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Ben‐Ishay Y, Barak Y, Feintuch A, Ouari O, Pierro A, Mileo E, Su X, Goldfarb D. Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy. Protein Sci 2024; 33:e4903. [PMID: 38358137 PMCID: PMC10868451 DOI: 10.1002/pro.4903] [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: 11/14/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.
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Affiliation(s)
- Yasmin Ben‐Ishay
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Barak
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
| | - Akiva Feintuch
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Olivier Ouari
- CNRS, ICR, Institut de Chimie RadicalaireAix‐Marseille UniversitéMarseilleFrance
| | - Annalisa Pierro
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
- Present address:
Konstanz Research School Chemical Biology, Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Elisabetta Mileo
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
| | - Xun‐Cheng Su
- State Key Laboratory of Elemento‐organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular RecognitionCollege of Chemistry, Nankai UniversityTianjinChina
| | - Daniella Goldfarb
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
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2
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Bogetti X, Saxena S. Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics. Chempluschem 2024; 89:e202300506. [PMID: 37801003 DOI: 10.1002/cplu.202300506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/07/2023]
Abstract
Electron paramagnetic resonance (EPR) has become a powerful probe of conformational heterogeneity and dynamics of biomolecules. In this Review, we discuss different computational modeling techniques that enrich the interpretation of EPR measurements of dynamics or distance restraints. A variety of spin labels are surveyed to provide a background for the discussion of modeling tools. Molecular dynamics (MD) simulations of models containing spin labels provide dynamical properties of biomolecules and their labels. These simulations can be used to predict EPR spectra, sample stable conformations and sample rotameric preferences of label sidechains. For molecular motions longer than milliseconds, enhanced sampling strategies and de novo prediction software incorporating or validated by EPR measurements are able to efficiently refine or predict protein conformations, respectively. To sample large-amplitude conformational transition, a coarse-grained or an atomistic weighted ensemble (WE) strategy can be guided with EPR insights. Looking forward, we anticipate an integrative strategy for efficient sampling of alternate conformations by de novo predictions, followed by validations by systematic EPR measurements and MD simulations. Continuous pathways between alternate states can be further sampled by WE-MD including all intermediate states.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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3
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Pierro A, Tamburrini KC, Leguenno H, Gerbaud G, Etienne E, Guigliarelli B, Belle V, Zambelli B, Mileo E. In-cell investigation of the conformational landscape of the GTPase UreG by SDSL-EPR. iScience 2023; 26:107855. [PMID: 37766968 PMCID: PMC10520941 DOI: 10.1016/j.isci.2023.107855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/07/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
UreG is a cytosolic GTPase involved in the maturation network of urease, an Ni-containing bacterial enzyme. Previous investigations in vitro showed that UreG features a flexible tertiary organization, making this protein the first enzyme discovered to be intrinsically disordered. To determine whether this heterogeneous behavior is maintained in the protein natural environment, UreG structural dynamics was investigated directly in intact bacteria by in-cell EPR. This approach, based on site-directed spin labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy, enables the study of proteins in their native environment. The results show that UreG maintains heterogeneous structural landscape in-cell, existing in a conformational ensemble of two major conformers, showing either random coil-like or compact properties. These data support the physiological relevance of the intrinsically disordered nature of UreG and indicates a role of protein flexibility for this specific enzyme, possibly related to the regulation of promiscuous protein interactions for metal ion delivery.
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Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Ketty Concetta Tamburrini
- Aix Marseille Univ, CNRS, AFMB, 13009 Marseille, France
- INRAE, Aix Marseille Univ, BBF, 13009 Marseille, France
| | - Hugo Leguenno
- Aix Marseille Univ, CNRS, IMM, Microscopy Core Facility, 13009 Marseille, France
| | | | | | | | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
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4
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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.
