pulse dipolar spectroscopy (PDS) is used to elucidate spin-spin distances at nanometre-scale by measuring dipole-dipole interactions between paramagnetic centres. The PDS methods of Double Electron Electron Resonance (DEER) and Relaxation Induced Dipolar Modulation Enhancement (RIDME) are employed, and their results compared, for the measurement of the dipolar coupling between nitroxide spin labels and copper-II (Cu(II)) paramagnetic centres within the copper amine oxidase from Arthrobacter globiformis (AGAO). The distance distribution results obtained indicate that two distinct distances can be measured, with the longer of these at c.a. 5 nm. Conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed. Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00723-021-01321-6.
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Affiliation(s)
- Hannah Russell
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
| | - Rachel Stewart
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
| | | | | | - Thembaninkosi G. Gaule
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Janet E. Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
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11
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Gamble Jarvi A, Bogetti X, Singewald K, Ghosh S, Saxena S. Going the dHis-tance: Site-Directed Cu 2+ Labeling of Proteins and Nucleic Acids. Acc Chem Res 2021; 54:1481-1491. [PMID: 33476119 DOI: 10.1021/acs.accounts.0c00761] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this Account, we showcase site-directed Cu2+ labeling in proteins and DNA, which has opened new avenues for the measurement of the structure and dynamics of biomolecules using electron paramagnetic resonance (EPR) spectroscopy. In proteins, the spin label is assembled in situ from natural amino acid residues and a metal complex and requires no post-expression synthetic modification or purification procedures. The labeling scheme exploits a double histidine (dHis) motif, which utilizes endogenous or site-specifically mutated histidine residues to coordinate a Cu2+ complex. Pulsed EPR measurements on such Cu2+-labeled proteins potentially yield distance distributions that are up to 5 times narrower than the common protein spin label-the approach, thus, overcomes the inherent limitation of the current technology, which relies on a spin label with a highly flexible side chain. This labeling scheme provides a straightforward method that elucidates biophysical information that is costly, complicated, or simply inaccessible by traditional EPR labels. Examples include the direct measurement of protein backbone dynamics at β-sheet sites, which are largely inaccessible through traditional spin labels, and rigid Cu2+-Cu2+ distance measurements that enable higher precision in the analysis of protein conformations, conformational changes, interactions with other biomolecules, and the relative orientations of two labeled protein subunits. Likewise, a Cu2+ label has been developed for use in DNA, which is small, is nucleotide independent, and is positioned within the DNA helix. The placement of the Cu2+ label directly reports on the biologically relevant backbone distance. Additionally, for both of these labeling techniques, we have developed models for interpretation of the EPR distance information, primarily utilizing molecular dynamics (MD) simulations. Initial results using force fields developed for both protein and DNA labels have agreed with experimental results, which has been a major bottleneck for traditional spin labels. Looking ahead, we anticipate new combinations of MD and EPR to further our understanding of protein and DNA conformational changes, as well as working synergistically to investigate protein-DNA interactions.
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Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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12
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Tkach I, Diederichsen U, Bennati M. Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:143-157. [PMID: 33640998 PMCID: PMC8071797 DOI: 10.1007/s00249-021-01508-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 12/01/2022]
Abstract
Electron paramagnetic resonance (EPR)-based pulsed dipolar spectroscopy measures the dipolar interaction between paramagnetic centers that are separated by distances in the range of about 1.5-10 nm. Its application to transmembrane (TM) peptides in combination with modern spin labelling techniques provides a valuable tool to study peptide-to-lipid interactions at a molecular level, which permits access to key parameters characterizing the structural adaptation of model peptides incorporated in natural membranes. In this mini-review, we summarize our approach for distance and orientation measurements in lipid environment using novel semi-rigid TOPP [4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-L-phenylglycine] labels specifically designed for incorporation in TM peptides. TOPP labels can report single peak distance distributions with sub-angstrom resolution, thus offering new capabilities for a variety of TM peptide investigations, such as monitoring of various helix conformations or measuring of tilt angles in membranes.
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Affiliation(s)
- Igor Tkach
- Max Planck Institute for Biophysical Chemistry, RG Electron-Spin Resonance Spectroscopy, 37077, Göttingen, Germany.
| | - Ulf Diederichsen
- Department of Organic and Biomolecular Chemistry, University of Göttingen, 37077, Göttingen, Germany
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, RG Electron-Spin Resonance Spectroscopy, 37077, Göttingen, Germany
- Department of Organic and Biomolecular Chemistry, University of Göttingen, 37077, Göttingen, Germany
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13
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PELDOR/DEER: An Electron Paramagnetic Resonance Method to Study Membrane Proteins in Lipid Bilayers. Methods Mol Biol 2021. [PMID: 33582999 DOI: 10.1007/978-1-0716-0724-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Every membrane protein is involved in close interactions with the lipid environment of cellular membranes. The annular lipids, that are in direct contact with the polypeptide, can in principle be seen as an integral part of its structure, akin to the first hydration shell of soluble proteins. It is therefore desirable to investigate the structure of membrane proteins and especially their conformational flexibility under conditions that are as close as possible to their native state. This can be achieved by reconstituting the protein into proteoliposomes, nanodiscs, or bicelles. In recent years, PELDOR/DEER spectroscopy has proved to be a very useful method to study the structure and function of membrane proteins in such artificial membrane environments. The technique complements both X-ray crystallography and cryo-EM and can be used in combination with virtually any artificial membrane environment and under certain circumstances even in native membranes. Of the above-mentioned membrane mimics, bicelles are currently the least often used for PELDOR studies, although they offer some advantages, especially their ease of use. Here, we provide a step-by-step protocol for studying a bicelle reconstituted membrane protein with PELDOR/DEER spectroscopy.
