1
|
Torricella F, Vitali V, Banci L. A systematic study on the effect of protonation and deuteration on electron spin Tm/ T2 in a cellular context. Phys Chem Chem Phys 2024. [PMID: 39037427 DOI: 10.1039/d4cp00599f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
In recent years, DEER experiments in pulsed EPR have garnered interest for their precise distance distribution insights in cellular and buffer setups. These measurements linked to electron spin Tm/T2 values of the labelled sample are impacted by the cellular environment being fully protonated or deuterated, as demonstrated in the present study.
Collapse
Affiliation(s)
- Francesco Torricella
- Magnetic Resonance Center, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy.
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, Maryland 20892-0520, USA
| | - Valentina Vitali
- Magnetic Resonance Center, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy.
- Dipartimento di Chimica, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanza Magnetiche di Metallo Proteine, 50019 Sesto Fiorentino, Italy
- Dipartimento di Chimica, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
2
|
Bizet M, Byrne D, Biaso F, Gerbaud G, Etienne E, Briola G, Guigliarelli B, Urban P, Dorlet P, Kalai T, Truan G, Martinho M. Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid. Chemistry 2024; 30:e202304307. [PMID: 38277424 DOI: 10.1002/chem.202304307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/28/2024]
Abstract
The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH• and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.
Collapse
Affiliation(s)
- Maxime Bizet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix Marseille Univ, CNRS, IMM, 13402, Marseille, France
| | - Frédéric Biaso
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Emilien Etienne
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Giuseppina Briola
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Philippe Urban
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Pierre Dorlet
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| | - Tamas Kalai
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Pécs, PO Box 99 Szigeti st. 12, H-7602 7624, Pécs, Hungary
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Marlène Martinho
- Aix Marseille Univ, CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 13402, Marseille, France
| |
Collapse
|
3
|
Dubroca T, Wang X, Mentink-Vigier F, Trociewitz B, Starck M, Parker D, Sherwin MS, Hill S, Krzystek J. Terahertz EPR spectroscopy using a 36-tesla high-homogeneity series-connected hybrid magnet. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107480. [PMID: 37331305 DOI: 10.1016/j.jmr.2023.107480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/24/2023] [Accepted: 05/13/2023] [Indexed: 06/20/2023]
Abstract
Electron Paramagnetic Resonance (EPR) is a powerful technique to study materials and biological samples on an atomic scale. High-field EPR in particular enables extracting very small g-anisotropies in organic radicals and half-filled 3d and 4f metal ions such as MnII (3d5) or GdIII (4f7), and resolving EPR signals from unpaired spins with very close g-values, both of which provide high-resolution details of the local atomic environment. Before the recent commissioning of the high-homogeneity Series Connected Hybrid magnet (SCH, superconducting + resistive) at the National High Magnetic Field Laboratory (NHMFL), the highest-field, high-resolution EPR spectrometer available was limited to 25 T using a purely resistive "Keck" magnet at the NHMFL. Herein, we report the first EPR experiments performed using the SCH magnet capable of reaching the field of 36 T, corresponding to an EPR frequency of 1 THz for g = 2. The magnet's intrinsic homogeneity (25 ppm, that is 0.9 mT at 36 T over 1 cm diameter, 1 cm length cylinder) was previously established by NMR. We characterized the magnet's temporal stability (5 ppm, which is 0.2 mT at 36 T over one-minute, the typical acquisition time) using 2,2-diphenyl-1-picrylhydrazyl (DPPH). This high resolution enables resolving the weak g-anisotropy of 1,3-bis(diphenylene)-2-phenylallyl (BDPA), Δg = 2.5 × 10-4 obtained from measurements at 932 GHz and 33 T. Subsequently, we recorded EPR spectra at multiple frequencies for two GdIII complexes with potential applications as spin labels. We demonstrated a significant reduction in line broadening in Gd[DTPA], attributed to second order zero field splitting, and a resolution enhancement of g-tensor anisotropy for Gd[sTPATCN]-SL.