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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
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5
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Bogetti X, Bogetti A, Casto J, Rule G, Chong L, Saxena S. Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation. Protein Sci 2023; 32:e4770. [PMID: 37632831 PMCID: PMC10503414 DOI: 10.1002/pro.4770] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/14/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
The catalytic activity of human glutathione S-transferase A1-1 (hGSTA1-1), a homodimeric detoxification enzyme, is dependent on the conformational dynamics of a key C-terminal helix α9 in each monomer. However, the structural details of how the two monomers interact upon binding of substrates is not well understood and the structure of the ligand-free state of the hGSTA1-1 homodimer has not been resolved. Here, we used a combination of electron paramagnetic resonance (EPR) distance measurements and weighted ensemble (WE) simulations to characterize the conformational ensemble of the ligand-free state at the atomic level. EPR measurements reveal a broad distance distribution between a pair of Cu(II) labels in the ligand-free state that gradually shifts and narrows as a function of increasing ligand concentration. These shifts suggest changes in the relative positioning of the two α9 helices upon ligand binding. WE simulations generated unbiased pathways for the seconds-timescale transition between alternate states of the enzyme, leading to the generation of atomically detailed structures of the ligand-free state. Notably, the simulations provide direct observations of negative cooperativity between the monomers of hGSTA1-1, which involve the mutually exclusive docking of α9 in each monomer as a lid over the active site. We identify key interactions between residues that lead to this negative cooperativity. Negative cooperativity may be essential for interaction of hGSTA1-1 with a wide variety of toxic substrates and their subsequent neutralization. More broadly, this work demonstrates the power of integrating EPR distances with WE rare-events sampling strategy to gain mechanistic information on protein function at the atomic level.
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Affiliation(s)
- Xiaowei Bogetti
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Anthony Bogetti
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Joshua Casto
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Gordon Rule
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
| | - Lillian Chong
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Sunil Saxena
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
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6
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Wang XW, Zhang X, Cui CY, Li B, Goldfarb D, Yang Y, Su XC. Stabilizing Nitroxide Spin Labels for Structural and Conformational Studies of Biomolecules by Maleimide Treatment. Chemistry 2023; 29:e202301350. [PMID: 37354082 DOI: 10.1002/chem.202301350] [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: 04/28/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/26/2023]
Abstract
Nitroxide (NO) spin radicals are effective in characterizing structures, interactions and dynamics of biomolecules. The EPR applications in cell lysates or intracellular milieu require stable spin labels, but NO radicals are unstable in such conditions. We showed that the destabilization of NO radicals in cell lysates or even in cells is caused by NADPH/NADH related enzymes, but not by the commonly believed reducing reagents such as GSH. Maleimide stabilizes the NO radicals in the cell lysates by consumption of the NADPH/NADH that are essential for the enzymes involved in destabilizing NO radicals, instead of serving as the solo thiol scavenger. The maleimide treatment retains the crowding properties of the intracellular components and allows to perform long-time EPR measurements of NO labeled biomolecules close to the intracellular conditions. The strategy of maleimide treatment on cell lysates for the EPR applications has been demonstrated on double electron-electron resonance (DEER) measurements on a number of NO labeled protein samples. The method opens a broad application range for the NO labeled biomolecules by EPR in conditions that resemble the intracellular milieu.
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Affiliation(s)
- Xi-Wei Wang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xing Zhang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chao-Yu Cui
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - 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
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7
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultrafast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. J Am Chem Soc 2023; 145:14608-14620. [PMID: 37364003 PMCID: PMC10440187 DOI: 10.1021/jacs.3c00967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Site-directed spin-labeling (SDSL)─in combination with double electron-electron resonance (DEER) spectroscopy─has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. DEER combined with in situ SDSL in live cells is challenging since current bioorthogonal labeling approaches are too slow to allow for complete labeling with low concentrations of spin label prior to loss of signal from cellular reduction. Here, we overcome this limitation by genetically encoding a novel family of small, tetrazine-bearing noncanonical amino acids (Tet-v4.0) at multiple sites in proteins expressed in Escherichia coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans-cyclooctene (sTCO)-functionalized nitroxides─including a gem-diethyl-substituted nitroxide with enhanced stability in cells─with rate constants that can exceed 106 M-1 s-1. The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro. Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and support assignment of the conformational state of an MBP mutant within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification.
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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8
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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.
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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.