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14
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Bretschneider M, Spindler PE, Rogozhnikova OY, Trukhin DV, Endeward B, Kuzhelev AA, Bagryanskaya E, Tormyshev VM, Prisner TF. Multiquantum Counting of Trityl Radicals. J Phys Chem Lett 2020; 11:6286-6290. [PMID: 32667797 DOI: 10.1021/acs.jpclett.0c01615] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We demonstrate a series of multitrityl radical compounds where accurate spin-counting by pulsed electron paramagnetic resonance (EPR) can be achieved at X-band (9 GHz) frequencies, even for molecules with very short and flexible linkers. Multiquantum filter experiments, well-known from NMR, were used to count the number of coupled electron spins in these compounds. The six pulse double quantum filter sequence used in EPR for distance determinations in biradicals was used. Precise phase settings to separate higher quantum coherences were achieved by an arbitrary waveform generator. The trityl radicals have narrow spectral width so that homogeneous excitation of all spins by the pulses is possible. The transversal relaxation times of higher quantum coherences of trityl radicals are sufficiently long to allow their detection. Our results on model compounds show the potential of this approach to determine oligomeric states in protein complexes in their native environment using functionalized trityl spin labels.
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Affiliation(s)
- Matthias Bretschneider
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60323 Frankfurt, Germany
| | - Phillip E Spindler
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60323 Frankfurt, Germany
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60323 Frankfurt, Germany
| | - Andrey A Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Elena Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60323 Frankfurt, Germany
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15
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Sahu ID, Lorigan GA. Electron Paramagnetic Resonance as a Tool for Studying Membrane Proteins. Biomolecules 2020; 10:E763. [PMID: 32414134 PMCID: PMC7278021 DOI: 10.3390/biom10050763] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins possess a variety of functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is extremely difficult to probe the structure and dynamic properties of membrane proteins using traditional biophysical techniques, particularly in their native environments. Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a very powerful and rapidly growing biophysical technique to study pertinent structural and dynamic properties of membrane proteins with no size restrictions. In this review, we will briefly discuss the most commonly used EPR techniques and their recent applications for answering structure and conformational dynamics related questions of important membrane protein systems.
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Affiliation(s)
- Indra D. Sahu
- Natural Science Division, Campbellsville University, Campbellsville, KY 42718, USA
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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16
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Radu V, Price JC, Levett SJ, Narayanasamy KK, Bateman-Price TD, Wilson PB, Mather ML. Dynamic Quantum Sensing of Paramagnetic Species Using Nitrogen-Vacancy Centers in Diamond. ACS Sens 2020; 5:703-710. [PMID: 31867948 PMCID: PMC7106109 DOI: 10.1021/acssensors.9b01903] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022]
Abstract
Naturally occurring paramagnetic species (PS), such as free radicals and paramagnetic metalloproteins, play an essential role in a multitude of critical physiological processes including metabolism, cell signaling, and immune response. These highly dynamic species can also act as intrinsic biomarkers for a variety of disease states, while synthetic paramagnetic probes targeted to specific sites on biomolecules enable the study of functional information such as tissue oxygenation and redox status in living systems. The work presented herein describes a new sensing method that exploits the spin-dependent emission of photoluminescence (PL) from an ensemble of nitrogen-vacancy centers in diamond for rapid, nondestructive detection of PS in living systems. Uniquely this approach involves simple measurement protocols that assess PL contrast with and without the application of microwaves. The method is demonstrated to detect concentrations of paramagnetic salts in solution and the widely used magnetic resonance imaging contrast agent gadobutrol with a limit of detection of less than 10 attomol over a 100 μm × 100 μm field of view. Real-time monitoring of changes in the concentration of paramagnetic salts is demonstrated with image exposure times of 20 ms. Further, dynamic tracking of chemical reactions is demonstrated via the conversion of low-spin cyanide-coordinated Fe3+ to hexaaqua Fe3+ under acidic conditions. Finally, the capability to map paramagnetic species in model cells with subcellular resolution is demonstrated using lipid membranes containing gadolinium-labeled phospholipids under ambient conditions in the order of minutes. Overall, this work introduces a new sensing approach for the realization of fast, sensitive imaging of PS in a widefield format that is readily deployable in biomedical settings. Ultimately, this new approach to nitrogen vacancy-based quantum sensing paves the way toward minimally invasive real-time mapping and observation of free radicals in in vitro cellular environments.
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Affiliation(s)
- Valentin Radu
- Optics
and Photonics Research Group, Faculty of Engineering, University Park, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Joshua Colm Price
- Optics
and Photonics Research Group, Faculty of Engineering, University Park, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Simon James Levett
- Optics
and Photonics Research Group, Faculty of Engineering, University Park, University of Nottingham, Nottingham NG7 2RD, U.K.
| | | | - Thomas David Bateman-Price
- Optics
and Photonics Research Group, Faculty of Engineering, University Park, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Philippe Barrie Wilson
- Leicester
School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, U.K.
| | - Melissa Louise Mather
- Optics
and Photonics Research Group, Faculty of Engineering, University Park, University of Nottingham, Nottingham NG7 2RD, U.K.
