1
|
Sanders G, Borbat PP, Georgieva ER. Conformations of influenza A M2 protein in DOPC/DOPS and E. coli native lipids and proteins. Biophys J 2024; 123:2584-2593. [PMID: 38932458 PMCID: PMC11365223 DOI: 10.1016/j.bpj.2024.06.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/21/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
We compared the conformations of the transmembrane domain (TMD) of influenza A M2 (IM2) protein reconstituted in 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPC/DOPS) bilayers to those in isolated Escherichia coli (E. coli) membranes, having preserved its native proteins and lipids. IM2 is a single-pass transmembrane protein known to assemble into a homo-tetrameric proton channel. To represent this channel, we made a construct containing the IM2's TMD region flanked by the juxtamembrane residues. The single cysteine substitution, L43C, of leucine located in the bilayer polar region was paramagnetically tagged with a methanethiosulfonate nitroxide label for the electron spin resonance (ESR) study. For this particular residue, we probed the conformations of the spin-labeled IM2 reconstituted in DOPC/DOPS and isolated E. coli membranes using continuous-wave ESR and double electron-electron resonance (DEER) spectroscopy. The total protein-to-lipid molar ratio spanned the range from 1:230 to 1:10,400. The continuous-wave ESR spectra corresponded to very slow spin-label motion in both environments. In all cases, the DEER data were reconstructed into distance distributions with well-resolved peaks at 1.68 and 2.37 nm in distance and amplitude ratios of 1.41 ± 0.2 and 2:1, respectively. This suggests four nitroxide spin labels located at the corners of a square, indicative of an axially symmetric tetramer. The distance modeling of DEER data with molecular modeling software applied to the NMR molecular structures (PDB: 2L0J) confirmed the symmetry and closed state of the C-terminal exit pore of the IM2 TMD tetramer in agreement with the model. Thus, we can conclude that, under conditions of pH 7.4 used in this study, IM2 TMD has similar conformations in model lipid bilayers and membranes made of native E. coli lipids and proteins of comparable thickness and fluidity, notwithstanding the complexity of the E. coli membranes caused by their lipid diversity and the abundance of integral and peripheral membrane proteins.
Collapse
Affiliation(s)
- Griffin Sanders
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, ACERT, Cornell University, Ithaca, New York
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas.
| |
Collapse
|
2
|
Adams MC, Schiltz C, Sun J, Hosford C, Johnson V, Pan H, Borbat P, Freed J, Thomason L, Court C, Court D, Chappie J. The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins. Nucleic Acids Res 2024; 52:4659-4675. [PMID: 38554102 PMCID: PMC11077077 DOI: 10.1093/nar/gkae212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/01/2024] Open
Abstract
RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron-electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.
Collapse
Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jing Sun
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Virginia M Johnson
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hao Pan
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Lynn C Thomason
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Carolyn Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Donald L Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
3
|
Esteban-Hofer L, Emmanouilidis L, Yulikov M, Allain FHT, Jeschke G. Ensemble structure of the N-terminal domain (1-267) of FUS in a biomolecular condensate. Biophys J 2024; 123:538-554. [PMID: 38279531 PMCID: PMC10938082 DOI: 10.1016/j.bpj.2024.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/06/2023] [Accepted: 01/22/2024] [Indexed: 01/28/2024] Open
Abstract
Solutions of some proteins phase separate into a condensed state of high protein concentration and a dispersed state of low concentration. Such behavior is observed in living cells for a number of RNA-binding proteins that feature intrinsically disordered domains. It is relevant for cell function via the formation of membraneless organelles and transcriptional condensates. On a basic level, the process can be studied in vitro on protein domains that are necessary and sufficient for liquid-liquid phase separation (LLPS). We have performed distance distribution measurements by electron paramagnetic resonance for 13 sections in an N-terminal domain (NTD) construct of the protein fused in sarcoma (FUS), consisting of the QGSY-rich domain and the RGG1 domain, in the denatured, dispersed, and condensed state. Using 10 distance distribution restraints for ensemble modeling and three such restraints for model validation, we have found that FUS NTD behaves as a random-coil polymer under good-solvent conditions in both the dispersed and condensed state. Conformation distribution in the biomolecular condensate is virtually indistinguishable from the one in an unrestrained ensemble, with the latter one being based on only residue-specific Ramachandran angle distributions. Over its whole length, FUS NTD is slightly more compact in the condensed than in the dispersed state, which is in line with the theory for random coils in good solvent proposed by de Gennes, Daoud, and Jannink. The estimated concentration in the condensate exceeds the overlap concentration resulting from this theory. The QGSY-rich domain is slightly more extended, slightly more hydrated, and has slightly higher propensity for LLPS than the RGG1 domain. Our results support previous suggestions that LLPS of FUS is driven by multiple transient nonspecific hydrogen bonding and π-sp2 interactions.
Collapse
Affiliation(s)
- Laura Esteban-Hofer
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | | | - Maxim Yulikov
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | | | - Gunnar Jeschke
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland.
| |
Collapse
|
4
|
Sanders G, Borbat PP, Georgieva ER. A comparative study of influenza A M2 protein conformations in DOPC/DOPS liposomes and in native E. coli membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574681. [PMID: 38260371 PMCID: PMC10802500 DOI: 10.1101/2024.01.08.574681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
We compared the conformations of the transmembrane domain (TMD) of influenza A M2 (IAM2) protein reconstituted at pH 7.4 in DOPC/DOPS bilayers to those in isolated E. coli membranes, having preserved its native proteins and lipids. IAM2 is a single-pass transmembrane protein known to assemble into homo-tetrameric proton channel. To represent this channel, we made a construct containing the IAM2's TMD region flanked by the juxtamembrane residues. The single cysteine substitute, L43C, of leucine located in the bilayer polar region was paramagnetically tagged with a methanethiosulfonate nitroxide label for the ESR (electron spin resonance) study. We compared the conformations of the spin-labeled IAM2 residing in DOPC/DOPS and native E. coli membranes using continuous-wave (CW) ESR and double electron-electron resonance (DEER) spectroscopy. The total protein-to-lipid molar ratio spanned the range from 1:230 to 1:10,400⩦ The CW ESR spectra corresponded to a nearly rigid limit spin label dynamics in both environments. In all cases, the DEER data were reconstructed into the distance distributions showing well-resolved peaks at 1.68 nm and 2.37 nm. The peak distance ratio was 1.41±0.2 and the amplitude ratio was 2:1. This is what one expects from four nitroxide spin-labels located at the corners of a square, indicative of an axially symmetric tetramer. Distance modeling of DEER data with molecular modeling software applied to the NMR molecular structures (PDB: 2L0J) confirmed the symmetry and closed state of the C-terminal exit pore of the IAM2 tetramer in agreement with the NMR model. Thus, we can conclude that IAM2 TMD has similar conformations in model and native E. coli membranes of comparable thickness and fluidity, notwithstanding the complexity of the E. coli membranes caused by their lipid diversity and the abundance of integral and peripheral membrane proteins.
Collapse
Affiliation(s)
- Griffin Sanders
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409
| | - Peter P. Borbat
- Department of Chemistry and Chemical Biology and ACERT, Cornell University, Ithaca NY 14853
| | - Elka R. Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Kazemi S, Lopata A, Kniss A, Pluska L, Güntert P, Sommer T, Prisner TF, Collauto A, Dötsch V. Efficient determination of the accessible conformation space of multi-domain complexes based on EPR PELDOR data. JOURNAL OF BIOMOLECULAR NMR 2023; 77:261-269. [PMID: 37966668 PMCID: PMC10687113 DOI: 10.1007/s10858-023-00426-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/25/2023] [Indexed: 11/16/2023]
Abstract
Many proteins can adopt multiple conformations which are important for their function. This is also true for proteins and domains that are covalently linked to each other. One important example is ubiquitin, which can form chains of different conformations depending on which of its lysine side chains is used to form an isopeptide bond with the C-terminus of another ubiquitin molecule. Similarly, ubiquitin gets covalently attached to active-site residues of E2 ubiquitin-conjugating enzymes. Due to weak interactions between ubiquitin and its interaction partners, these covalent complexes adopt multiple conformations. Understanding the function of these complexes requires the characterization of the entire accessible conformation space and its modulation by interaction partners. Long-range (1.8-10 nm) distance restraints obtained by EPR spectroscopy in the form of probability distributions are ideally suited for this task as not only the mean distance but also information about the conformation dynamics is encoded in the experimental data. Here we describe a computational method that we have developed based on well-established structure determination software using NMR restraints to calculate the accessible conformation space using PELDOR/DEER data.
Collapse
Affiliation(s)
- Sina Kazemi
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
- Signals GmbH & Co. KG, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Anna Lopata
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
- Department of Molecular Immunology and Toxicology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest, Hungary
| | - Andreas Kniss
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Lukas Pluska
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin-Buch, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
- Institute of Molecular Physical Science, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Thomas Sommer
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin-Buch, Germany
- Institute for Biology, Humboldt Universität zu Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany.
| | - Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ, UK.