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9
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Pelletier R, Danylchuk DI, Benaissa H, Broch F, Vauchelles R, Gautier A, Klymchenko AS. Genetic Targeting of Solvatochromic Dyes for Probing Nanoscale Environments of Proteins in Organelles. Anal Chem 2023. [PMID: 37229557 DOI: 10.1021/acs.analchem.3c00515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A variety of protein tags are available for genetically encoded protein labeling, which allow their precise localization and tracking inside the cells. A new dimension in protein imaging can be offered by combining protein tags with polarity-sensitive fluorescent probes, which provide information about local nanoscale environments of target proteins within the subcellular compartments (organelles). Here, we designed three fluorescent probes based on solvatochromic nile red dye, conjugated to a HaloTag reactive targeting group through polyethylene glycol linkers of varying lengths. The probe with medium linker length, NR12-Halo, was found to label specifically a large variety of proteins localized in defined cell compartments, such as plasma membranes (outer and inner leaflets), endoplasmic reticulum, Golgi apparatus, cytosol, microtubules, actin, and chromatin. Owing to its polarity-sensitive fluorophore, the probe clearly distinguished the proteins localized within apolar lipid membranes from other proteins. Moreover, it revealed dramatic changes in the environment during the life cycle of proteins from biosynthesis to their expected localization and, finally, to recycling inside lysosomes. Heterogeneity in the local polarity of some membrane proteins also suggested a formation of low-polar protein aggregates, for example, within cell-cell contacts. The approach also showed that mechanical stress (cell shrinking by osmotic shock) induced a general polarity decrease in membrane proteins, probably due to the condensation of biomolecules. Finally, the nanoenvironment of some membrane proteins was affected by a polyunsaturated fatty acid diet, which provided the bridge between organization of lipids and proteins. The developed solvatochromic HaloTag probe constitutes a promising tool for probing nanoscale environments of proteins and their interactions within subcellular structures.
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Affiliation(s)
- Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Hela Benaissa
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Fanny Broch
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Romain Vauchelles
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Arnaud Gautier
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
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10
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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.
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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.
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11
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Casto J, Bogetti X, Hunter HR, Hasanbasri Z, Saxena S. "Store-bought is fine": Sensitivity considerations using shaped pulses for DEER measurements on Cu(II) labels. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 349:107413. [PMID: 36867974 DOI: 10.1016/j.jmr.2023.107413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/27/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
The narrow excitation bandwidth of monochromic pulses is a sensitivity limitation for pulsed dipolar spectroscopy on Cu(II)-based measurements. In response, frequency-swept pulses with large excitation bandwidths have been adopted to probe a greater range of the EPR spectrum. However, much of the work utilizing frequency-swept pulses in Cu(II) distance measurements has been carried out on home-built spectrometers and equipment. Herein, we carry out systematic Cu(II) based distance measurements to demonstrate the capability of chirp pulses on commercial instrumentation. More importantly we delineate sensitivity considerations under acquisition schemes that are necessary for robust distance measurements using Cu(II) labels for proteins. We show that a 200 MHz sweeping bandwidth chirp pulse can improve the sensitivity of long-range distance measurements by factors of three to four. The sensitivity of short-range distances only increases slightly due to special considerations for the chirp pulse duration relative to the period length of the modulated dipolar signal. Enhancements in sensitivity also dramatically reduce measurement collection times enabling rapid collection of orientationally averaged Cu(II) distance measurements in under two hours.
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Affiliation(s)
- Joshua Casto
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Hannah R Hunter
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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12
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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.
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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
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13
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Huang K, Fang X. A review on recent advances in methods for site-directed spin labeling of long RNAs. Int J Biol Macromol 2023; 239:124244. [PMID: 37001783 DOI: 10.1016/j.ijbiomac.2023.124244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
RNAs are important biomolecules that play essential roles in various cellular processes and are crucially linked with many human diseases. The key to elucidate the mechanisms underlying their biological functions and develop RNA-based therapeutics is to investigate RNA structure and dynamics and their connections to function in detail using a variety of approaches. Magnetic resonance techniques including paramagnetic nuclear magnetic resonance (NMR) and electron magnetic resonance (EPR) spectroscopies have proved to be powerful tools to gain insights into such properties. The prerequisites for paramagnetic NMR and EPR studies on RNAs are to achieve site-specific spin labeling of the intrinsically diamagnetic RNAs, which however is not trivial, especially for long ones. In this review, we present some covalent labeling strategies that allow site-specific introduction of electron spins to long RNAs. Generally, these strategies include assembly of long RNAs via enzymatic ligation of short oligonucleotides, co- and post-transcriptional site-specific labeling empowered with the unnatural base pair system, and direct enzymatic functionalization of natural RNAs. We introduce a few case studies to discuss the advantages and limitations of each strategy, and to provide a vision for the future development.