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17
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Sahu ID, Dixit G, Reynolds WD, Kaplevatsky R, Harding BD, Jaycox CK, McCarrick RM, Lorigan GA. Characterization of the Human KCNQ1 Voltage Sensing Domain (VSD) in Lipodisq Nanoparticles for Electron Paramagnetic Resonance (EPR) Spectroscopic Studies of Membrane Proteins. J Phys Chem B 2020; 124:2331-2342. [PMID: 32130007 DOI: 10.1021/acs.jpcb.9b11506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Membrane proteins are responsible for conducting essential biological functions that are necessary for the survival of living organisms. In spite of their physiological importance, limited structural information is currently available as a result of challenges in applying biophysical techniques for studying these protein systems. Electron paramagnetic resonance (EPR) spectroscopy is a very powerful technique to study the structural and dynamic properties of membrane proteins. However, the application of EPR spectroscopy to membrane proteins in a native membrane-bound state is extremely challenging due to the complexity observed in inhomogeneity sample preparation and the dynamic motion of the spin label. Detergent micelles are very popular membrane mimetics for membrane proteins due to their smaller size and homogeneity, providing high-resolution structure analysis by solution NMR spectroscopy. However, it is important to test whether the protein structure in a micelle environment is the same as that of its membrane-bound state. Lipodisq nanoparticles or styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) have been introduced as a potentially good membrane-mimetic system for structural studies of membrane proteins. Recently, we reported on the EPR characterization of the KCNE1 membrane protein having a single transmembrane incorporated into lipodisq nanoparticles. In this work, lipodisq nanoparticles were used as a membrane mimic system for probing the structural and dynamic properties of the more complicated membrane protein system human KCNQ1 voltage sensing domain (Q1-VSD) having four transmembrane helices using site-directed spin-labeling EPR spectroscopy. Characterization of spin-labeled Q1-VSD incorporated into lipodisq nanoparticles was carried out using CW-EPR spectral line shape analysis and pulsed EPR double-electron electron resonance (DEER) measurements. The CW-EPR spectra indicate an increase in spectral line broadening with the addition of the styrene-maleic acid (SMA) polymer which approaches close to the rigid limit providing a homogeneous stabilization of the protein-lipid complex. Similarly, EPR DEER measurements indicated a superior quality of distance measurement with an increase in the phase memory time (Tm) values upon incorporation of the sample into lipodisq nanoparticles when compared to proteoliposomes. These results are consistent with the solution NMR structural studies on the Q1-VSD. This study will be beneficial for researchers working on investigating the structural and dynamic properties of more complicated membrane protein systems using lipodisq nanoparticles.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States.,Natural Science Division, Campbellsville University, Campbellsville, Kentucky 42718, United States
| | - Gunjan Dixit
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Warren D Reynolds
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Ryan Kaplevatsky
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Benjamin D Harding
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Colleen K Jaycox
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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18
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Heinz M, Erlenbach N, Stelzl LS, Thierolf G, Kamble NR, Sigurdsson ST, Prisner TF, Hummer G. High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Res 2020; 48:924-933. [PMID: 31777925 PMCID: PMC6954412 DOI: 10.1093/nar/gkz1096] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/01/2019] [Accepted: 11/20/2019] [Indexed: 12/25/2022] Open
Abstract
Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.
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Affiliation(s)
- Marcel Heinz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Lukas S Stelzl
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Grace Thierolf
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Nilesh R Kamble
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavk, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavk, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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19
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Abdullin D, Brehm P, Fleck N, Spicher S, Grimme S, Schiemann O. Pulsed EPR Dipolar Spectroscopy on Spin Pairs with one Highly Anisotropic Spin Center: The Low-Spin Fe III Case. Chemistry 2019; 25:14388-14398. [PMID: 31386227 PMCID: PMC6900076 DOI: 10.1002/chem.201902908] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/05/2019] [Indexed: 02/01/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) dipolar spectroscopy (PDS) offers several methods for measuring dipolar coupling constants and thus the distance between electron spin centers. Up to now, PDS measurements have been mostly applied to spin centers whose g-anisotropies are moderate and therefore have a negligible effect on the dipolar coupling constants. In contrast, spin centers with large g-anisotropy yield dipolar coupling constants that depend on the g-values. In this case, the usual methods of extracting distances from the raw PDS data cannot be applied. Here, the effect of the g-anisotropy on PDS data is studied in detail on the example of the low-spin Fe3+ ion. First, this effect is described theoretically, using the work of Bedilo and Maryasov (Appl. Magn. Reson. 2006, 30, 683-702) as a basis. Then, two known Fe3+ /nitroxide compounds and one new Fe3+ /trityl compound were synthesized and PDS measurements were carried out on them using a method called relaxation induced dipolar modulation enhancement (RIDME). Based on the theoretical results, a RIDME data analysis procedure was developed, which facilitated the extraction of the inter-spin distance and the orientation of the inter-spin vector relative to the Fe3+ g-tensor frame from the RIDME data. The accuracy of the determined distances and orientations was confirmed by comparison with MD simulations. This method can thus be applied to the highly relevant class of metalloproteins with, for example, low-spin Fe3+ ions.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Philipp Brehm
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
- Current address: Institute of Inorganic ChemistryUniversity of Bonn53115BonnGermany
| | - Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Sebastian Spicher
- Mulliken Center for Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
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20
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Bondarenko V, Wells MM, Chen Q, Singewald KC, Saxena S, Xu Y, Tang P. 19F Paramagnetic Relaxation-Based NMR for Quaternary Structural Restraints of Ion Channels. ACS Chem Biol 2019; 14:2160-2165. [PMID: 31525026 DOI: 10.1021/acschembio.9b00692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quaternary distance restraints are essential to define the three-dimensional structures of protein assemblies. These distances often fall within a range of 10-18 Å, which challenges the high and low measurement limits of conventional nuclear magnetic resonance (NMR) and double electron-electron resonance electron spin resonance spectroscopies. Here, we report the use of 19F paramagnetic relaxation enhancement (PRE) NMR in combination with 19F/paramagnetic labeling to equivalent sites in different subunits of a protein complex in micelles to determine intersubunit distances. The feasibility of this strategy was evaluated on a pentameric ligand-gated ion channel, for which we found excellent agreement of the 19F PRE NMR results with previous structural information. The study suggests that 19F PRE NMR is a viable tool in extracting distance restraints to define quaternary structures.