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany.
| |
Collapse
|
7
|
Mandato A, Hasanbasri Z, Saxena S. Double Quantum Coherence ESR at Q-Band Enhances the Sensitivity of Distance Measurements at Submicromolar Concentrations. J Phys Chem Lett 2023; 14:8909-8915. [PMID: 37768093 PMCID: PMC10577775 DOI: 10.1021/acs.jpclett.3c02372] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Recently, there have been remarkable improvements in pulsed ESR sensitivity, paving the way for broader applicability of ESR in the measurement of biological distance constraints, for instance, at physiological concentrations and in more complex systems. Nevertheless, submicromolar distance measurements with the commonly used nitroxide spin label take multiple days. Therefore, there remains a need for rapid and reliable methods of measuring distances between spins at nanomolar concentrations. In this work, we demonstrate the power of double quantum coherence (DQC) experiments at Q-band frequencies. With the help of short and intense pulses, we showcase DQC signals on nitroxide-labeled proteins with modulation depths close to 100%. We show that the deep dipolar modulations aid in the resolution of bimodal distance distributions. Finally, we establish that distance measurements with protein concentrations as low as 25 nM are feasible. This limit is approximately 4-fold lower than previously possible. We anticipate that nanomolar concentration measurements will lead to further advancements in the use of ESR, especially in cellular contexts.
Collapse
Affiliation(s)
- Alysia Mandato
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
8
|
Rudolph M, Tampé R, Joseph B. Time-Resolved Mn 2+ -NO and NO-NO Distance Measurements Reveal That Catalytic Asymmetry Regulates Alternating Access in an ABC Transporter. Angew Chem Int Ed Engl 2023; 62:e202307091. [PMID: 37459565 DOI: 10.1002/anie.202307091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
ATP-binding cassette (ABC) transporters shuttle diverse substrates across biological membranes. Transport is often achieved through a transition between an inward-facing (IF) and an outward-facing (OF) conformation of the transmembrane domains (TMDs). Asymmetric nucleotide-binding sites (NBSs) are present among several ABC subfamilies and their functional role remains elusive. Here we addressed this question using concomitant NO-NO, Mn2+ -NO, and Mn2+ -Mn2+ pulsed electron-electron double-resonance spectroscopy of TmrAB in a time-resolved manner. This type-IV ABC transporter undergoes a reversible transition in the presence of ATP with a significantly faster forward transition. The impaired degenerate NBS stably binds Mn2+ -ATP, and Mn2+ is preferentially released at the active consensus NBS. ATP hydrolysis at the consensus NBS considerably accelerates the reverse transition. Both NBSs fully open during each conformational cycle and the degenerate NBS may regulate the kinetics of this process.
Collapse
Affiliation(s)
- Michael Rudolph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Benesh Joseph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| |
Collapse
|
9
|
Majeed S, Dang L, Islam MM, Ishola O, Borbat PP, Ludtke SJ, Georgieva ER. HIV-1 Vpu protein forms stable oligomers in aqueous solution via its transmembrane domain self-association. Sci Rep 2023; 13:14691. [PMID: 37673923 PMCID: PMC10483038 DOI: 10.1038/s41598-023-41873-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/01/2023] [Indexed: 09/08/2023] Open
Abstract
We report our findings on the assembly of the HIV-1 protein Vpu into soluble oligomers. Vpu is a key HIV-1 protein. It has been considered exclusively a single-pass membrane protein. Previous observations show that this protein forms stable oligomers in aqueous solution, but details about these oligomers still remain obscure. This is an interesting and rather unique observation, as the number of proteins transitioning between soluble and membrane embedded states is limited. In this study we made use of protein engineering, size exclusion chromatography, cryoEM and electron paramagnetic resonance (EPR) spectroscopy to better elucidate the nature of the soluble oligomers. We found that Vpu oligomerizes via its N-terminal transmembrane domain (TM). CryoEM suggests that the oligomeric state most likely is a hexamer/heptamer equilibrium. Both cryoEM and EPR suggest that, within the oligomer, the distal C-terminal region of Vpu is highly flexible. Our observations are consistent with both the concept of specific interactions among TM helices or the core of the oligomers being stabilized by hydrophobic forces. While this study does not resolve all of the questions about Vpu oligomers or their functional role in HIV-1 it provides new fundamental information about the size and nature of the oligomeric interactions.
Collapse
Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Lan Dang
- Graduate Program in Quantitative and Computational Biosciences, Graduate School of Biomedical Sciences at Baylor College of Medicine, Houston, TX, USA
| | - Md Majharul Islam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Olamide Ishola
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology and ACERT, Cornell University, Ithaca, NY, 14853, USA
| | - Steven J Ludtke
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA.
- Center for Membrane Protein Research, TTU Health Science Center, Lubbock, TX, 79430, USA.
| |
Collapse
|
10
|
Endeward B, Bretschneider M, Trenkler P, Prisner TF. Implementation and applications of shaped pulses in EPR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 136-137:61-82. [PMID: 37716755 DOI: 10.1016/j.pnmrs.2023.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/12/2023] [Accepted: 04/26/2023] [Indexed: 09/18/2023]
Abstract
In this review, we describe the application of shaped pulses for EPR spectroscopy. Pulses generated by fast arbitrary waveform generators are mostly used in the field of EPR spectroscopy for broadband (200 MHz-1 GHz) excitation of paramagnetic species. The implementation and optimization of such broadband pulses in existing EPR spectrometers, often designed and optimized for short rectangular microwave pulses, is demanding. Therefore, a major part of this review will describe in detail the implementation, testing and optimization of shaped pulses in existing EPR spectrometers. Additionally, we review applications using such pulses for broadband inversion of longitudinal magnetization as well as for the creation and manipulation of transverse magnetization in the field of dipolar and hyperfine EPR spectroscopy. They demonstrate the great potential of shaped pulses to improve the performance of pulsed EPR experiments. We give a brief theoretical description of shaped pulses and their limitations, especially for adiabatic pulses, most often used in EPR. We believe that this review can on the one hand be of practical use to EPR groups starting to work with such pulses, and on the other hand give readers an overview of the state of the art of shaped pulse applications in EPR spectroscopy.
Collapse
Affiliation(s)
- Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
| | - Matthias Bretschneider
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
| | - Paul Trenkler
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
11
|
Majeed S, Dang L, Islam MM, Ishola O, Borbat PP, Ludtke SJ, Georgieva ER. HIV-1 Vpu protein forms stable oligomers in aqueous solution via its transmembrane domain self-association. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539839. [PMID: 37214796 PMCID: PMC10197565 DOI: 10.1101/2023.05.08.539839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report our findings on the assembly of the HIV-1 protein Vpu into soluble oligomers. Vpu is a key to HIV-1 protein. It has been considered exclusively a single-pass membrane protein. However, we revealed that this protein forms stable oligomers in aqueous solution, which is an interesting and rather unique observation, as the number of proteins transitioning between soluble and membrane embedded states is limited. Therefore, we undertook a study to characterize these oligomers by utilizing protein engineering, size exclusion chromatography, cryoEM and electron paramagnetic resonance (EPR) spectroscopy. We found that Vpu oligomerizes via its N-terminal transmembrane domain (TM). CryoEM analyses suggest that the oligomeric state most likely is a hexamer or hexamer-to-heptamer equilibrium. Both cryoEM and EPR suggest that, within the oligomer, the distant C-terminal region of Vpu is highly flexible. To the best of our knowledge, this is the first comprehensive study on soluble Vpu. We propose that these oligomers are stabilized via possibly hydrophobic interactions between Vpu TMs. Our findings contribute valuable information about this protein properties and about protein supramolecular complexes formation. The acquired knowledge could be further used in protein engineering, and could also help to uncover possible physiological function of these Vpu oligomers.
Collapse
Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Lan Dang
- Graduate Program in Quantitative and Computational Biosciences, Graduate School of Biomedical Sciences at Baylor College of Medicine, Houston, Texas, USA
| | - Md Majharul Islam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Olamide Ishola
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Peter P. Borbat
- Department of Chemistry and Chemical Biology and ACERT, Cornell University, Ithaca, NY 14853, USA
| | - Steven J. Ludtke
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elka R. Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Center for Membrane Protein Research, TTU Health Science Center, Lubbock, TX 79430, USA
| |
Collapse
|
12
|
Wort JL, Ackermann K, Giannoulis A, Bode BE. Enhanced sensitivity for pulse dipolar EPR spectroscopy using variable-time RIDME. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107460. [PMID: 37167826 DOI: 10.1016/j.jmr.2023.107460] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/03/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Pulse dipolar EPR spectroscopy (PDS) measurements are an important complementary tool in structural biology and are increasingly applied to macromolecular assemblies implicated in human health and disease at physiological concentrations. This requires ever higher sensitivity, and recent advances have driven PDS measurements into the mid-nanomolar concentration regime, though optimization and acquisition of such measurements remains experimentally demanding and time expensive. One important consideration is that constant-time acquisition represents a hard limit for measurement sensitivity, depending on the maximum measured distance. Determining this distance a priori has been facilitated by machine-learning structure prediction (AlphaFold2 and RoseTTAFold) but is often confounded by non-representative behaviour in frozen solution that may mandate multiple rounds of optimization and acquisition. Herein, we endeavour to simultaneously enhance sensitivity and streamline PDS measurement optimization to one-step by benchmarking a variable-time acquisition RIDME experiment applied to CuII-nitroxide and CuII-CuII model systems. Results demonstrate marked sensitivity improvements of both 5- and 6-pulse variable-time RIDME of between 2- and 5-fold over the constant-time analogues.