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14
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Mittal S, Dutta S, Shukla D. Reconciling membrane protein simulations with experimental DEER spectroscopy data. Phys Chem Chem Phys 2023; 25:6253-6262. [PMID: 36757376 DOI: 10.1039/d2cp02890e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Spectroscopy experiments are crucial to study membrane proteins for which traditional structure determination methods still prove challenging. Double electron-electron resonance (DEER) spectroscopy experiments provide protein residue-pair distance distributions that are indicative of their conformational heterogeneity. Atomistic molecular dynamics (MD) simulations are another tool that have been proven to be vital to study the structural dynamics of membrane proteins such as to identify inward-open, occluded, and outward-open conformations of transporter membrane proteins, among other partially open or closed states of the protein. Yet, studies have reported that there is no direct consensus between the distributional data from DEER experiments and MD simulations, which has challenged validation of structures obtained from long-timescale simulations and using simulations to design experiments. Current coping strategies for comparisons rely on heuristics, such as mapping the nearest matching peaks between two ensembles or biased simulations. Here we examine the differences in residue-pair distance distributions arising due to the choice of membranes around the protein and covalent modification of a pair of residues to nitroxide spin labels in DEER experiments. Through comparing MD simulations of two proteins, PepTSo and LeuT-both of which have been characterized using DEER experiments previously-we show that the proteins' dynamics are similar despite the choice of the detergent micelle as a membrane mimetic in DEER experiments. On the other hand, covalently modified residues show slight local differences in their dynamics and a huge divergence when the oxygen atom pair distances between spin labeled residues are measured rather than protein backbone distances. Given the computational expense associated with pairwise MTSSL labeled MD simulations, we examine the use of biased simulations to explore the conformational dynamics of the spin labels only to reveal that such simulations alter the underlying protein dynamics. Our study identifies the main cause for the mismatch between DEER experiments and MD simulations and will accelerate the development of potential mitigation strategies to improve the match.
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Affiliation(s)
- Shriyaa Mittal
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Soumajit Dutta
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Diwakar Shukla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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15
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Hasanbasri Z, Poncelet M, Hunter H, Driesschaert B, Saxena S. A new 13C trityl-based spin label enables the use of DEER for distance measurements. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 347:107363. [PMID: 36620971 PMCID: PMC9928843 DOI: 10.1016/j.jmr.2022.107363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Triarylmethyl (TAM)-based labels, while still underutilized, are a powerful class of labels for pulsed-Electron Spin Resonance (ESR) distance measurements. They feature slow relaxation rates for long-lasting signals, high stability for cellular experiments, and narrow spectral features for efficient excitation of the spins. However, the typical narrow line shape limits the available distance measurements to only single-frequency experiments, such as Double Quantum Coherence (DQC) and Relaxation Induced Dipolar Modulation Enhancement (RIDME), which can be complicated to perform or hard to process. Therefore, widespread usage of TAM labels can be enhanced by the use of Double Electron-Electron Resonance (DEER) distance measurements. In this work, we developed a new spin label, 13C1-mOX063-d24, with a 13C isotope as the radical center. Due to the resolved hyperfine splitting, the spectrum is sufficiently broadened to permit DEER-based experiments at Q-band spectrometers. Additionally, this new label can be incorporated orthogonally with Cu(II)-based protein label. The orthogonal labeling scheme enables DEER distance measurement at X-band frequencies. Overall, the new trityl label allows for DEER-based distance measurements that complement existing TAM-label DQC and RIDME experiments.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Martin Poncelet
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, WV 26506, United States
| | - Hannah Hunter
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, WV 26506, United States; C. Eugene Bennett Department of Chemistry West Virginia University, Morgantown, WV 26506, United States.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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16
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultra-Fast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525763. [PMID: 36747808 PMCID: PMC9901033 DOI: 10.1101/2023.01.26.525763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Studying protein structures and dynamics directly in the cellular environments in which they function is essential to fully understand the molecular mechanisms underlying cellular processes. Site-directed spin-labeling (SDSL)-in combination with double electron-electron resonance (DEER) spectroscopy-has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. In-cell DEER spectroscopy on proteins in mammalian cells has thus far not been possible due to the notable challenges of spin-labeling in live cells. In-cell SDSL requires exquisite biorthogonality, high labeling reaction rates and low background signal from unreacted residual spin label. While the bioorthogonal reaction must be highly specific and proceed under physiological conditions, many spin labels display time-dependent instability in the reducing cellular environment. Additionally, high concentrations of spin label can be toxic. Thus, an exceptionally fast bioorthogonal reaction is required that can allow for complete labeling with low concentrations of spin-label prior to loss of signal. Here we utilized genetic code expansion to site-specifically encode a novel family of small, tetrazine-bearing non-canonical amino acids (Tet-v4.0) at multiple sites in green fluorescent protein (GFP) and maltose binding protein (MBP) expressed both in E. coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans -cyclooctene (sTCO)-functionalized nitroxides-including a gem -diethyl-substituted nitroxide with enhanced stability in cells-with rate constants that can exceed 10 6 M -1 s -1 . The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live HEK293T cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide added directly to the culture medium. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro . Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and successfully discerned the conformational state of MBP within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification. TOC
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
- Equal contributors
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
- Equal contributors
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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17
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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.