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Affiliation(s)
- Vasyl Bondarenko
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Marta M. Wells
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qiang Chen
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin C. Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yan Xu
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pei Tang
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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21
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Leone V, Waclawska I, Kossmann K, Koshy C, Sharma M, Prisner TF, Ziegler C, Endeward B, Forrest LR. Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP. J Gen Physiol 2019; 151:381-394. [PMID: 30728216 PMCID: PMC6400524 DOI: 10.1085/jgp.201812111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 11/26/2018] [Accepted: 01/11/2019] [Indexed: 11/20/2022] Open
Abstract
Mechanistic understanding of dynamic membrane proteins such as transporters, receptors, and channels requires accurate depictions of conformational ensembles, and the manner in which they interchange as a function of environmental factors including substrates, lipids, and inhibitors. Spectroscopic techniques such as electron spin resonance (ESR) pulsed electron-electron double resonance (PELDOR), also known as double electron-electron resonance (DEER), provide a complement to atomistic structures obtained from x-ray crystallography or cryo-EM, since spectroscopic data reflect an ensemble and can be measured in more native solvents, unperturbed by a crystal lattice. However, attempts to interpret DEER data are frequently stymied by discrepancies with the structural data, which may arise due to differences in conditions, the dynamics of the protein, or the flexibility of the attached paramagnetic spin labels. Recently, molecular simulation techniques such as EBMetaD have been developed that create a conformational ensemble matching an experimental distance distribution while applying the minimal possible bias. Moreover, it has been proposed that the work required during an EBMetaD simulation to match an experimentally determined distribution could be used as a metric with which to assign conformational states to a given measurement. Here, we demonstrate the application of this concept for a sodium-coupled transport protein, BetP. Because the probe, protein, and lipid bilayer are all represented in atomic detail, the different contributions to the work, such as the extent of protein backbone movements, can be separated. This work therefore illustrates how ranking simulations based on EBMetaD can help to bridge the gap between structural and biophysical data and thereby enhance our understanding of membrane protein conformational mechanisms.
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Affiliation(s)
- Vanessa Leone
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | | | - Katharina Kossmann
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Regensburg, Germany
| | - Caroline Koshy
- Max Planck Institute for Biophysics, Frankfurt am Main, Germany
| | - Monika Sharma
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Regensburg, Germany
| | - Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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22
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Erlenbach N, Grünewald C, Krstic B, Heckel A, Prisner TF. "End-to-end" stacking of small dsRNA. RNA (NEW YORK, N.Y.) 2019; 25:239-246. [PMID: 30404925 PMCID: PMC6348986 DOI: 10.1261/rna.068130.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/06/2018] [Indexed: 05/08/2023]
Abstract
PELDOR (pulsed electron-electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the "end-to-end" stacking of small double-stranded (ds) RNAs. For this study, the dsRNA molecules were only singly labeled with the spin label TPA to avoid multispin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π-π interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From these data, the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we demonstrate by PELDOR experiments quantitatively.
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Affiliation(s)
- Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Bisera Krstic
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
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23
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Ritsch I, Hintz H, Jeschke G, Godt A, Yulikov M. Improving the accuracy of Cu(ii)–nitroxide RIDME in the presence of orientation correlation in water-soluble Cu(ii)–nitroxide rulers. Phys Chem Chem Phys 2019; 21:9810-9830. [DOI: 10.1039/c8cp06573j] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Detailed analysis of artefacts in the Cu(ii)–nitroxide RIDME experiments, related to orientation averaging, echo-crossing, ESEEM and background-correction is presented.
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Affiliation(s)
- Irina Ritsch
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
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24
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Riederer EA, Focke PJ, Georgieva ER, Akyuz N, Matulef K, Borbat PP, Freed JH, Blanchard SC, Boudker O, Valiyaveetil FI. A facile approach for the in vitro assembly of multimeric membrane transport proteins. eLife 2018; 7:36478. [PMID: 29889023 PMCID: PMC6025958 DOI: 10.7554/elife.36478] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
Membrane proteins such as ion channels and transporters are frequently homomeric. The homomeric nature raises important questions regarding coupling between subunits and complicates the application of techniques such as FRET or DEER spectroscopy. These challenges can be overcome if the subunits of a homomeric protein can be independently modified for functional or spectroscopic studies. Here, we describe a general approach for in vitro assembly that can be used for the generation of heteromeric variants of homomeric membrane proteins. We establish the approach using GltPh, a glutamate transporter homolog that is trimeric in the native state. We use heteromeric GltPh transporters to directly demonstrate the lack of coupling in substrate binding and demonstrate how heteromeric transporters considerably simplify the application of DEER spectroscopy. Further, we demonstrate the general applicability of this approach by carrying out the in vitro assembly of VcINDY, a Na+-coupled succinate transporter and CLC-ec1, a Cl-/H+ antiporter.
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Affiliation(s)
- Erika A Riederer
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
| | - Paul J Focke
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
| | - Elka R Georgieva
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, Unites States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, United States
| | | | - Kimberly Matulef
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, Unites States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, Unites States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, United States
| | | | - Olga Boudker
- Weill Cornell Medicine, New York, United States.,Howard Hughes Medical Institute, Maryland, United States
| | - Francis I Valiyaveetil
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
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25
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Xiao K, Zhao Y, Choi M, Liu H, Blanc A, Qian J, Cahill TJ, Li X, Xiao Y, Clark LJ, Li S. Revealing the architecture of protein complexes by an orthogonal approach combining HDXMS, CXMS, and disulfide trapping. Nat Protoc 2018; 13:1403-1428. [PMID: 29844522 DOI: 10.1038/nprot.2018.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many cellular functions necessitate structural assemblies of two or more associated proteins. The structural characterization of protein complexes using standard methods, such as X-ray crystallography, is challenging. Herein, we describe an orthogonal approach using hydrogen-deuterium-exchange mass spectrometry (HDXMS), cross-linking mass spectrometry (CXMS), and disulfide trapping to map interactions within protein complexes. HDXMS measures changes in solvent accessibility and hydrogen bonding upon complex formation; a decrease in HDX rate could account for newly formed intermolecular or intramolecular interactions. To distinguish between inter- and intramolecular interactions, we use a CXMS method to determine the position of direct interface regions by trapping intermolecular residues in close proximity to various cross-linkers (e.g., disuccinimidyl adipate (DSA)) of different lengths and reactive groups. Both MS-based experiments are performed on high-resolution mass spectrometers (e.g., an Orbitrap Elite hybrid mass spectrometer). The physiological relevance of the interactions identified through HDXMS and CXMS is investigated by transiently co-expressing cysteine mutant pairs, one mutant on each protein at the discovered interfaces, in an appropriate cell line, such as HEK293. Disulfide-trapped protein complexes are formed within cells spontaneously or are facilitated by addition of oxidation reagents such as H2O2 or diamide. Western blotting analysis, in the presence and absence of reducing reagents, is used to determine whether the disulfide bonds are formed in the proposed complex interface in physiologically relevant milieus. The procedure described here requires 1-2 months. We demonstrate this approach using the β2-adrenergic receptor-β-arrestin1 complex as the model system.