Collapse
Affiliation(s)
- Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Angeliki Giannoulis
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Scotland.
| |
Collapse
|
13
|
Choi YM, Ajjaji D, Fleming KD, Borbat PP, Jenkins ML, Moeller BE, Fernando S, Bhatia SR, Freed JH, Burke JE, Thiam AR, Airola MV. Structural insights into perilipin 3 membrane association in response to diacylglycerol accumulation. Nat Commun 2023; 14:3204. [PMID: 37268630 PMCID: PMC10238389 DOI: 10.1038/s41467-023-38725-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/12/2023] [Indexed: 06/04/2023] Open
Abstract
Lipid droplets (LDs) are dynamic organelles that contain an oil core mainly composed of triglycerides (TAG) that is surrounded by a phospholipid monolayer and LD-associated proteins called perilipins (PLINs). During LD biogenesis, perilipin 3 (PLIN3) is recruited to nascent LDs as they emerge from the endoplasmic reticulum. Here, we analyze how lipid composition affects PLIN3 recruitment to membrane bilayers and LDs, and the structural changes that occur upon membrane binding. We find that the TAG precursors phosphatidic acid and diacylglycerol (DAG) recruit PLIN3 to membrane bilayers and define an expanded Perilipin-ADRP-Tip47 (PAT) domain that preferentially binds DAG-enriched membranes. Membrane binding induces a disorder to order transition of alpha helices within the PAT domain and 11-mer repeats, with intramolecular distance measurements consistent with the expanded PAT domain adopting a folded but dynamic structure upon membrane binding. In cells, PLIN3 is recruited to DAG-enriched ER membranes, and this requires both the PAT domain and 11-mer repeats. This provides molecular details of PLIN3 recruitment to nascent LDs and identifies a function of the PAT domain of PLIN3 in DAG binding.
Collapse
Affiliation(s)
- Yong Mi Choi
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Dalila Ajjaji
- Laboratoire de Physique de l'École normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8N 1A1, Canada
| | - Peter P Borbat
- National Biomedical Resource for Advanced Electron Spin Resonance Technology (ACERT), Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8N 1A1, Canada
| | - Brandon E Moeller
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8N 1A1, Canada
| | - Shaveen Fernando
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Surita R Bhatia
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jack H Freed
- National Biomedical Resource for Advanced Electron Spin Resonance Technology (ACERT), Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8N 1A1, Canada.
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
| | - Abdou Rachid Thiam
- Laboratoire de Physique de l'École normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
| | - Michael V Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
| |
Collapse
|
14
|
Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
Collapse
Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| |
Collapse
|
15
|
Majeed S, Adetuyi O, Borbat PP, Majharul Islam M, Ishola O, Zhao B, Georgieva ER. Insights into the oligomeric structure of the HIV-1 Vpu protein. J Struct Biol 2023; 215:107943. [PMID: 36796461 PMCID: PMC10257199 DOI: 10.1016/j.jsb.2023.107943] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
The HIV-1-encoded protein Vpu forms an oligomeric ion channel/pore in membranes and interacts with host proteins to support the virus lifecycle. However, Vpu molecular mechanisms are currently not well understood. Here, we report on the Vpu oligomeric organization under membrane and aqueous conditions and provide insights into how the Vpu environment affects the oligomer formation. For these studies, we designed a maltose-binding protein (MBP)-Vpu chimera protein and produced it in E. coli in soluble form. We analyzed this protein using analytical size-exclusion chromatography (SEC), negative staining electron microscopy (nsEM), and electron paramagnetic resonance (EPR) spectroscopy. Surprisingly, we found that MBP-Vpu formed stable oligomers in solution, seemingly driven by Vpu transmembrane domain self-association. A coarse modeling of nsEM data as well as SEC and EPR data suggests that these oligomers most likely are pentamers, similar to what was reported regarding membrane-bound Vpu. We also noticed reduced MBP-Vpu oligomer stability upon reconstitution of the protein in β-DDM detergent and mixtures of lyso-PC/PG or DHPC/DHPG. In these cases, we observed greater oligomer heterogeneity, with MBP-Vpu oligomeric order generally lower than in solution; however, larger oligomers were also present. Notably, we found that in lyso-PC/PG, above a certain protein concentration, MBP-Vpu assembles into extended structures, which had not been reported for Vpu. Therefore, we captured various Vpu oligomeric forms, which can shed light on Vpu quaternary organization. Our findings could be useful in understanding Vpu organization and function in cellular membranes and could provide information regarding the biophysical properties of single-pass transmembrane proteins.
Collapse
Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Oluwatosin Adetuyi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology and ACERT, Cornell University, Ithaca, NY 14853, United States
| | - Md Majharul Islam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Olamide Ishola
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States
| | - Bo Zhao
- College of Arts & Sciences Microscopy (CASM), Texas Tech University, Lubbock, TX 79409, United States
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, United States.
| |
Collapse
|
16
|
Pierro A, Drescher M. Dance with spins: site-directed spin labeling coupled to electron paramagnetic resonance spectroscopy directly inside cells. Chem Commun (Camb) 2023; 59:1274-1284. [PMID: 36633152 PMCID: PMC9890500 DOI: 10.1039/d2cc05907j] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023]
Abstract
Depicting how biomolecules move and interact within their physiological environment is one of the hottest topics of structural biology. This Feature Article gives an overview of the most recent advances in Site-directed Spin Labeling coupled to Electron Paramagnetic Resonance spectroscopy (SDSL-EPR) to study biomolecules in living cells. The high sensitivity, the virtual absence of background, and the versatility of spin-labeling strategies make this approach one of the most promising techniques for the study of biomolecules in physiologically relevant environments. After presenting the milestones achieved in this field, we present a summary of the future goals and ambitions of this community.
Collapse
Affiliation(s)
- Annalisa Pierro
- Department of Chemistry, University of Konstanz, and Konstanz Research School Chemical Biology, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Malte Drescher
- Department of Chemistry, University of Konstanz, and Konstanz Research School Chemical Biology, Universitätsstraße 10, 78457 Konstanz, Germany.
| |
Collapse
|
17
|
Ketter S, Joseph B. Gd 3+-Trityl-Nitroxide Triple Labeling and Distance Measurements in the Heterooligomeric Cobalamin Transport Complex in the Native Lipid Bilayers. J Am Chem Soc 2023; 145:960-966. [PMID: 36599418 PMCID: PMC9853854 DOI: 10.1021/jacs.2c10080] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Indexed: 01/06/2023]
Abstract
Increased efforts are being made for observing proteins in their native environments. Pulsed electron-electron double resonance spectroscopy (PELDOR, also known as DEER) is a powerful tool for this purpose. Conventionally, PELDOR employs an identical spin pair, which limits the output to a single distance for monomeric samples. Here, we show that the Gd3+-trityl-nitroxide (NO) three-spin system is a versatile tool to study heterooligomeric membrane protein complexes, even within their native membrane. This allowed for an independent determination of four different distances (Gd3+-trityl, Gd3+-NO, trityl-NO, and Gd3+-Gd3+) within the same sample. We demonstrate the feasibility of this approach by observing sequential ligand binding and the dynamics of complex formation in the cobalamin transport system involving four components (cobalamin, BtuB, TonB, and BtuF). Our results reveal that TonB binding alone is sufficient to release cobalamin from BtuB in the native asymmetric bilayers. This approach provides a potential tool for the structural and quantitative analysis of dynamic protein-protein interactions in oligomeric complexes, even within their native surroundings.
Collapse
Affiliation(s)
- Sophie Ketter
- Institute of Biophysics,
Department of Physics and Centre for Biomolecular Magnetic Resonance
(BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 1, Frankfurt 60438, Germany
| | - Benesh Joseph
- Institute of Biophysics,
Department of Physics and Centre for Biomolecular Magnetic Resonance
(BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 1, Frankfurt 60438, Germany
| |
Collapse
|
18
|
Seal M, Feintuch A, Goldfarb D. The effect of spin-lattice relaxation on DEER background decay. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 345:107327. [PMID: 36410061 DOI: 10.1016/j.jmr.2022.107327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
The common approach to background removal in double electron-electron resonance (DEER) measurements on frozen solutions with a three-dimensional homogeneous distribution of doubly labeled biomolecules is to fit the background to an exponential decay function. Excluded volume effects or distribution in a dimension lower than three, such as proteins in a membrane, can lead to a stretched exponential decay. In this work, we show that in cases of spin labels with short spin-lattice relaxation time, up to an order of magnitude longer than the DEER trace length, relevant for metal-based spin labels, spin flips that take place during the DEER evolution time affect the background decay shape. This was demonstrated using a series of temperature-dependent DEER measurements on frozen solutions of a nitroxide radical, a Gd(III) complex, Cu(II) ions, and a bis-Gd(III) model complex. As expected, the background decay was exponential for the nitroxide, whereas deviations were noted for Gd(III) and Cu(II). Based on the theoretical approach of Keller et al. (Phys. Chem. Chem. Phys. 21 (2019) 8228-8245), which addresses the effect of spin-lattice relaxation-induced spin flips during the evolution time, we show that the background decay can be fitted to an exponent including a linear and quadratic term in t, which is the position of the pump pulse. Analysis of the data in terms of the probability of spontaneous spin flips induced by spin-lattice relaxation showed that this approach worked well for the high temperature range studied for Gd(III) and Cu(II). At the low temperature range, the spin flips that occured during the DEER evolution time for Gd(III) exceeded the measured spin-lattice relaxation rate and include contributions from spin flips due to another mechanisms, most likely nuclear spin diffusion.