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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.
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18
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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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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.
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19
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Scherer A, Yao X, Qi M, Wiedmaier M, Godt A, Drescher M. Increasing the Modulation Depth of Gd III-Based Pulsed Dipolar EPR Spectroscopy (PDS) with Porphyrin-Gd III Laser-Induced Magnetic Dipole Spectroscopy. J Phys Chem Lett 2022; 13:10958-10964. [PMID: 36399541 PMCID: PMC9720741 DOI: 10.1021/acs.jpclett.2c02138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Distance determination with pulsed EPR has become an important technique for the structural investigation of biomacromolecules, with double electron-electron resonance spectroscopy (DEER) as the most important method. GdIII-based spin labels are one of the most frequently used spin labels for DEER owing to their stability against reduction, high magnetic moment, and absence of orientation selection. A disadvantage of GdIII-GdIII DEER is the low modulation depth due to the broad EPR spectrum of GdIII. Here, we introduce laser-induced magnetic dipole spectroscopy (LaserIMD) with a spin pair consisting of GdIII(PymiMTA) and a photoexcited porphyrin as an alternative technique. We show that the excited state of the porphyrin is not disturbed by the presence of the GdIII complex and that herewith modulation depths of almost 40% are possible. This is significantly higher than the value of 7.2% that was achieved with GdIII-GdIII DEER.
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Affiliation(s)
- Andreas Scherer
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Xuemei Yao
- Faculty
of Chemistry and Center of Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Mian Qi
- Faculty
of Chemistry and Center of Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Max Wiedmaier
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Adelheid Godt
- Faculty
of Chemistry and Center of Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Malte Drescher
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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20
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Protein delivery to living cells by thermal stimulation for biophysical investigation. Sci Rep 2022; 12:17190. [PMID: 36229511 PMCID: PMC9561116 DOI: 10.1038/s41598-022-21103-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
Studying biomolecules in their native environment represents the ideal sample condition for structural biology investigations. Here we present a novel protocol which allows to delivery proteins into eukaryotic cells through a mild thermal stimulation. The data presented herein show the efficacy of this approach for delivering proteins in the intracellular environment of mammalian cells reaching a concentration range suitable for successfully applying biophysical methods, such as double electron electron resonance (DEER) measurements for characterising protein conformations.
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21
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Tessmer MH, Canarie ER, Stoll S. Comparative evaluation of spin-label modeling methods for protein structural studies. Biophys J 2022; 121:3508-3519. [PMID: 35957530 PMCID: PMC9515001 DOI: 10.1016/j.bpj.2022.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Site-directed spin-labeling electron paramagnetic resonance spectroscopy is a powerful technique for the investigation of protein structure and dynamics. Accurate spin-label modeling methods are essential to make full quantitative use of site-directed spin-labeling electron paramagnetic resonance data for protein modeling and model validation. Using a set of double electron-electron resonance data from seven different site pairs on maltodextrin/maltose-binding protein under two different conditions using five different spin labels, we compare the ability of two widely used spin-label modeling methods, based on accessible volume sampling and rotamer libraries, to predict experimental distance distributions. We present a spin-label modeling approach inspired by canonical side-chain modeling methods and compare modeling accuracy with the established methods.
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Affiliation(s)
- Maxx H Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington
| | | | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington.