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Affiliation(s)
- Kunhong Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Vascular Medicine Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Biomedical Mass Spectrometry Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yang Zhao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Minjung Choi
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Hongda Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adi Blanc
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Jiang Qian
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Thomas J Cahill
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Xue Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Yunfang Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lisa J Clark
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sheng Li
- Department of Chemistry, University of California at San Diego, La Jolla, California, USA
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26
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Sahu ID, Lorigan GA. Site-Directed Spin Labeling EPR for Studying Membrane Proteins. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3248289. [PMID: 29607317 PMCID: PMC5828257 DOI: 10.1155/2018/3248289] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/21/2017] [Indexed: 01/13/2023]
Abstract
Site-directed spin labeling (SDSL) in combination with electron paramagnetic resonance (EPR) spectroscopy is a rapidly expanding powerful biophysical technique to study the structural and dynamic properties of membrane proteins in a native environment. Membrane proteins are responsible for performing important functions in a wide variety of complicated biological systems that are responsible for the survival of living organisms. In this review, a brief introduction of the most popular SDSL EPR techniques and illustrations of recent applications for studying pertinent structural and dynamic properties on membrane proteins will be discussed.
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Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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27
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Affiliation(s)
- Katrin Ackermann
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and EaStCHEM School of Chemistry, University of St Andrews, St Andrews, KY16 9ST, Scotland
| | - Bela E. Bode
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and EaStCHEM School of Chemistry, University of St Andrews, St Andrews, KY16 9ST, Scotland
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28
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Pliotas C. Ion Channel Conformation and Oligomerization Assessment by Site-Directed Spin Labeling and Pulsed-EPR. Methods Enzymol 2017; 594:203-242. [PMID: 28779841 DOI: 10.1016/bs.mie.2017.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mechanosensitive (MS) ion channels are multimeric integral membrane proteins that respond to increased lipid bilayer tension by opening their nonselective pores to release solutes and relieve increased cytoplasmic pressure. These systems undergo major conformational changes during gating and the elucidation of their mechanism requires a deep understanding of the interplay between lipids and proteins. Lipids are responsible for transmitting lateral tension to MS channels and therefore play a key role in obtaining a molecular-detail model for mechanosensation. Site-directed spin labeling combined with electron paramagnetic resonance (EPR) spectroscopy is a powerful spectroscopic tool in the study of proteins. The main bottleneck for its use relates to challenges associated with successful isolation of the protein of interest, introduction of paramagnetic labels on desired sites, and access to specialized instrumentation and expertise. The design of sophisticated experiments, which combine a variety of existing EPR methodologies to address a diversity of specific questions, require knowledge of the limitations and strengths, characteristic of each particular EPR method. This chapter is using the MS ion channels as paradigms and focuses on the application of different EPR techniques to ion channels, in order to investigate oligomerization, conformation, and the effect of lipids on their regulation. The methodology we followed, from the initial strategic selection of mutants and sample preparation, including protein purification, spin labeling, reconstitution into lipid mimics to the complete set-up of the pulsed-EPR experiments, is described in detail.
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29
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Oligomeric Structure of Anabaena Sensory Rhodopsin in a Lipid Bilayer Environment by Combining Solid-State NMR and Long-range DEER Constraints. J Mol Biol 2017; 429:1903-1920. [DOI: 10.1016/j.jmb.2017.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/27/2017] [Accepted: 05/06/2017] [Indexed: 11/22/2022]
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30
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Sahu ID, Zhang R, Dunagan MM, Craig AF, Lorigan GA. Characterization of KCNE1 inside Lipodisq Nanoparticles for EPR Spectroscopic Studies of Membrane Proteins. J Phys Chem B 2017; 121:5312-5321. [DOI: 10.1021/acs.jpcb.7b01705] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Indra D. Sahu
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Rongfu Zhang
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Megan M. Dunagan
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Andrew F. Craig
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Gary A. Lorigan
- Department of Chemistry and
Biochemistry, Miami University, Oxford, Ohio 45056, United States
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31
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Schmidt T, Wälti MA, Baber JL, Hustedt EJ, Clore GM. Long Distance Measurements up to 160 Å in the GroEL Tetradecamer Using Q-Band DEER EPR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609617] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics; National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda MD 20892-0520 USA
| | - Marielle A. Wälti
- Laboratory of Chemical Physics; National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda MD 20892-0520 USA
| | - James L. Baber
- Laboratory of Chemical Physics; National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda MD 20892-0520 USA
| | - Eric J. Hustedt
- Department of Molecular Physiology and Biophysics; Vanderbilt University; Nashville TN 37232 USA
| | - G. Marius Clore
- Laboratory of Chemical Physics; National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda MD 20892-0520 USA
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32
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Schmidt T, Wälti MA, Baber JL, Hustedt EJ, Clore GM. Long Distance Measurements up to 160 Å in the GroEL Tetradecamer Using Q-Band DEER EPR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:15905-15909. [PMID: 27860003 DOI: 10.1002/anie.201609617] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 11/06/2022]
Abstract
Current distance measurements between spin-labels on multimeric protonated proteins using double electron-electron resonance (DEER) EPR spectroscopy are generally limited to the 15-60 Å range. Here we show how DEER experiments can be extended to dipolar evolution times of ca. 80 μs, permitting distances up to 170 Å to be accessed in multimeric proteins. The method relies on sparse spin-labeling, supplemented by deuteration of protein and solvent, to minimize the deleterious impact of multispin effects and substantially increase the apparent spin-label phase memory relaxation time, complemented by high sensitivity afforded by measurements at Q-band. We demonstrate the approach using the tetradecameric molecular machine GroEL as an example. Two engineered surface-exposed mutants, R268C and E315C, are used to measure pairwise distance distributions with mean values ranging from 20 to 100 Å and from 30 to 160 Å, respectively, both within and between the two heptameric rings of GroEL. The measured distance distributions are consistent with the known crystal structure of apo GroEL. The methodology presented here should significantly expand the use of DEER for the structural characterization of conformational changes in higher order oligomers.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Marielle A Wälti
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - James L Baber
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Eric J Hustedt
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
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33
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Valera S, Ackermann K, Pliotas C, Huang H, Naismith JH, Bode BE. Accurate Extraction of Nanometer Distances in Multimers by Pulse EPR. Chemistry 2016; 22:4700-3. [PMID: 26865468 PMCID: PMC4848767 DOI: 10.1002/chem.201505143] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 12/15/2022]
Abstract
Pulse electron paramagnetic resonance (EPR) is gaining increasing importance in structural biology. The PELDOR (pulsed electron–electron double resonance) method allows extracting distance information on the nanometer scale. Here, we demonstrate the efficient extraction of distances from multimeric systems such as membrane‐embedded ion channels where data analysis is commonly hindered by multi‐spin effects.