Collapse
Affiliation(s)
- Manas Seal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Born A, Soetbeer J, Henen MA, Breitgoff F, Polyhach Y, Jeschke G, Vögeli B. Ligand-specific conformational change drives interdomain allostery in Pin1. Nat Commun 2022; 13:4546. [PMID: 35927276 PMCID: PMC9352728 DOI: 10.1038/s41467-022-32340-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Pin1 is a two-domain cell regulator that isomerizes peptidyl-prolines. The catalytic domain (PPIase) and the other ligand-binding domain (WW) sample extended and compact conformations. Ligand binding changes the equilibrium of the interdomain conformations, but the conformational changes that lead to the altered domain sampling were unknown. Prior evidence has supported an interdomain allosteric mechanism. We recently introduced a magnetic resonance-based protocol that allowed us to determine the coupling of intra- and interdomain structural sampling in apo Pin1. Here, we describe ligand-specific conformational changes that occur upon binding of pCDC25c and FFpSPR. pCDC25c binding doubles the population of the extended states compared to the virtually identical populations of the apo and FFpSPR-bound forms. pCDC25c binding to the WW domain triggers conformational changes to propagate via the interdomain interface to the catalytic site, while FFpSPR binding displaces a helix in the PPIase that leads to repositioning of the PPIase catalytic loop.
Collapse
Affiliation(s)
- Alexandra Born
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Morkos A Henen
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA.,Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Frauke Breitgoff
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich, Switzerland
| | - Beat Vögeli
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO, USA.
| |
Collapse
|
21
|
Ackermann K, Wort JL, Bode BE. Pulse dipolar EPR for determining nanomolar binding affinities. Chem Commun (Camb) 2022; 58:8790-8793. [PMID: 35837993 PMCID: PMC9350988 DOI: 10.1039/d2cc02360a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein interaction studies often require very low concentrations and highly sensitive biophysical methods. Here, we demonstrate that pulse dipolar electron paramagnetic resonance spectroscopy allows measuring dissociation constants in the nanomolar range. This approach is appealing for concentration-limited biomolecular systems and medium-to-high-affinity binding studies, demonstrated here at 50 nanomolar protein concentration. CuII-nitroxide RIDME measurements at 100 nM protein concentration allow reliable extraction of dissociation constants and distances, while measurements at 50 nM protein concentration allow reliable extraction of dissociation constants only.![]()
Collapse
Affiliation(s)
- 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, Scotland, UK.
| | - Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
| |
Collapse
|
22
|
Fábregas-Ibáñez L, Jeschke G, Stoll S. Compactness regularization in the analysis of dipolar EPR spectroscopy data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 339:107218. [PMID: 35439683 DOI: 10.1016/j.jmr.2022.107218] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Dipolar electron paramagnetic resonance (EPR) experiments, such as double electron-electron resonance (DEER), measure distributions of nanometer-scale distances between paramagnetic centers, which are valuable for structural characterization of proteins and other macromolecular systems. One challenge in the least-squares fitting analysis of dipolar EPR data is the separation of the inter-molecular contribution (background) and the intra-molecular contribution. For noisy experimental traces of insufficient length, this separation is not unique, leading to identifiability problems for the background model parameters and the long-distance region of the intra-molecular distance distribution. Here, we introduce a regularization approach that mitigates this by including an additional penalty term in the objective function that is proportional to the variance of the distance distribution and thereby penalizes non-compact distributions. We examine the reliability of this approach statistically on a large set of synthetic data and illustrate it with an experimental example. The results show that the introduction of compactness can improve identifiability.
Collapse
Affiliation(s)
- Luis Fábregas-Ibáñez
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland.
| | - Gunnar Jeschke
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Stefan Stoll
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA
| |
Collapse
|
23
|
Born A, Henen MA, Nichols PJ, Vögeli B. On the use of residual dipolar couplings in multi-state structure calculation of two-domain proteins. MAGNETIC RESONANCE LETTERS 2022; 2:61-68. [PMID: 35734611 PMCID: PMC9210859 DOI: 10.1016/j.mrl.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Residual dipolar couplings (RDCs) are powerful nuclear magnetic resonance (NMR) probes for the structure calculation of biomacromolecules. Typically, an alignment tensor that defines the orientation of the entire molecule relative to the magnetic field is determined either before refinement of individual bond vectors or simultaneously with this refinement. For single-domain proteins this approach works well since all bond vectors can be described within the same coordinate frame, which is given by the alignment tensor. However, novel approaches are sought after for systems where no universal alignment tensor can be used. Here, we present an approach that can be applied to two-domain proteins that enables the calculation of multiple states within each domain as well as with respect to the relative positions of the two domains.
Collapse
Affiliation(s)
- Alexandra Born
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
| | - Morkos A. Henen
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Parker J. Nichols
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
| | - Beat Vögeli
- University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, 12801 East 17 Avenue, Aurora, CO 80045, USA
| |
Collapse
|
24
|
Abstract
Different types of spin labels are currently available for structural studies of biomolecules both in vitro and in cells using Electron Paramagnetic Resonance (EPR) and pulse dipolar spectroscopy (PDS). Each type of label has its own advantages and disadvantages, that will be addressed in this chapter. The spectroscopically distinct properties of the labels have fostered new applications of PDS aimed to simultaneously extract multiple inter-label distances on the same sample. In fact, combining different labels and choosing the optimal strategy to address their inter-label distances can increase the information content per sample, and this is pivotal to better characterize complex multi-component biomolecular systems. In this review, we provide a brief background of the spectroscopic properties of the four most common orthogonal spin labels for PDS measurements and focus on the various methods at disposal to extract homo- and hetero-label distances in proteins. We also devote a section to possible artifacts arising from channel crosstalk and provide few examples of applications in structural biology.
Collapse
|
25
|
Richardson KH, Seif-Eddine M, Sills A, Roessler MM. Controlling and exploiting intrinsic unpaired electrons in metalloproteins. Methods Enzymol 2022; 666:233-296. [PMID: 35465921 DOI: 10.1016/bs.mie.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Electron paramagnetic resonance spectroscopy encompasses a versatile set of techniques that allow detailed insight into intrinsically occurring paramagnetic centers in metalloproteins and enzymes that undergo oxidation-reduction reactions. In this chapter, we discuss the process from isolating the protein to acquiring and analyzing pulse EPR spectra, adopting a practical perspective. We start with considerations when preparing the protein sample, explain techniques and procedures available for determining the reduction potential of the redox-active center of interest and provide details on methodologies to trap a given paramagnetic state for detailed pulse EPR studies, with an emphasis on biochemical and spectroscopic tools available when multiple EPR-active species are present. We elaborate on some of the most commonly used pulse EPR techniques and the choices the user has to make, considering advantages and disadvantages and how to avoid pitfalls. Examples are provided throughout.
Collapse
Affiliation(s)
| | - Maryam Seif-Eddine
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Adam Sills
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Maxie M Roessler
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom.
| |
Collapse
|
26
|
Fábregas-Ibáñez L, Tessmer MH, Jeschke G, Stoll S. Dipolar pathways in dipolar EPR spectroscopy. Phys Chem Chem Phys 2022; 24:2504-2520. [PMID: 35023519 PMCID: PMC8920025 DOI: 10.1039/d1cp03305k] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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. To determine these distributions from the experimental signal, it is critical to employ an accurate model of the signal. For dilute samples of doubly spin-labeled molecules, the signal is a product of an intramolecular and an intermolecular contribution. We present a general model based on dipolar pathways valid for dipolar EPR experiments with spin-1/2 labels. Our results show that the intramolecular contribution consists of a sum and the intermolecular contribution consists of a product over individual dipolar pathway contributions. We examine several commonly used dipolar EPR experiments in terms of dipolar pathways and show experimental results confirming the theoretical predictions. This multi-pathway model makes it possible to analyze a wide range of dipolar EPR experiments within a single theoretical framework.