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22
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Bogetti X, Hasanbasri Z, Hunter HR, Saxena S. An optimal acquisition scheme for Q-band EPR distance measurements using Cu 2+-based protein labels. Phys Chem Chem Phys 2022; 24:14727-14739. [PMID: 35574729 DOI: 10.1039/d2cp01032a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recent advances in site-directed Cu2+ labeling of proteins and nucleic acids have added an attractive new methodology to measure the structure-function relationship in biomolecules. Despite the promise, accessing the higher sensitivity of Q-band Double Electron Electron Resonance (DEER) has been challenging for Cu2+ labels designed for proteins. Q-band DEER experiments on this label typically require many measurements at different magnetic fields, since the pulses can excite only a few orientations at a given magnetic field. Herein, we analyze such orientational effects through simulations and show that three DEER measurements, at strategically selected magnetic fields, are generally sufficient to acquire an orientational-averaged DEER time trace for this spin label at Q-band. The modeling results are experimentally verified on Cu2+ labeled human glutathione S-transferase (hGSTA1-1). The DEER distance distribution measured at the Q-band shows good agreement with the distance distribution sampled by molecular dynamics (MD) simulations and X-band experiments. The concordance of MD sampled distances and experimentally measured distances adds growing evidence that MD simulations can accurately predict distances for the Cu2+ labels, which remains a key bottleneck for the commonly used nitroxide label. In all, this minimal collection scheme reduces data collection time by as much as six-fold and is generally applicable to many octahedrally coordinated Cu2+ systems. Furthermore, the concepts presented here may be applied to other metals and pulsed EPR experiments.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
| | - Hannah R Hunter
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
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23
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Goldfarb D. Exploring protein conformations in vitro and in cell with EPR distance measurements. Curr Opin Struct Biol 2022; 75:102398. [PMID: 35667279 DOI: 10.1016/j.sbi.2022.102398] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/20/2022] [Accepted: 04/30/2022] [Indexed: 11/18/2022]
Abstract
The electron-electron double resonance (DEER) method, which provides distance distributions between two spin labels, attached site specifically to biomolecules (proteins and nucleic acids), is currently a well-recognized biophysical tool in structural biology. The most commonly used spin labels are based on nitroxide stable radicals, conjugated to the proteins primarily via native or engineered cysteine residues. However, in recent years, new spin labels, along with different labeling chemistries, have been introduced, driven in part by the desire to study structural and dynamical properties of biomolecules in their native environment, the cell. This mini-review focuses on these new spin labels, which allow for DEER on orthogonal spin labels, and on the state of the art methods for in-cell DEER distance measurements.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 761001, Israel
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24
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Teucher M, Sidabras JW, Schnegg A. Milliwatt three- and four-pulse double electron electron resonance for protein structure determination. Phys Chem Chem Phys 2022; 24:12528-12540. [PMID: 35579184 DOI: 10.1039/d1cp05508a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) experiments for protein structure determination using double electron-electron resonance (DEER) spectroscopy rely on high-power microwave amplifiers (>300 W) to create the short pulse lengths needed to excite a sizable portion of the spectrum. The recently introduced self-resonant microhelix combines a high B1 conversion efficiency with an intrinsically large bandwidth (low Q-value) and a high absolute sensitivity. We report dead times in 3-pulse DEER experiments as low as 14 ± 2 ns achieved using less than 1 W of power at X-band (nominally 9.5 GHz) for experiments on a molecular ruler and a T4 lysozyme sample for concentrations down to 100 μM. These low-power experiments were performed using an active volume 120 times smaller than that of a standard pulse EPR resonator, while only a 11-fold decrease in the signal-to-noise ratio was observed. Small build sizes, as realized with the microhelix, give access to volume-limited samples, while shorter dead times allow the investigation of fast relaxing spin species. With the significantly reduced dead times, the 3-pulse DEER experiment can be revisited. Here, we show experimentally that 3-pulse DEER offers superior sensitivity over 4-pulse DEER. We assert that the microhelix paves the road for low-cost benchtop X-band pulse EPR spectrometers by eliminating the need for high-power amplifiers, accelerating the adoption of pulse EPR to a broader community.
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Affiliation(s)
- Markus Teucher
- EPR Research Group, Max Planck Institute for Chemical Energy Conversion, Stift-straße 34-36, Mülheim an der Ruhr, 45470, Germany.
| | - Jason W Sidabras
- EPR Research Group, Max Planck Institute for Chemical Energy Conversion, Stift-straße 34-36, Mülheim an der Ruhr, 45470, Germany.
| | - Alexander Schnegg
- EPR Research Group, Max Planck Institute for Chemical Energy Conversion, Stift-straße 34-36, Mülheim an der Ruhr, 45470, Germany.
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25
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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.
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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.
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26
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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.
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27
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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.
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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.
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28
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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29
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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30
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Asanbaeva N, Sukhanov A, Diveikina AA, Rogozhnikova O, Trukhin DV, Tormyshev VM, Chubarov AS, Maryasov AG, Genaev A, Shernyukov AV, Salnikov GE, Lomzov AA, Pyshnyi DV, Bagryanskaya E. Application of W-band 19F electron nuclear double resonance (ENDOR) spectroscopy to distance measurement using a trityl spin probe and a fluorine label. Phys Chem Chem Phys 2022; 24:5982-6001. [DOI: 10.1039/d1cp05445g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently, Marina Bennati and coworkers (Angew. Chemie - Int. Ed., 2020, 59, 373–379., A. J. Magn. Reson., 2021, 333, 107091) proposed to use electron nuclear double resonance (ENDOR) spectroscopy in...