Collapse
Affiliation(s)
- Thierry Dubroca
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA.
| | - Xiaoling Wang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Center for Molecular Magnetic Quantum Materials, University of Florida, Gainesville, FL 32611, USA
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Bianca Trociewitz
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Matthieu Starck
- Department of Chemistry, University of Durham, Durham DH13LE, UK
| | - David Parker
- Department of Chemistry, University of Durham, Durham DH13LE, UK
| | - Mark S Sherwin
- Department of Physics, University of California Santa Barbara, CA 93106, USA
| | - Stephen Hill
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Center for Molecular Magnetic Quantum Materials, University of Florida, Gainesville, FL 32611, USA; Department of Physics, Florida State University, Tallahassee FL 32306, USA
| | - J Krzystek
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA.
| |
Collapse
|
4
|
Rogers CJ, Bogdanov A, Seal M, Thornton ME, Su XC, Natrajan LS, Goldfarb D, Bowen AM. Frequency swept pulses for the enhanced resolution of ENDOR spectra detecting on higher spin transitions of Gd(III). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 351:107447. [PMID: 37119743 DOI: 10.1016/j.jmr.2023.107447] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 05/29/2023]
Abstract
Half-Integer High Spin (HIHS) systems with zero-field splitting (ZFS) parameters below 1 GHz are generally dominated by the spin |─1/2>→|+1/2 > central transition (CT). Accordingly, most pulsed Electron Paramagnetic Resonance (EPR) experiments are performed at this position for maximum sensitivity. However, in certain cases it can be desirable to detect higher spin transitions away from the CT in such systems. Here, we describe the use of frequency swept Wideband, Uniform Rate, Smooth Truncation (WURST) pulses for transferring spin population from the CT, and other transitions, of Gd(III) to the neighbouring higher spin transition |─3/2>→|─1/2 > at Q- and W-band frequencies. Specifically, we demonstrate this approach to enhance the sensitivity of 1H Mims Electron-Nuclear Double Resonance (ENDOR) measurements on two model Gd(III) aryl substituted 1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid (DO3A) complexes, focusing on transitions other than the CT. We show that an enhancement factor greater than 2 is obtained for both complexes at Q- and W-band frequencies by the application of two polarising pulses prior to the ENDOR sequence. This is in agreement with simulations of the spin dynamics of the system during WURST pulse excitation. The technique demonstrated here should allow more sensitive experiments to be measured away from the CT at higher operating temperatures, and be combined with any relevant pulse sequence.
Collapse
Affiliation(s)
- Ciarán J Rogers
- Department of Chemistry, Photon Science Institute and the National Research Facility for Electron Paramagnetic Resonance, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, UK
| | - Alexey Bogdanov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Manas Seal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Matthew E Thornton
- Department of Chemistry, Photon Science Institute and the National Research Facility for Electron Paramagnetic Resonance, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, UK
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition College of Chemistry, Nankai University, Tianjin 300071, China
| | - Louise S Natrajan
- Department of Chemistry, Photon Science Institute and the National Research Facility for Electron Paramagnetic Resonance, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, UK
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Alice M Bowen
- Department of Chemistry, Photon Science Institute and the National Research Facility for Electron Paramagnetic Resonance, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, UK.
| |
Collapse
|
5
|
Dunleavy R, Chandrasekaran S, Crane BR. Enzymatic Spin-Labeling of Protein N- and C-Termini for Electron Paramagnetic Resonance Spectroscopy. Bioconjug Chem 2023:10.1021/acs.bioconjchem.3c00029. [PMID: 36921260 PMCID: PMC10502183 DOI: 10.1021/acs.bioconjchem.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for investigating the structure and dynamics of proteins. The introduction of paramagnetic moieties at specific positions in a protein enables precise measurement of local structure and dynamics. This technique, termed site-directed spin-labeling, has traditionally been performed using cysteine-reactive radical-containing probes. However, large proteins are more likely to contain multiple cysteine residues and cysteine labeling at specific sites may be infeasible or impede function. To address this concern, we applied three peptide-ligating enzymes (sortase, asparaginyl endopeptidase, and inteins) for nitroxide labeling of N- and C-termini of select monomeric and dimeric proteins. Continuous wave and pulsed EPR (double electron electron resonance) experiments reveal specific attachment of nitroxide probes to ether N-termini (OaAEP1) or C-termini (sortase and intein) across three test proteins (CheY, CheA, and iLOV), thereby enabling a straightforward, highly specific, and general method for protein labeling. Importantly, the linker length (3, 5, and 9 residues for OaAEP1, intein, and sortase reactions, respectively) between the probe and the target protein has a large impact on the utility of distance measurements by pulsed EPR, with longer linkers leading to broader distributions. As these methods are only dependent on accessible N- and C-termini, we anticipate application to a wide range of protein targets for biomolecular EPR spectroscopy.