Collapse
Affiliation(s)
- Luis Fábregas-Ibáñez
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Maxx H Tessmer
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA.
| | - Gunnar Jeschke
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stefan Stoll
- University of Washington, Department of Chemistry, Seattle, WA 98195, USA.
| |
Collapse
|
27
|
Endeward B, Hu Y, Bai G, Liu G, Prisner TF, Fang X. Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy. Biophys J 2022; 121:37-43. [PMID: 34896070 PMCID: PMC8758415 DOI: 10.1016/j.bpj.2021.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/23/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy is powerful in structure and dynamics study of biological macromolecules by providing distance distribution information ranging from 1.8 to 6 nm, providing that the biomolecules are site-specifically labeled with paramagnetic tags. However, long distances up to 16 nm have been measured on perdeuterated and spin-labeled proteins in deuterated solvent by PELDOR. Here we demonstrate long-range distance measurement on a large RNA, the 97-nucleotide 3'SL RNA element of the Dengue virus 2 genome, by combining a posttranscriptional site-directed spin labeling method using an unnatural basepair system with RNA perdeuteration by enzymatic synthesis using deuterated nucleotides. The perdeuteration removes the coupling of the electron spins of the nitroxide spin labels from the proton nuclear spin system of the RNA and does extend the observation time windows of PELDOR up to 50 μs. This enables one to determine long distances up to 14 nm for large RNAs and their conformational flexibility.
Collapse
Affiliation(s)
- Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt, Germany
| | - Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 10086, China
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 10019, China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 10019, China
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt, Germany,Corresponding author
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 10086, China,Corresponding author
| |
Collapse
|
28
|
Soetbeer J, Ibáñez LF, Berkson Z, Polyhach Y, Jeschke G. Regularized dynamical decoupling noise spectroscopy - a decoherence descriptor for radicals in glassy matrices. Phys Chem Chem Phys 2021; 23:21664-21676. [PMID: 34581335 PMCID: PMC8494271 DOI: 10.1039/d1cp03103a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022]
Abstract
Decoherence arises from a fluctuating spin environment, captured by its noise spectrum S(ω). Dynamical decoupling (DD) with n π pulses extends the dephasing time if the associated filter function attenuates S(ω). Inversely, DD noise spectroscopy (DDNS) reconstructs S(ω) from DD data by approximating the filters pass band by a δ-function. This restricts application to qubit-like spin systems with inherently long dephasing times and/or many applicable pulses. We introduce regularized DDNS to lift this limitation and thereby infer S(ω) from DD traces of paramagnetic centers in glassy o-terphenyl and water-glycerol matrices recorded with n ≤ 5. For nitroxide radicals at low temperatures, we utilize deuteration to identify distinct matrix- and spin center-induced spectral features. The former extends up to a matrix-specific cut-off frequency and characterizes nuclear spin diffusion. We demonstrate that rotational tunneling of intramolecular methyl groups drives the latter process, whereas at elevated temperatures S(ω) reflects the classical methyl group reorientation. Ultimately, S(ω) visualizes and quantifies variations in the electron spins couplings and thus reports on the underlying spin dynamics as a powerful decoherence descriptor.
Collapse
Affiliation(s)
- Janne Soetbeer
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8049 Zürich, Switzerland.
| | - Luis Fábregas Ibáñez
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8049 Zürich, Switzerland.
| | - Zachariah Berkson
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8049 Zürich, Switzerland.
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8049 Zürich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8049 Zürich, Switzerland.
| |
Collapse
|
29
|
Born A, Soetbeer J, Breitgoff F, Henen MA, Sgourakis N, Polyhach Y, Nichols PJ, Strotz D, Jeschke G, Vögeli B. Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance. J Am Chem Soc 2021; 143:16055-16067. [PMID: 34579531 DOI: 10.1021/jacs.1c06289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteins composed of multiple domains allow for structural heterogeneity and interdomain dynamics that may be vital for function. Intradomain structures and dynamics can influence interdomain conformations and vice versa. However, no established structure determination method is currently available that can probe the coupling of these motions. The protein Pin1 contains separate regulatory and catalytic domains that sample "extended" and "compact" states, and ligand binding changes this equilibrium. Ligand binding and interdomain distance have been shown to impact the activity of Pin1, suggesting interdomain allostery. In order to characterize the conformational equilibrium of Pin1, we describe a novel method to model the coupling between intra- and interdomain dynamics at atomic resolution using multistate ensembles. The method uses time-averaged nuclear magnetic resonance (NMR) restraints and double electron-electron resonance (DEER) data that resolve distance distributions. While the intradomain calculation is primarily driven by exact nuclear Overhauser enhancements (eNOEs), J couplings, and residual dipolar couplings (RDCs), the relative domain distribution is driven by paramagnetic relaxation enhancement (PREs), RDCs, interdomain NOEs, and DEER. Our data support a 70:30 population of the compact and extended states in apo Pin1. A multistate ensemble describes these conformations simultaneously, with distinct conformational differences located in the interdomain interface stabilizing the compact or extended states. We also describe correlated conformations between the catalytic site and interdomain interface that may explain allostery driven by interdomain contact.
Collapse
Affiliation(s)
- Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Janne Soetbeer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Frauke Breitgoff
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States.,Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Nikolaos Sgourakis
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| | - Dean Strotz
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, ETH-Hönggerberg, Zürich CH-8093, Switzerland
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, Colorado 80045, United States
| |
Collapse
|
30
|
Thorsen MK, Lai A, Lee MW, Hoogerheide DP, Wong GCL, Freed JH, Heldwein EE. Highly Basic Clusters in the Herpes Simplex Virus 1 Nuclear Egress Complex Drive Membrane Budding by Inducing Lipid Ordering. mBio 2021; 12:e0154821. [PMID: 34425706 PMCID: PMC8406295 DOI: 10.1128/mbio.01548-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/28/2021] [Indexed: 02/01/2023] Open
Abstract
During replication of herpesviruses, capsids escape from the nucleus into the cytoplasm by budding at the inner nuclear membrane. This unusual process is mediated by the viral nuclear egress complex (NEC) that deforms the membrane around the capsid by oligomerizing into a hexagonal, membrane-bound scaffold. Here, we found that highly basic membrane-proximal regions (MPRs) of the NEC alter lipid order by inserting into the lipid headgroups and promote negative Gaussian curvature. We also find that the electrostatic interactions between the MPRs and the membranes are essential for membrane deformation. One of the MPRs is phosphorylated by a viral kinase during infection, and the corresponding phosphomimicking mutations block capsid nuclear egress. We show that the same phosphomimicking mutations disrupt the NEC-membrane interactions and inhibit NEC-mediated budding in vitro, providing a biophysical explanation for the in vivo phenomenon. Our data suggest that the NEC generates negative membrane curvature by both lipid ordering and protein scaffolding and that phosphorylation acts as an off switch that inhibits the membrane-budding activity of the NEC to prevent capsid-less budding. IMPORTANCE Herpesviruses are large viruses that infect nearly all vertebrates and some invertebrates and cause lifelong infections in most of the world's population. During replication, herpesviruses export their capsids from the nucleus into the cytoplasm by an unusual mechanism in which the viral nuclear egress complex (NEC) deforms the nuclear membrane around the capsid. However, how membrane deformation is achieved is unclear. Here, we show that the NEC from herpes simplex virus 1, a prototypical herpesvirus, uses clusters of positive charges to bind membranes and order membrane lipids. Reducing the positive charge or introducing negative charges weakens the membrane deforming ability of the NEC. We propose that the virus employs electrostatics to deform nuclear membrane around the capsid and can control this process by changing the NEC charge through phosphorylation. Blocking NEC-membrane interactions could be exploited as a therapeutic strategy.
Collapse
Affiliation(s)
- Michael K. Thorsen
- Department of Molecular Biology and Microbiology, Graduate Program in Cellular, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Alex Lai
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York, USA
| | - Michelle W. Lee
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Gerard C. L. Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Jack H. Freed
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York, USA
| | - Ekaterina E. Heldwein
- Department of Molecular Biology and Microbiology, Graduate Program in Cellular, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
31
|
Ackermann K, Wort JL, Bode BE. Nanomolar Pulse Dipolar EPR Spectroscopy in Proteins: Cu II-Cu II and Nitroxide-Nitroxide Cases. J Phys Chem B 2021; 125:5358-5364. [PMID: 33998795 PMCID: PMC7611071 DOI: 10.1021/acs.jpcb.1c03666] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The study of ever more complex biomolecular assemblies implicated in human health and disease is facilitated by a suite of complementary biophysical methods. Pulse dipolar electron paramagnetic resonance spectroscopy (PDS) is a powerful tool that provides highly precise geometric constraints in frozen solutions; however, the drive toward PDS at physiologically relevant sub-μM concentrations is limited by the currently achievable concentration sensitivity. Recently, PDS using a combination of nitroxide- and CuII-based spin labels allowed measuring a 500 nM concentration of a model protein. Using commercial instrumentation and spin labels, we demonstrate CuII-CuII and nitroxide-nitroxide PDS measurements at protein concentrations below previous examples reaching 500 and 100 nM, respectively. These results demonstrate the general feasibility of sub-μM PDS measurements at short to intermediate distances (∼1.5 to 3.5 nm), and are of particular relevance for applications where the achievable concentration is limiting.