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Affiliation(s)
- Silvia Valera
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Katrin Ackermann
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Christos Pliotas
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Hexian Huang
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Bela E Bode
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK. .,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.
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34
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Meyer V, Swanson MA, Clouston LJ, Boratyński PJ, Stein RA, Mchaourab HS, Rajca A, Eaton SS, Eaton GR. Room-temperature distance measurements of immobilized spin-labeled protein by DEER/PELDOR. Biophys J 2016; 108:1213-9. [PMID: 25762332 DOI: 10.1016/j.bpj.2015.01.015] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/17/2014] [Accepted: 01/14/2015] [Indexed: 11/18/2022] Open
Abstract
Nitroxide spin labels are used for double electron-electron resonance (DEER) measurements of distances between sites in biomolecules. Rotation of gem-dimethyls in commonly used nitroxides causes spin echo dephasing times (Tm) to be too short to perform DEER measurements at temperatures between ∼80 and 295 K, even in immobilized samples. A spirocyclohexyl spin label has been prepared that has longer Tm between 80 and 295 K in immobilized samples than conventional labels. Two of the spirocyclohexyl labels were attached to sites on T4 lysozyme introduced by site-directed spin labeling. Interspin distances up to ∼4 nm were measured by DEER at temperatures up to 160 K in water/glycerol glasses. In a glassy trehalose matrix the Tm for the doubly labeled T4 lysozyme was long enough to measure an interspin distance of 3.2 nm at 295 K, which could not be measured for the same protein labeled with the conventional 1-oxyl-2,2,5,5-tetramethyl-3-pyrroline-3-(methyl)methanethio-sulfonate label.
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Affiliation(s)
- Virginia Meyer
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado
| | - Michael A Swanson
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado
| | - Laura J Clouston
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska
| | | | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado.
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35
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Abdullin D, Hagelueken G, Schiemann O. Determination of nitroxide spin label conformations via PELDOR and X-ray crystallography. Phys Chem Chem Phys 2016; 18:10428-37. [DOI: 10.1039/c6cp01307d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PELDOR is used to unravel the position and orientation of MTSSL in six singly-labelled azurin mutants. A comparison with X-ray structures of the mutants shows good agreement with respect to the position and orientation of the nitroxide group.
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Affiliation(s)
- D. Abdullin
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - G. Hagelueken
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - O. Schiemann
- Institute of Physical and Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
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36
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Abstract
Membrane proteins are very important in controlling bioenergetics, functional activity, and initializing signal pathways in a wide variety of complicated biological systems. They also represent approximately 50% of the potential drug targets. EPR spectroscopy is a very popular and powerful biophysical tool that is used to study the structural and dynamic properties of membrane proteins. In this article, a basic overview of the most commonly used EPR techniques and examples of recent applications to answer pertinent structural and dynamic related questions on membrane protein systems will be presented.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States of America
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37
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Endeward B, Marko A, Denysenkov VP, Sigurdsson ST, Prisner TF. Advanced EPR Methods for Studying Conformational Dynamics of Nucleic Acids. Methods Enzymol 2015; 564:403-25. [PMID: 26477259 DOI: 10.1016/bs.mie.2015.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) spectroscopy has become an important tool for structural characterization of biomolecules allowing measurement of the distances between two paramagnetic spin labels attached to a biomolecule in the 2-8 nm range. In this chapter, we will focus on applications of this approach to investigate tertiary structure elements as well as conformational dynamics of nucleic acid molecules. Both aspects take advantage of using specific spin labels that are rigidly attached to the nucleobases, as they allow obtaining not only the distance but also the relative orientation between both nitroxide moieties with high accuracy. Thus, not only the distance but additionally the three Euler angles between both the nitroxide axis systems and the two polar angles of the interconnecting vector with respect to the nitroxide axis systems can be extracted from a single pair of spin labels. To extract all these parameters independently and unambiguously, a set of multifrequency/multifield pulsed EPR experiments have to be performed. We will describe the experimental procedure as well as newly developed spin labels, which are helpful to disentangle all these parameters, and tools which we have developed to analyze such data sets. The procedures and analyses will be illustrated by examples from our laboratory.
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Affiliation(s)
- B Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - A Marko
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - V P Denysenkov
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - S Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Reykjavık, Iceland
| | - T F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.