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31
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Overall SA, Barnes AB. Biomolecular Perturbations in In-Cell Dynamic Nuclear Polarization Experiments. Front Mol Biosci 2021; 8:743829. [PMID: 34751246 PMCID: PMC8572051 DOI: 10.3389/fmolb.2021.743829] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022] Open
Abstract
In-cell DNP is a growing application of NMR to the study of biomolecular structure and function within intact cells. An important unresolved question for in-cell DNP spectroscopy is the integrity of cellular samples under the cryogenic conditions of DNP. Despite the rich literature around cryopreservation of cells in the fields of stem cell/embryonic cell therapeutics, cell line preservation and in cryo-EM applications, the effect of cryopreservation procedures on DNP parameters is unclear. In this report we investigate cell survival and apoptosis in the presence of cryopreserving agents and DNP radicals. We also assess the effects of these reagents on cellular enhancements. We show that the DNP radical AMUPol has no effect on membrane permeability and does not induce apoptosis. Furthermore, the standard aqueous glass forming reagent, comprised of 60/30/10 d8-glycerol/D2O/H2O (DNP juice), rapidly dehydrates cells and induces apoptosis prior to freezing, reducing structural integrity of the sample prior to DNP analysis. Preservation with d6-DMSO at 10% v/v provided similar DNP enhancements per √unit time compared to glycerol preservation with superior maintenance of cell size and membrane integrity prior to freezing. DMSO preservation also greatly enhanced post-thaw survival of cells slow-frozen at 1°C/min. We therefore demonstrate that in-cell DNP-NMR studies should be done with d6-DMSO as cryoprotectant and raise important considerations for the progression of in-cell DNP-NMR towards the goal of high quality structural studies.
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Affiliation(s)
- Sarah A Overall
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
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32
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Ovcherenko SS, Chinak OA, Chechushkov AV, Dobrynin SA, Kirilyuk IA, Krumkacheva OA, Richter VA, Bagryanskaya EG. Uptake of Cell-Penetrating Peptide RL2 by Human Lung Cancer Cells: Monitoring by Electron Paramagnetic Resonance and Confocal Laser Scanning Microscopy. Molecules 2021; 26:5442. [PMID: 34576913 PMCID: PMC8470091 DOI: 10.3390/molecules26185442] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 11/21/2022] Open
Abstract
RL2 is a recombinant analogue of a human κ-casein fragment, capable of penetrating cells and inducing apoptosis of cancer cells with no toxicity to normal cells. The exact mechanism of RL2 penetration into cells remains unknown. In this study, we investigated the mechanism of RL2 penetration into human lung cancer A549 cells by a combination of electron paramagnetic resonance (EPR) spectroscopy and confocal laser scanning microscopy. EPR spectra of A549 cells incubated with RL2 (sRL2) spin-labeled by a highly stable 3-carboxy-2,2,5,5-tetraethylpyrrolidine-1-oxyl radical were found to contain three components, with their contributions changing with time. The combined EPR and confocal-microscopy data allowed us to assign these three forms of sRL2 to the spin-labeled protein sticking to the membrane of the cell and endosomes, to the spin-labeled protein in the cell interior, and to spin labeled short peptides formed in the cell because of protein digestion. EPR spectroscopy enabled us to follow the kinetics of transformations between different forms of the spin-labeled protein at a minimal spin concentration (3-16 μM) in the cell. The prospects of applications of spin-labeled cell-penetrating peptides to EPR imaging, DNP, and magnetic resonance imaging are discussed, as is possible research on an intrinsically disordered protein in the cell by pulsed dipolar EPR spectroscopy.
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Affiliation(s)
- Sergey S. Ovcherenko
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (S.S.O.); (S.A.D.); (I.A.K.)
| | - Olga A. Chinak
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (O.A.C.); (A.V.C.); (V.A.R.)
| | - Anton V. Chechushkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (O.A.C.); (A.V.C.); (V.A.R.)
| | - Sergey A. Dobrynin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (S.S.O.); (S.A.D.); (I.A.K.)
| | - Igor A. Kirilyuk
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (S.S.O.); (S.A.D.); (I.A.K.)
| | | | - Vladimir A. Richter
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (O.A.C.); (A.V.C.); (V.A.R.)
| | - Elena G. Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (S.S.O.); (S.A.D.); (I.A.K.)