Collapse
|
32
|
Casto J, Mandato A, Saxena S. dHis-troying Barriers: Deuteration Provides a Pathway to Increase Sensitivity and Accessible Distances for Cu 2+ Labels. J Phys Chem Lett 2021; 12:4681-4685. [PMID: 33979151 DOI: 10.1021/acs.jpclett.1c01002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recently, site-directed Cu2+ labeling has emerged as an incisive biophysical tool to directly report on distance constraints that pertain to the structure, conformational transitions, and dynamics of proteins and nucleic acids. However, short phase memory times inherent to the Cu2+ labels limit measurable distances to 4-5 nm. In this work we systematically examine different methods to dampen electron-nuclear and electron-electron coupled interactions to decrease rapid relaxation. We show that using Cu2+ spin concentrations up to ca. 800 μM has an invariant effect on relaxation and that increasing the cryoprotectant concentration reduces contributions of solvent protons to relaxation. On the other hand, the deuteration of protein and solvent dramatically increases the duration of the dipolar modulated signal by over 6-fold to 32 μs. Based on this increase in signal longevity, distances up to 9 nm and beyond can potentially be measured with Cu2+ labels.
Collapse
Affiliation(s)
- Joshua Casto
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alysia Mandato
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
33
|
NMR and EPR reveal a compaction of the RNA-binding protein FUS upon droplet formation. Nat Chem Biol 2021; 17:608-614. [PMID: 33686294 DOI: 10.1038/s41589-021-00752-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/22/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023]
Abstract
Many RNA-binding proteins undergo liquid-liquid phase separation, which underlies the formation of membraneless organelles, such as stress granules and P-bodies. Studies of the molecular mechanism of phase separation in vitro are hampered by the coalescence and sedimentation of organelle-sized droplets interacting with glass surfaces. Here, we demonstrate that liquid droplets of fused in sarcoma (FUS)-a protein found in cytoplasmic aggregates of amyotrophic lateral sclerosis and frontotemporal dementia patients-can be stabilized in vitro using an agarose hydrogel that acts as a cytoskeleton mimic. This allows their spectroscopic characterization by liquid-phase NMR and electron paramagnetic resonance spectroscopy. Protein signals from both dispersed and condensed phases can be observed simultaneously, and their respective proportions can be quantified precisely. Furthermore, the agarose hydrogel acts as a cryoprotectant during shock-freezing, which facilitates pulsed electron paramagnetic resonance measurements at cryogenic temperatures. Surprisingly, double electron-electron resonance measurements revealed a compaction of FUS in the condensed phase.
Collapse
|
34
|
Bahrenberg T, Jahn SM, Feintuch A, Stoll S, Goldfarb D. The decay of the refocused Hahn echo in double electron-electron resonance (DEER) experiments. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:161-173. [PMID: 37904783 PMCID: PMC10539729 DOI: 10.5194/mr-2-161-2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/13/2021] [Indexed: 11/01/2023]
Abstract
Double electron-electron resonance (DEER) is a pulse electron paramagnetic resonance (EPR) technique that measures distances between paramagnetic centres. It utilizes a four-pulse sequence based on the refocused Hahn spin echo. The echo decays with increasing pulse sequence length 2 ( τ 1 + τ 2 ) , where τ 1 and τ 2 are the two time delays. In DEER, the value of τ 2 is determined by the longest inter-spin distance that needs to be resolved, and τ 1 is adjusted to maximize the echo amplitude and, thus, sensitivity. We show experimentally that, for typical spin centres (nitroxyl, trityl, and Gd(III)) diluted in frozen protonated solvents, the largest refocused echo amplitude for a given τ 2 is obtained neither at very short τ 1 (which minimizes the pulse sequence length) nor at τ 1 = τ 2 (which maximizes dynamic decoupling for a given total sequence length) but rather at τ 1 values smaller than τ 2 . Large-scale spin dynamics simulations based on the coupled cluster expansion (CCE), including the electron spin and several hundred neighbouring protons, reproduce the experimentally observed behaviour almost quantitatively. They show that electron spin dephasing is driven by solvent protons via the flip-flop coupling among themselves and their hyperfine couplings to the electron spin.
Collapse
Affiliation(s)
- Thorsten Bahrenberg
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Samuel M. Jahn
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| |
Collapse
|
35
|
Soetbeer J, Millen M, Zouboulis K, Hülsmann M, Godt A, Polyhach Y, Jeschke G. Dynamical decoupling in water-glycerol glasses: a comparison of nitroxides, trityl radicals and gadolinium complexes. Phys Chem Chem Phys 2021; 23:5352-5369. [PMID: 33635938 DOI: 10.1039/d1cp00055a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our previous study on nitroxides in o-terphenyl (OTP) revealed two separable decoherence processes at low temperatures, best captured by the sum of two stretched exponentials (SSE) model. Dynamical decoupling (DD) extends both associated dephasing times linearly for 1 to 5 refocusing pulses [Soetbeer et al., Phys. Chem. Chem. Phys., 2018, 20, 1615]. Here we demonstrate an analogous DD behavior of water-soluble nitroxides in water-glycerol glass by using nitroxide and/or solvent deuteration for component assignment. Compared to the conventional Hahn experiment, we show that Carr-Purcell and Uhrig DD schemes are superior in resolving and identifying active dephasing mechanisms. Thereby, we observe a partial coherence loss to intramolecular nitroxide and trityl nuclei that can be alleviated, while the zero field splitting-induced losses for gadolinium labels cannot be refocused and contribute even at the central transition of this spin-7/2 system. Independent of the studied spin system, Uhrig DD leads to a characteristic convex dephasing envelope in both protonated water-glycerol and OTP glass, thus outperforming the Carr-Purcell scheme.
Collapse
Affiliation(s)
- Janne Soetbeer
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland.
| | - Marthe Millen
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland.
| | - Konstantin Zouboulis
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland.
| | - Miriam Hülsmann
- Bielefeld University, Department of Chemistry, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Adelheid Godt
- Bielefeld University, Department of Chemistry, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Yevhen Polyhach
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland.
| |
Collapse
|
36
|
Georgieva ER. Protein Conformational Dynamics upon Association with the Surfaces of Lipid Membranes and Engineered Nanoparticles: Insights from Electron Paramagnetic Resonance Spectroscopy. Molecules 2020; 25:E5393. [PMID: 33218036 PMCID: PMC7698768 DOI: 10.3390/molecules25225393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Detailed study of conformational rearrangements and dynamics of proteins is central to our understanding of their physiological functions and the loss of function. This review outlines the applications of the electron paramagnetic resonance (EPR) technique to study the structural aspects of proteins transitioning from a solution environment to the states in which they are associated with the surfaces of biological membranes or engineered nanoobjects. In the former case these structural transitions generally underlie functional protein states. The latter case is mostly relevant to the application of protein immobilization in biotechnological industries, developing methods for protein purification, etc. Therefore, evaluating the stability of the protein functional state is particularly important. EPR spectroscopy in the form of continuous-wave EPR or pulse EPR distance measurements in conjunction with protein spin labeling provides highly versatile and sensitive tools to characterize the changes in protein local dynamics as well as large conformational rearrangements. The technique can be widely utilized in studies of both protein-membrane and engineered nanoobject-protein complexes.
Collapse
Affiliation(s)
- Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| |
Collapse
|
37
|
Muok AR, Chua TK, Srivastava M, Yang W, Maschmann Z, Borbat PP, Chong J, Zhang S, Freed JH, Briegel A, Crane BR. Engineered chemotaxis core signaling units indicate a constrained kinase-off state. Sci Signal 2020; 13:13/657/eabc1328. [PMID: 33172954 DOI: 10.1126/scisignal.abc1328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacterial chemoreceptors, the histidine kinase CheA, and the coupling protein CheW form transmembrane molecular arrays with remarkable sensing properties. The receptors inhibit or stimulate CheA kinase activity depending on the presence of attractants or repellants, respectively. We engineered chemoreceptor cytoplasmic regions to assume a trimer of receptor dimers configuration that formed well-defined complexes with CheA and CheW and promoted a CheA kinase-off state. These mimics of core signaling units were assembled to homogeneity and investigated by site-directed spin-labeling with pulse-dipolar electron-spin resonance spectroscopy (PDS), small-angle x-ray scattering, targeted protein cross-linking, and cryo-electron microscopy. The kinase-off state was especially stable, had relatively low domain mobility, and associated the histidine substrate and docking domains with the kinase core, thus preventing catalytic activity. Together, these data provide an experimentally restrained model for the inhibited state of the core signaling unit and suggest that chemoreceptors indirectly sequester the kinase and substrate domains to limit histidine autophosphorylation.
Collapse
Affiliation(s)
- Alise R Muok
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Wen Yang
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Zach Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Petr P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Jenna Chong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Sheng Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
38
|
Fábregas Ibáñez L, Jeschke G, Stoll S. DeerLab: a comprehensive software package for analyzing dipolar electron paramagnetic resonance spectroscopy data. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:209-224. [PMID: 34568875 PMCID: PMC8462493 DOI: 10.5194/mr-1-209-2020] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/21/2020] [Indexed: 05/09/2023]
Abstract
Dipolar EPR spectroscopy (DEER and other techniques) enables the structural characterization of macromolecular and biological systems by measurement of distance distributions between unpaired electrons on a nanometer scale. The inference of these distributions from the measured signals is challenging due to the ill-posed nature of the inverse problem. Existing analysis tools are scattered over several applications with specialized graphical user interfaces. This renders comparison, reproducibility, and method development difficult. To remedy this situation, we present DeerLab, an open-source software package for analyzing dipolar EPR data that is modular and implements a wide range of methods. We show that DeerLab can perform one-step analysis based on separable non-linear least squares, fit dipolar multi-pathway models to multi-pulse DEER data, run global analysis with non-parametric distributions, and use a bootstrapping approach to fully quantify the uncertainty in the analysis.