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38
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Prisner TF, Marko A, Sigurdsson ST. Conformational dynamics of nucleic acid molecules studied by PELDOR spectroscopy with rigid spin labels. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 252:187-98. [PMID: 25701439 DOI: 10.1016/j.jmr.2014.12.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 05/22/2023]
Abstract
Nucleic acid molecules can adopt a variety of structures and exhibit a large degree of conformational flexibility to fulfill their various functions in cells. Here we describe the use of Pulsed Electron-Electron Double Resonance (PELDOR or DEER) to investigate nucleic acid molecules where two cytosine analogs have been incorporated as spin probes. Because these new types of spin labels are rigid and incorporated into double stranded DNA and RNA molecules, there is no additional flexibility of the spin label itself present. Therefore the magnetic dipole-dipole interaction between both spin labels encodes for the distance as well as for the mutual orientation between the spin labels. All of this information can be extracted by multi-frequency/multi-field PELDOR experiments, which gives very precise and valuable information about the structure and conformational flexibility of the nucleic acid molecules. We describe in detail our procedure to obtain the conformational ensembles and show the accuracy and limitations with test examples and application to double-stranded DNA.
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Affiliation(s)
- T F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany.
| | - A Marko
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany
| | - S Th Sigurdsson
- Science Institute, University of Iceland, Reykjavik, Iceland
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39
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40
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Klare JP, Steinhoff HJ. Spin Labeling Studies of Transmembrane Signaling and Transport. Methods Enzymol 2015; 564:315-47. [DOI: 10.1016/bs.mie.2015.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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41
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42
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Ward R, Pliotas C, Branigan E, Hacker C, Rasmussen A, Hagelueken G, Booth IR, Miller S, Lucocq J, Naismith JH, Schiemann O. Probing the structure of the mechanosensitive channel of small conductance in lipid bilayers with pulsed electron-electron double resonance. Biophys J 2014; 106:834-42. [PMID: 24559986 PMCID: PMC3944623 DOI: 10.1016/j.bpj.2014.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/16/2023] Open
Abstract
Mechanosensitive channel proteins are important safety valves against osmotic shock in bacteria, and are involved in sensing touch and sound waves in higher organisms. The mechanosensitive channel of small conductance (MscS) has been extensively studied. Pulsed electron-electron double resonance (PELDOR or DEER) of detergent-solubilized protein confirms that as seen in the crystal structure, the outer ring of transmembrane helices do not pack against the pore-forming helices, creating an apparent void. The relevance of this void to the functional form of MscS in the bilayer is the subject of debate. Here, we report PELDOR measurements of MscS reconstituted into two lipid bilayer systems: nanodiscs and bicelles. The distance measurements from multiple mutants derived from the PELDOR data are consistent with the detergent-solution arrangement of the protein. We conclude, therefore, that the relative positioning of the transmembrane helices is preserved in mimics of the cell bilayer, and that the apparent voids are not an artifact of detergent solution but a property of the protein that will have to be accounted for in any molecular mechanism of gating.
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Affiliation(s)
- Richard Ward
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Christos Pliotas
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Emma Branigan
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Christian Hacker
- School of Medicine, University of St. Andrews, St. Andrews, Scotland
| | - Akiko Rasmussen
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Ian R Booth
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Samantha Miller
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - John Lucocq
- School of Medicine, University of St. Andrews, St. Andrews, Scotland
| | - James H Naismith
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland.
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany; Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland.
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43
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Gophane DB, Endeward B, Prisner TF, Sigurdsson ST. Conformationally restricted isoindoline-derived spin labels in duplex DNA: distances and rotational flexibility by pulsed electron-electron double resonance spectroscopy. Chemistry 2014; 20:15913-9. [PMID: 25296640 DOI: 10.1002/chem.201403726] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/10/2014] [Indexed: 12/25/2022]
Abstract
Three structurally related isoindoline-derived spin labels that have different mobilities were incorporated into duplex DNA to systematically study the effect of motion on orientation-dependent pulsed electron-electron double resonance (PELDOR) measurements. To that end, a new nitroxide spin label, (ExIm)U, was synthesized and incorporated into DNA oligonucleotides. (ExIm)U is the first example of a conformationally unambiguous spin label for nucleic acids, in which the nitroxide N-O bond lies on the same axis as the three single bonds used to attach the otherwise rigid isoindoline-based spin label to a uridine base. Continuous-wave (CW) EPR measurements of (ExIm)U confirm a very high rotational mobility of the spin label in duplex DNA relative to the structurally related spin label (Im)U, which has restricted mobility due to an intramolecular hydrogen bond. The X-band CW-EPR spectra of (ExIm)U can be used to identify mismatches in duplex DNA. PELDOR distance measurements between pairs of the spin labels (Im)U, (Ox)U, and (ExIm)U in duplex DNA showed a strong angular dependence for (Im)U, a medium dependence for (Ox)U, and no orientation effect for (ExIm)U. Thus, precise distances can be extracted from (ExIm)U without having to take orientational effects into account.
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Affiliation(s)
- Dnyaneshwar B Gophane
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik (Iceland), Fax: (+354)5528911
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44
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Sahu ID, Kroncke BM, Zhang R, Dunagan MM, Smith HJ, Craig A, McCarrick RM, Sanders CR, Lorigan GA. Structural investigation of the transmembrane domain of KCNE1 in proteoliposomes. Biochemistry 2014; 53:6392-401. [PMID: 25234231 PMCID: PMC4196734 DOI: 10.1021/bi500943p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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KCNE1 is a single-transmembrane protein
of the KCNE family that modulates the function of voltage-gated potassium
channels, including KCNQ1. Hereditary mutations in KCNE1 have been
linked to diseases such as long QT syndrome (LQTS), atrial fibrillation,
sudden infant death syndrome, and deafness. The transmembrane domain
(TMD) of KCNE1 plays a key role in mediating the physical association
with KCNQ1 and in subsequent modulation of channel gating kinetics
and conductance. However, the mechanisms associated with these roles
for the TMD remain poorly understood, highlighting a need for experimental
structural studies. A previous solution NMR study of KCNE1 in LMPG
micelles revealed a curved transmembrane domain, a structural feature
proposed to be critical to KCNE1 function. However, this curvature
potentially reflects an artifact of working in detergent micelles.