Collapse
Affiliation(s)
- Robert Dunleavy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
6
|
Bode BE, Fusco E, Nixon R, Buch CD, Weihe H, Piligkos S. Dipolar-Coupled Entangled Molecular 4f Qubits. J Am Chem Soc 2023; 145:2877-2883. [PMID: 36695706 PMCID: PMC9912257 DOI: 10.1021/jacs.2c10902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We demonstrate by use of continuous wave- and pulse-electron paramagnetic resonance spectroscopy on oriented single crystals of magnetically dilute YbIII ions in Yb0.01Lu0.99(trensal) that molecular entangled two-qubit systems can be constructed by exploiting dipolar interactions between neighboring YbIII centers. Furthermore, we show that the phase memory time and Rabi frequencies of these dipolar-interaction-coupled entangled two-qubit systems are comparable to the ones of the corresponding single qubits.
Collapse
Affiliation(s)
- Bela E. Bode
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, and Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St AndrewsKY16 9ST, U.K.,
| | - Edoardo Fusco
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, and Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St AndrewsKY16 9ST, U.K.
| | - Rachel Nixon
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, and Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St AndrewsKY16 9ST, U.K.
| | - Christian D. Buch
- Department
of Chemistry, University of Copenhagen, CopenhagenDK-2100, Denmark
| | - Høgni Weihe
- Department
of Chemistry, University of Copenhagen, CopenhagenDK-2100, Denmark
| | - Stergios Piligkos
- Department
of Chemistry, University of Copenhagen, CopenhagenDK-2100, Denmark,
| |
Collapse
|
7
|
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
|
8
|
Hofmann L, Mandato A, Saxena S, Ruthstein S. The use of EPR spectroscopy to study transcription mechanisms. Biophys Rev 2022; 14:1141-1159. [PMID: 36345280 PMCID: PMC9636360 DOI: 10.1007/s12551-022-01004-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 02/08/2023] Open
Abstract
Electron paramagnetic resonance (EPR) spectroscopy has become a promising structural biology tool to resolve complex and dynamic biological mechanisms in-vitro and in-cell. Here, we focus on the advantages of continuous wave (CW) and pulsed EPR distance measurements to resolve transcription processes and protein-DNA interaction. The wide range of spin-labeling approaches that can be used to follow structural changes in both protein and DNA render EPR a powerful method to study protein-DNA interactions and structure-function relationships in other macromolecular complexes. EPR-derived data goes well beyond static structural information and thus serves as the method of choice if dynamic insight is needed. Herein, we describe the conceptual details of the theory and the methodology and illustrate the use of EPR to study the protein-DNA interaction of the copper-sensitive transcription factor, CueR.
Collapse
Affiliation(s)
- L. Hofmann
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat-Gan, Israel
| | - A. Mandato
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA USA
| | - S. Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA USA
| | - S. Ruthstein
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat-Gan, Israel
| |
Collapse
|
9
|
Hofmann L, Ruthstein S. EPR Spectroscopy Provides New Insights into Complex Biological Reaction Mechanisms. J Phys Chem B 2022; 126:7486-7494. [PMID: 36137278 PMCID: PMC9549461 DOI: 10.1021/acs.jpcb.2c05235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In the last 20 years, the use of electron paramagnetic
resonance
(EPR) has made a pronounced and lasting impact in the field of structural
biology. The advantage of EPR spectroscopy over other structural techniques
is its ability to target even minor conformational changes in any
biomolecule or macromolecular complex, independent of its size or
complexity, or whether it is in solution or in the cell during a biological
or chemical reaction. Here, we focus on the use of EPR spectroscopy
to study transmembrane transport and transcription mechanisms. We
discuss experimental and analytical concerns when referring to studies
of two biological reaction mechanisms, namely, transfer of copper
ions by the human copper transporter hCtr1 and the mechanism of action
of the Escherichia coli copper-dependent
transcription factor CueR. Last, we elaborate on future avenues in
the field of EPR structural biology.