Collapse
Affiliation(s)
- Luis Fábregas Ibáñez
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
39
|
Taguchi Y, Saio T, Kohda D. Distance Distribution between Two Iodine Atoms Derived from Small-Angle X-ray Scattering Interferometry for Analyzing a Conformational Ensemble of Heavy Atom-Labeled Small Molecules. J Phys Chem Lett 2020; 11:5451-5456. [PMID: 32558579 DOI: 10.1021/acs.jpclett.0c01107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
To obtain unbiased information about the dynamic conformational ensemble of a molecule in solution, one promising approach is small-angle X-ray scattering (SAXS). Conventionally, SAXS data are converted to a pair distribution function, which describes the distance distribution between all pairs of atoms within a molecule. If two strong X-ray scatterers are introduced and the background contributions from the other atoms are suppressed, then the distance distribution between the two scatterers provides spatial information about a flexible molecule. Gold nanocrystals can provide such information for distances of >50 Å. Here, we synthesized a chemical compound containing two iodine atoms attached to the ends of a flexible polyethylene glycol chain and used the relevant singly labeled and unlabeled compounds to suppress the background contribution. This is a feasibility demonstration to prove that the distance distribution in the range of 10-30 Å can be experimentally accessed by SAXS.
Collapse
Affiliation(s)
- Yuya Taguchi
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Tomohide Saio
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| |
Collapse
|
40
|
Lindemann WR, Mijalis AJ, Alonso JL, Borbat PP, Freed JH, Arnaout MA, Pentelute BL, Ortony JH. Conformational Dynamics in Extended RGD-Containing Peptides. Biomacromolecules 2020; 21:2786-2794. [PMID: 32469507 PMCID: PMC7388056 DOI: 10.1021/acs.biomac.0c00506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RGD is a prolific example of a tripeptide used in biomaterials for cell adhesion, but the potency of free or surface-bound RGD tripeptide is orders-of-magnitude less than the RGD domain within natural proteins. We designed a set of peptides with varying lengths, composed of fragments of fibronectin protein whose central three residues are RGD, in order to vary their conformational behavior without changing the binding site's chemical environment. With these peptides, we measure the conformational dynamics and transient structure of the active site. Our studies reveal how flanking residues affect conformational behavior and integrin binding. We find that disorder of the binding site is important to the potency of RGD peptides and that transient hydrogen bonding near the RGD site affects both the energy landscape roughness of the peptides and peptide binding. This phenomenon is independent of longer-range folding interactions and helps explain why short binding sequences, including RGD itself, do not fully replicate the integrin-targeting properties of extracellular matrix proteins. Our studies reinforce that peptide binding is a holistic event and fragments larger than those directly involved in binding should be considered in the design of peptide epitopes for functional biomaterials.
Collapse
Affiliation(s)
- William R Lindemann
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alexander J Mijalis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - José L Alonso
- Leukocyte Biology and Inflammation Program, Division of Nephrology and Department of Medicine, Massachusetts General Hospital, 149 13th Street, Charlestown, Massachusetts 02129, United States
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - M Amin Arnaout
- Leukocyte Biology and Inflammation Program, Division of Nephrology and Department of Medicine, Massachusetts General Hospital, 149 13th Street, Charlestown, Massachusetts 02129, United States
- Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Julia H Ortony
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
41
|
Wili N, Hintz H, Vanas A, Godt A, Jeschke G. Distance measurement between trityl radicals by pulse dressed electron paramagnetic resonance with phase modulation. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:75-87. [PMID: 37904888 PMCID: PMC10500722 DOI: 10.5194/mr-1-75-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/29/2020] [Indexed: 11/01/2023]
Abstract
Distance measurement in the nanometre range is among the most important applications of pulse electron paramagnetic resonance today, especially in biological applications. The longest distance that can be measured by all presently used pulse sequences is determined by the phase memory time T m of the observed spins. Here we show that one can measure the dipolar coupling during strong microwave irradiation by using an appropriate frequency- or phase-modulation scheme, i.e. by applying pulse sequences in the nutating frame. This decouples the electron spins from the surrounding nuclear spins and thus leads to significantly longer relaxation times of the microwave-dressed spins (i.e. the rotating frame relaxation times T 1 ρ and T 2 ρ ) compared to T m . The electron-electron dipolar coupling is not decoupled as long as both spins are excited, which can be implemented for trityl radicals at Q-band frequencies (35 GHz, 1.2 T). We show results for two bis-trityl rulers with inter-electron distances of about 4.1 and 5.3 nm and discuss technical challenges and possible next steps.
Collapse
Affiliation(s)
- Nino Wili
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Agathe Vanas
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Scherer A, Tischlik S, Weickert S, Wittmann V, Drescher M. Optimising broadband pulses for DEER depends on concentration and distance range of interest. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:59-74. [PMID: 37904889 PMCID: PMC10500711 DOI: 10.5194/mr-1-59-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/26/2020] [Indexed: 11/01/2023]
Abstract
EPR distance determination in the nanometre region has become an important tool for studying the structure and interaction of macromolecules. Arbitrary waveform generators (AWGs), which have recently become commercially available for EPR spectrometers, have the potential to increase the sensitivity of the most common technique, double electron-electron resonance (DEER, also called PELDOR), as they allow the generation of broadband pulses. There are several families of broadband pulses, which are different in general pulse shape and the parameters that define them. Here, we compare the most common broadband pulses. When broadband pulses lead to a larger modulation depth, they also increase the background decay of the DEER trace. Depending on the dipolar evolution time, this can significantly increase the noise level towards the end of the form factor and limit the potential increase in the modulation-to-noise ratio (MNR). We found asymmetric hyperbolic secant (HS{ 1 , 6 } ) pulses to perform best for short DEER traces, leading to a MNR improvement of up to 86 % compared to rectangular pulses. For longer traces we found symmetric hyperbolic secant (HS{ 1 , 1 } ) pulses to perform best; however, the increase compared to rectangular pulses goes down to 43 %.
Collapse
Affiliation(s)
- Andreas Scherer
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
| | - Sonja Tischlik
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
| | - Sabrina Weickert
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology,
University of Konstanz, Konstanz, Germany
| |
Collapse
|
44
|
Yang Z, Stein RA, Ngendahimana T, Pink M, Rajca S, Jeschke G, Eaton SS, Eaton GR, Mchaourab HS, Rajca A. Supramolecular Approach to Electron Paramagnetic Resonance Distance Measurement of Spin-Labeled Proteins. J Phys Chem B 2020; 124:3291-3299. [PMID: 32227839 DOI: 10.1021/acs.jpcb.0c00743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We demonstrate a host-guest molecular recognition approach to advance double electron-electron resonance (DEER) distance measurements of spin-labeled proteins. We synthesized an iodoacetamide derivative of 2,6-diazaadamantane nitroxide (DZD) spin label that could be doubly incorporated into T4 Lysozyme (T4L) by site-directed spin labeling with efficiency up to 50% per cysteine. The rigidity of the fused ring structure and absence of mobile methyl groups increase the spin echo dephasing time (Tm) at temperatures above 80 K. This enables DEER measurements of distances >4 nm in DZD-labeled T4L in glycerol/water at temperatures up to 150 K with increased sensitivity compared to that of a common spin label such as MTSL. Addition of β-cyclodextrin reduces the rotational correlation time of the label, slightly increases Tm, and most importantly, narrows (and slightly lengthens) the interspin distance distributions. The distance distributions are in good agreement with simulated distance distributions obtained by rotamer libraries. These results provide a foundation for developing supramolecular recognition to facilitate long-distance DEER measurements at near physiological temperatures.