Double electron electron resonance (DEER) measurements were conducted
on KCNE1 in LMPG micelles, POPC/POPG proteoliposomes, and POPC/POPG
lipodisq nanoparticles to directly compare the structure of the TMD
in a variety of different membrane environments. Experimentally derived
DEER distances coupled with simulated annealing molecular dynamic
simulations were used to probe the bilayer structure of the TMD of
KCNE1. The results indicate that the structure is helical in proteoliposomes
and is slightly curved, which is consistent with the previously determined
solution NMR structure in micelles. The evident resilience of the
curvature in the KCNE1 TMD leads us to hypothesize that the curvature
is likely to be maintained upon binding of the protein to the KCNQ1
channel.
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Affiliation(s)
- Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
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45
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Abdullin D, Hagelueken G, Hunter RI, Smith GM, Schiemann O. Geometric model-based fitting algorithm for orientation-selective PELDOR data. Mol Phys 2014. [DOI: 10.1080/00268976.2014.960494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | | | | | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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46
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Goldfarb D. Gd3+ spin labeling for distance measurements by pulse EPR spectroscopy. Phys Chem Chem Phys 2014; 16:9685-99. [DOI: 10.1039/c3cp53822b] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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47
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Joseph B, Korkhov VM, Yulikov M, Jeschke G, Bordignon E. Conformational cycle of the vitamin B12 ABC importer in liposomes detected by double electron-electron resonance (DEER). J Biol Chem 2013; 289:3176-85. [PMID: 24362024 DOI: 10.1074/jbc.m113.512178] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Double electron-electron resonance is used here to investigate intermediates of the transport cycle of the Escherichia coli vitamin B12 ATP-binding cassette importer BtuCD-F. Previously, we showed the ATP-induced opening of the cytoplasmic gate I in TM5 helices, later confirmed by the AMP-PNP-bound BtuCD-F crystal structure. Here, other key residues are analyzed in TM10 helices (positions 307 and 322) and in the cytoplasmic gate II, i.e. the loop between TM2 and TM3 (positions 82 and 85). Without BtuF, binding of ATP induces detectable changes at positions 307 and 85 in BtuCD in liposomes. Together with BtuF, ATP triggers the closure of the cytoplasmic gate II in liposomes (reported by both positions 82 and 85). This forms a sealed cavity in the translocation channel in agreement with the AMP-PNP·BtuCD-F x-ray structure. When vitamin B12 and AMP-PNP are simultaneously present, the extent of complex formation is reduced, but the short 82-82 interspin distance detected indicates that the substrate does not affect the closed conformation of this gate. The existence of the BtuCD-F complex under these conditions is verified with spectroscopically orthogonal nitroxide and Gd(III)-based labels. The cytoplasmic gate II remains closed also in the vanadate-trapped state, but it reopens in the ADP-bound state of the complex. Therefore, we suggest that the substrate likely trapped in ATP·BtuCD-F can be released after ATP hydrolysis but before the occluded ADP-bound conformation is reached.
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Affiliation(s)
- Benesh Joseph
- From the Laboratory of Physical Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10 and
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48
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Möbius K, Lubitz W, Savitsky A. High-field EPR on membrane proteins - crossing the gap to NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:1-49. [PMID: 24160760 DOI: 10.1016/j.pnmrs.2013.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 06/02/2023]
Abstract
In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.
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Affiliation(s)
- Klaus Möbius
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany; Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany.
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Branigan E, Pliotas C, Hagelueken G, Naismith JH. Quantification of free cysteines in membrane and soluble proteins using a fluorescent dye and thermal unfolding. Nat Protoc 2013; 8:2090-7. [PMID: 24091556 PMCID: PMC3836627 DOI: 10.1038/nprot.2013.128] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cysteine is an extremely useful site for selective attachment of labels to proteins for many applications, including the study of protein structure in solution by electron paramagnetic resonance (EPR), fluorescence spectroscopy and medical imaging. The demand for quantitative data for these applications means that it is important to determine the extent of the cysteine labeling. The efficiency of labeling is sensitive to the 3D context of cysteine within the protein. Where the label or modification is not directly measurable by optical or magnetic spectroscopy, for example, in cysteine modification to dehydroalanine, assessing labeling efficiency is difficult. We describe a simple assay for determining the efficiency of modification of cysteine residues, which is based on an approach previously used to determine membrane protein stability. The assay involves a reaction between the thermally unfolded protein and a thiol-specific coumarin fluorophore that is only fluorescent upon conjugation with thiols. Monitoring fluorescence during thermal denaturation of the protein in the presence of the dye identifies the temperature at which the maximum fluorescence occurs; this temperature differs among proteins. Comparison of the fluorescence intensity at the identified temperature between modified, unmodified (positive control) and cysteine-less protein (negative control) allows for the quantification of free cysteine. We have quantified both site-directed spin labeling and dehydroalanine formation. The method relies on a commonly available fluorescence 96-well plate reader, which rapidly screens numerous samples within 1.5 h and uses <100 μg of material. The approach is robust for both soluble and detergent-solubilized membrane proteins.
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Affiliation(s)
- Emma Branigan
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
| | - Christos Pliotas
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
| | - Gregor Hagelueken
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK
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50
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Milov AD, Tsvetkov YD, De Zotti M, Prinzivalli C, Biondi B, Formaggio F, Toniolo C, Gobbo M. Aggregation modes of the spin mono-labeled tylopeptin B and heptaibin peptaibiotics in frozen solutions of weak polarity as studied by PELDOR spectroscopy. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476613070056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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