Collapse
Affiliation(s)
- Lukas Hofmann
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| |
Collapse
|
10
|
Buch CD, Kundu K, Marbey JJ, van Tol J, Weihe H, Hill S, Piligkos S. Spin–Lattice Relaxation Decoherence Suppression in Vanishing Orbital Angular Momentum Qubits. J Am Chem Soc 2022; 144:17597-17603. [DOI: 10.1021/jacs.2c07057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian D. Buch
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Krishnendu Kundu
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Jonathan J. Marbey
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Johan van Tol
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Høgni Weihe
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Stephen Hill
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Stergios Piligkos
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| |
Collapse
|
11
|
Mekkattu Tharayil S, Mahawaththa MC, Feintuch A, Maleckis A, Ullrich S, Morewood R, Maxwell MJ, Huber T, Nitsche C, Goldfarb D, Otting G. Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:169-182. [PMID: 37904871 PMCID: PMC10539774 DOI: 10.5194/mr-3-169-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 11/01/2023]
Abstract
The paramagnetism of a lanthanoid tag site-specifically installed on a protein provides a rich source of structural information accessible by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy. Here we report a lanthanoid tag for selective reaction with cysteine or selenocysteine with formation of a (seleno)thioether bond and a short tether between the lanthanoid ion and the protein backbone. The tag is assembled on the protein in three steps, comprising (i) reaction with 4-fluoro-2,6-dicyanopyridine (FDCP); (ii) reaction of the cyano groups with α -cysteine, penicillamine or β -cysteine to complete the lanthanoid chelating moiety; and (iii) titration with a lanthanoid ion. FDCP reacts much faster with selenocysteine than cysteine, opening a route for selective tagging in the presence of solvent-exposed cysteine residues. Loaded with Tb 3 + and Tm 3 + ions, pseudocontact shifts were observed in protein NMR spectra, confirming that the tag delivers good immobilisation of the lanthanoid ion relative to the protein, which was also manifested in residual dipolar couplings. Completion of the tag with different 1,2-aminothiol compounds resulted in different magnetic susceptibility tensors. In addition, the tag proved suitable for measuring distance distributions in double electron-electron resonance experiments after titration with Gd 3 + ions.
Collapse
Affiliation(s)
| | - Mithun C. Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michael J. Maxwell
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
12
|
Keeley J, Choudhury T, Galazzo L, Bordignon E, Feintuch A, Goldfarb D, Russell H, Taylor MJ, Lovett JE, Eggeling A, Fábregas Ibáñez L, Keller K, Yulikov M, Jeschke G, Kuprov I. Neural networks in pulsed dipolar spectroscopy: A practical guide. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 338:107186. [PMID: 35344921 DOI: 10.1016/j.jmr.2022.107186] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
This is a methodological guide to the use of deep neural networks in the processing of pulsed dipolar spectroscopy (PDS) data encountered in structural biology, organic photovoltaics, photosynthesis research, and other domains featuring long-lived radical pairs and paramagnetic metal ions. PDS uses distance dependence of magnetic dipolar interactions; measuring a single well-defined distance is straightforward, but extracting distance distributions is a hard and mathematically ill-posed problem requiring careful regularisation and background fitting. Neural networks do this exceptionally well, but their "robust black box" reputation hides the complexity of their design and training - particularly when the training dataset is effectively infinite. The objective of this paper is to give insight into training against simulated databases, to discuss network architecture choices, to describe options for handling DEER (double electron-electron resonance) and RIDME (relaxation-induced dipolar modulation enhancement) experiments, and to provide a practical data processing flowchart.
Collapse
Affiliation(s)
- Jake Keeley
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Tajwar Choudhury
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva, Switzerland
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva, Switzerland
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hannah Russell
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
| | - Michael J Taylor
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
| | - Andrea Eggeling
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Luis Fábregas Ibáñez
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Katharina Keller
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom.
| |
Collapse
|
13
|
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
|
14
|
Jash C, Feintuch A, Nudelman S, Manukovsky N, Abdelkader EH, Bhattacharya S, Jeschke G, Otting G, Goldfarb D. DEER experiments reveal fundamental differences between calmodulin complexes with IQ and MARCKS peptides in solution. Structure 2022; 30:813-827.e5. [PMID: 35397204 DOI: 10.1016/j.str.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/09/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022]
Abstract
Calmodulin (CaM) is a calcium-binding protein that regulates the function of many proteins by indirectly conferring Ca2+ sensitivity, and it undergoes a large conformational change on partners' binding. We compared the solution binding mode of the target peptides MARCKS and IQ by double electron-electron resonance (DEER) distance measurements and paramagnetic NMR. We combined nitroxide and Gd(III) spin labels, including specific substitution of one of the Ca2+ ions in the CaM mutant N60D by a Gd(III) ion. The binding of MARCKS to holo-CaM resulted neither in a closed conformation nor in a unique relative orientation between the two CaM domains, in contrast with the crystal structure. Binding of IQ to holo-CaM did generate a closed conformation. Using elastic network modeling and 12 distance restraints obtained from multiple holo-CaM/IQ DEER data, we derived a model of the solution structure, which is in reasonable agreement with the crystal structure.