Collapse
Affiliation(s)
- Zhimin Yang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Maren Pink
- IUMSC, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| |
Collapse
|
45
|
Chavan TS, Cheng RC, Jiang T, Mathews II, Stein RA, Koehl A, Mchaourab HS, Tajkhorshid E, Maduke M. A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the CLC Cl -/H + transport cycle. eLife 2020; 9:53479. [PMID: 32310757 PMCID: PMC7253180 DOI: 10.7554/elife.53479] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 04/18/2020] [Indexed: 12/16/2022] Open
Abstract
Among coupled exchangers, CLCs uniquely catalyze the exchange of oppositely charged ions (Cl– for H+). Transport-cycle models to describe and explain this unusual mechanism have been proposed based on known CLC structures. While the proposed models harmonize with many experimental findings, gaps and inconsistencies in our understanding have remained. One limitation has been that global conformational change – which occurs in all conventional transporter mechanisms – has not been observed in any high-resolution structure. Here, we describe the 2.6 Å structure of a CLC mutant designed to mimic the fully H+-loaded transporter. This structure reveals a global conformational change to improve accessibility for the Cl– substrate from the extracellular side and new conformations for two key glutamate residues. Together with DEER measurements, MD simulations, and functional studies, this new structure provides evidence for a unified model of H+/Cl– transport that reconciles existing data on all CLC-type proteins. Cells are shielded from harmful molecules and other threats by a thin, flexible layer called the membrane. However, this barrier also prevents chloride, sodium, protons and other ions from moving in or out of the cell. Channels and transporters are two types of membrane proteins that form passageways for these charged particles. Channels let ions flow freely from one side of the membrane to the other. To do so, these proteins change their three-dimensional shape to open or close as needed. On the other hand, transporters actively pump ions across the membrane to allow the charged particles to accumulate on one side. The shape changes needed for that type of movement are different: the transporters have to open a passageway on one side of the membrane while closing it on the other side, alternating openings to one side or the other. In general, channels and transporters are not related to each other, but one exception is a group called CLCs proteins. Present in many organisms, this family contains a mixture of channels and transporters. For example, humans have nine CLC proteins: four are channels that allow chloride ions in and out, and five are ‘exchange transporters’ that make protons and chloride ions cross the membrane in opposite directions. These proteins let one type of charged particle move freely across the membrane, which generates energy that the transporter then uses to actively pump the other ion in the direction needed by the cell. Yet, the exact three-dimensional changes required for CLC transporters and channels to perform their roles are still unknown. To investigate this question, Chavan, Cheng et al. harnessed a technique called X-ray crystallography, which allows scientists to look at biological molecules at the level of the atom. This was paired with other methods to examine a CLC mutant that adopts the shape of a normal CLC transporter when it is loaded with a proton. The experiments revealed how various elements in the transporter move relative to each other to adopt a structure that allows protons and chloride ions to enter the protein from opposite sides of the membrane, using separate pathways. While obtained on a bacterial CLC, these results can be applied to other CLC channels and transporters (including those in humans), shedding light on how this family transports charged particles across membranes. From bone diseases to certain types of seizures, many human conditions are associated with poorly functioning CLCs. Understanding the way these structures change their shapes to perform their roles could help to design new therapies for these health problems.
Collapse
Affiliation(s)
- Tanmay S Chavan
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Ricky C Cheng
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, United States
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Antoine Koehl
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, United States
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Merritt Maduke
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| |
Collapse
|
46
|
Abdullin D, Schiemann O. Pulsed Dipolar EPR Spectroscopy and Metal Ions: Methodology and Biological Applications. Chempluschem 2020; 85:353-372. [DOI: 10.1002/cplu.201900705] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/16/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| |
Collapse
|
47
|
Goldfarb D. Pulse EPR in biological systems - Beyond the expert's courtyard. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:102-108. [PMID: 31337564 DOI: 10.1016/j.jmr.2019.07.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/07/2019] [Accepted: 07/08/2019] [Indexed: 05/14/2023]
Abstract
Application of EPR to biological systems includes many techniques and applications. In this short perspective, which dares to look into the future, I focus on pulse EPR, which is my field of expertise. Generally, pulse EPR techniques can be divided into two main groups: (1) hyperfine spectroscopy, which explores electron-nuclear interactions, and (2) pulse-dipolar (PD) EPR spectroscopy, which is based on electron-electron spin interactions. Here I focus on PD-EPR because it has a better chance of becoming a widely applied, easy-to-use table-top method to study the structural and dynamic aspects of bio-molecules. I will briefly introduce this technique, its current state of the art, the challenges it is facing, and finally I will describe futuristic scenarios of low-cost PD-EPR approaches that can cross the diffusion barrier from the core of experts to the bulk of the scientific community.
Collapse
Affiliation(s)
- Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
48
|
Jeschke G. Quo vadis EPR? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:36-41. [PMID: 31345773 DOI: 10.1016/j.jmr.2019.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/21/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Complexity of paramagnetic catalysts and materials increases, and the same applies to systems targeted by integrative structural biology. Hence, EPR spectroscopists must find ways to enhance information content of their data. I argue that a third major wave of method development in EPR spectroscopy, which is triggered by recent advances in digital electronics and computing, can achieve this. Transfer of NMR methods to EPR will go on, but part of the new EPR methodology will depend on completely new concepts.
Collapse
Affiliation(s)
- Gunnar Jeschke
- ETH Zurich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| |
Collapse
|
49
|
Joseph B, Jaumann EA, Sikora A, Barth K, Prisner TF, Cafiso DS. In situ observation of conformational dynamics and protein ligand-substrate interactions in outer-membrane proteins with DEER/PELDOR spectroscopy. Nat Protoc 2019; 14:2344-2369. [PMID: 31278399 PMCID: PMC6886689 DOI: 10.1038/s41596-019-0182-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 04/18/2019] [Indexed: 12/01/2022]
Abstract
Observing structure and conformational dynamics of membrane proteins at high-resolution in their native environments is challenging because of the lack of suitable techniques. We have developed an approach for high-precision distance measurements in the nanometer range for outer membrane proteins (OMPs) in intact E. coli and native membranes. OMPs in Gram-negative bacteria rarely have reactive cysteines. This enables in-situ labeling of engineered cysteines with a methanethiosulfonate functionalized nitroxide spin label (MTSL) with minimal background signals. Following overexpression of the target protein, spin labeling is performed with E. coli or isolated outer membranes (OM) under selective conditions. The interspin distances are measured in-situ using pulsed electron-electron double resonance spectroscopy (PELDOR or DEER). The residual background signals, which are problematic for in-situ structural biology, contributes specifically to the intermolecular part of the signal and can be selectively removed to extract the desired interspin distance distribution. The initial cloning stage can take 5–7 d and the subsequent protein expression, OM isolation, spin labeling, PELDOR experiment, and the data analysis typically take 4–5 d. The described protocol provides a general strategy for observing protein-ligand/substrate interactions, oligomerization, and conformational dynamics of OMPs in the native OM and intact E. coli. EDITORIAL SUMMARY This protocol describes how to label bacterial outer membrane proteins with spin labels to study conformational changes and their interaction with ligands and substrates in native membranes and cells using Pulsed Electron-Electron Double Resonance (PELDOR or DEER) spectroscopy. TWEET A new protocol for studying conformational changes and ligand/substrate interactions of bacterial outer membrane proteins in-situ. COVER TEASER Studying membrane protein conformations in-situ
Collapse
Affiliation(s)
- Benesh Joseph
- Institute of Biophysics, Department of Physics, University of Frankfurt, Frankfurt am Main, Germany. .,Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany.
| | - Eva A Jaumann
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Arthur Sikora
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, VA, USA
| | - Katja Barth
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, VA, USA
| |
Collapse
|
50
|
Dal Farra MG, Richert S, Martin C, Larminie C, Gobbo M, Bergantino E, Timmel CR, Bowen AM, Di Valentin M. Light-Induced Pulsed EPR Dipolar Spectroscopy on a Paradigmatic Hemeprotein. Chemphyschem 2019; 20:931-935. [PMID: 30817078 PMCID: PMC6618045 DOI: 10.1002/cphc.201900139] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 02/27/2019] [Indexed: 01/12/2023]
Abstract
Light-induced pulsed EPR dipolar spectroscopic methods allow the determination of nanometer distances between paramagnetic sites. Here we employ orthogonal spin labels, a chromophore triplet state and a stable radical, to carry out distance measurements in singly nitroxide-labeled human neuroglobin. We demonstrate that Zn-substitution of neuroglobin, to populate the Zn(II) protoporphyrin IX triplet state, makes it possible to perform light-induced pulsed dipolar experiments on hemeproteins, extending the use of light-induced dipolar spectroscopy to this large class of metalloproteins. The versatility of the method is ensured by the employment of different techniques: relaxation-induced dipolar modulation enhancement (RIDME) is applied for the first time to the photoexcited triplet state. In addition, an alternative pulse scheme for laser-induced magnetic dipole (LaserIMD) spectroscopy, based on the refocused-echo detection sequence, is proposed for accurate zero-time determination and reliable distance analysis.
Collapse
Affiliation(s)
| | - Sabine Richert
- Centre for Advanced Electron Spin Resonance (CAESR) Department of Chemistry, Inorganic Chemistry LaboratoryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
- current affiliation: Institute of Physical ChemistryUniversity of FreiburgAlbertstr. 2179104FreiburgGermany
| | - Caterina Martin
- Department of BiologyUniversity of Padovaviale G. Colombo 335121PadovaItaly
- current affiliation: Groningen Biomolecular Science and Biotechnology InstituteUniversity of Groningen9700 ABGroningenThe Netherlands
| | - Charles Larminie
- Centre for Advanced Electron Spin Resonance (CAESR) Department of Chemistry, Inorganic Chemistry LaboratoryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Marina Gobbo
- Department of Chemical SciencesUniversity of PadovaVia Marzolo 135131PadovaItaly
| | | | - Christiane R. Timmel
- Centre for Advanced Electron Spin Resonance (CAESR) Department of Chemistry, Inorganic Chemistry LaboratoryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Alice M. Bowen
- Centre for Advanced Electron Spin Resonance (CAESR) Department of Chemistry, Inorganic Chemistry LaboratoryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Marilena Di Valentin
- Department of Chemical SciencesUniversity of PadovaVia Marzolo 135131PadovaItaly
| |
Collapse
|