Collapse
Affiliation(s)
- Chandrima Jash
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Nudelman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Nurit Manukovsky
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Sudeshna Bhattacharya
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
15
|
Walke G, Aupič J, Kashoua H, Janoš P, Meron S, Shenberger Y, Qasem Z, Gevorkyan-Airapetov L, Magistrato A, Ruthstein S. Dynamical interplay between the human high-affinity copper transporter hCtr1 and its cognate metal ion. Biophys J 2022; 121:1194-1204. [PMID: 35202609 PMCID: PMC9034245 DOI: 10.1016/j.bpj.2022.02.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/12/2021] [Accepted: 02/17/2022] [Indexed: 11/02/2022] Open
Abstract
Abnormal cellular copper levels have been clearly implicated in genetic diseases, cancer, and neurodegeneration. Ctr1, a high affinity copper transporter, is an homotrimeric integral membrane protein that provides the main route for cellular copper uptake. Together with a sophisticated copper transport system, Ctr1 regulates Cu(I) metabolism in eukaryotes. Despite its pivotal role in normal cell function, the molecular mechanism of copper uptake and transport via Ctr1 remains elusive. In this study, electron paramagnetic resonance (EPR), UV-visible spectroscopy, and all-atom simulations were employed to explore Cu(I) binding to full-length human Ctr1 (hCtr1), thereby elucidating how metal binding at multiple distinct sites affects the hCtr1 conformational dynamics. We demonstrate that each hCtr1 monomer binds up to 5 Cu(I) ions and that progressive Cu(I) binding triggers a marked structural rearrangement in the hCtr1 C-terminal region. The observed Cu(I)-induced conformational remodelling suggests that the C-terminal region may play a dual role, serving both as a channel gate and as a shuttle mediating the delivery of Cu ions from the extracellular hCtr1 selectivity filter to intracellular metallochaperones. Our findings thus contribute to a more complete understanding of the mechanism of hCtr1-mediated Cu(I) uptake and provide a conceptual basis for developing mechanism-based therapeutics for treating pathological conditions linked to de-regulated copper metabolism.
Collapse
Affiliation(s)
- Gulshan Walke
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Jana Aupič
- Department National Research Council of Italy (CNR) - Institute of Material (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Hadeel Kashoua
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Pavel Janoš
- Department National Research Council of Italy (CNR) - Institute of Material (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Shelly Meron
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Yulia Shenberger
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Zena Qasem
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002
| | - Alessandra Magistrato
- Department National Research Council of Italy (CNR) - Institute of Material (IOM) c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy.
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan, Israel, 5290002.
| |
Collapse
|
16
|
Honrao C, Teissier N, Zhang B, Powers R, O’Day EM. Gadolinium-Based Paramagnetic Relaxation Enhancement Agent Enhances Sensitivity for NUS Multidimensional NMR-Based Metabolomics. Molecules 2021; 26:molecules26175115. [PMID: 34500549 PMCID: PMC8433644 DOI: 10.3390/molecules26175115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 01/03/2023] Open
Abstract
Gadolinium is a paramagnetic relaxation enhancement (PRE) agent that accelerates the relaxation of metabolite nuclei. In this study, we noted the ability of gadolinium to improve the sensitivity of two-dimensional, non-uniform sampled NMR spectral data collected from metabolomics samples. In time-equivalent experiments, the addition of gadolinium increased the mean signal intensity measurement and the signal-to-noise ratio for metabolite resonances in both standard and plasma samples. Gadolinium led to highly linear intensity measurements that correlated with metabolite concentrations. In the presence of gadolinium, we were able to detect a broad array of metabolites with a lower limit of detection and quantification in the low micromolar range. We also observed an increase in the repeatability of intensity measurements upon the addition of gadolinium. The results of this study suggest that the addition of a gadolinium-based PRE agent to metabolite samples can improve NMR-based metabolomics.
Collapse
Affiliation(s)
| | | | - Bo Zhang
- Olaris, Inc., Waltham, MA 02451, USA; (C.H.); (N.T.); (B.Z.)
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Correspondence: (R.P.); (E.M.O.)
| | - Elizabeth M. O’Day
- Olaris, Inc., Waltham, MA 02451, USA; (C.H.); (N.T.); (B.Z.)
- Correspondence: (R.P.); (E.M.O.)
| |
Collapse
|