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33
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Saio T, Hiramatsu S, Asada M, Nakagawa H, Shimizu K, Kumeta H, Nakamura T, Ishimori K. Conformational ensemble of a multidomain protein explored by Gd 3+ electron paramagnetic resonance. Biophys J 2021; 120:2943-2951. [PMID: 34242587 DOI: 10.1016/j.bpj.2021.06.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/07/2021] [Accepted: 06/28/2021] [Indexed: 10/20/2022] Open
Abstract
Despite their importance in function, the conformational state of proteins and its changes are often poorly understood, mainly because of the lack of an efficient tool. MurD, a 47-kDa protein enzyme responsible for peptidoglycan biosynthesis, is one of those proteins whose conformational states and changes during their catalytic cycle are not well understood. Although it has been considered that MurD takes a single conformational state in solution as shown by a crystal structure, the solution nuclear magnetic resonance (NMR) study suggested the existence of multiple conformational state of apo MurD in solution. However, the conformational distribution has not been evaluated. In this work, we investigate the conformational states of MurD by the use of electron paramagnetic resonance (EPR), especially intergadolinium distance measurement using double electron-electron resonance (DEER) measurement. The gadolinium ions are fixed on specific positions on MurD via a rigid double-arm paramagnetic lanthanide tag that has been originally developed for paramagnetic NMR. The combined use of NMR and EPR enables accurate interpretation of the DEER distance information to the structural information of MurD. The DEER distance measurement for apo MurD shows a broad distance distribution, whereas the presence of the inhibitor narrows the distance distribution. The results suggest that MurD exists in a wide variety of conformational states in the absence of ligands, whereas binding of the inhibitor eliminates variation in conformational states. The multiple conformational states of MurD were previously implied by NMR experiments, but our DEER data provided structural characterization of the conformational variety of MurD.
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Affiliation(s)
- Tomohide Saio
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan.
| | - Soya Hiramatsu
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Mizue Asada
- Instrument Center, Institute for Molecular Science, Okazaki, Japan
| | - Hiroshi Nakagawa
- Materials Sciences Research CenterTokai, Ibaraki, Japan; J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Kazumi Shimizu
- Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
| | | | | | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.
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34
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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.
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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
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35
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Hasanbasri Z, Singewald K, Gluth TD, Driesschaert B, Saxena S. Cleavage-Resistant Protein Labeling With Hydrophilic Trityl Enables Distance Measurements In-Cell. J Phys Chem B 2021; 125:5265-5274. [PMID: 33983738 DOI: 10.1021/acs.jpcb.1c02371] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sensitive in-cell distance measurements in proteins using pulsed-electron spin resonance (ESR) require reduction-resistant and cleavage-resistant spin labels. Among the reduction-resistant moieties, the hydrophilic trityl core known as OX063 is promising due to its long phase-memory relaxation time (Tm). This property leads to a sufficiently intense ESR signal for reliable distance measurements. Furthermore, the Tm of OX063 remains sufficiently long at higher temperatures, opening the possibility for measurements at temperatures above 50 K. In this work, we synthesized deuterated OX063 with a maleimide linker (mOX063-d24). We show that the combination of the hydrophilicity of the label and the maleimide linker enables high protein labeling that is cleavage-resistant in-cells. Distance measurements performed at 150 K using this label are more sensitive than the measurements at 80 K. The sensitivity gain is due to the significantly short longitudinal relaxation time (T1) at higher temperatures, which enables more data collection per unit of time. In addition to in vitro experiments, we perform distance measurements in Xenopus laevis oocytes. Interestingly, the Tm of mOX063-d24 is sufficiently long even in the crowded environment of the cell, leading to signals of appreciable intensity. Overall, mOX063-d24 provides highly sensitive distance measurements both in vitro and in-cells.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Teresa D Gluth
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Benoit Driesschaert
- Department of Pharmaceutical Sciences, School of Pharmacy & In Vivo Multifunctional Magnetic Resonance (IMMR) Center, Health Sciences Center, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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36
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Kucher S, Elsner C, Safonova M, Maffini S, Bordignon E. In-Cell Double Electron-Electron Resonance at Nanomolar Protein Concentrations. J Phys Chem Lett 2021; 12:3679-3684. [PMID: 33829785 DOI: 10.1021/acs.jpclett.1c00048] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is an established technique to site-specifically monitor conformational changes of spin-labeled biomolecules. Emerging in-cell EPR approaches aiming to address spin-labeled proteins in their native environment still struggle to reach a broad applicability and to target physiologically relevant protein concentrations. Here, we present a comparative in vitro and in-cell double electron-electron resonance (DEER) study demonstrating that nanomolar protein concentrations are at reach to measure distances up to 4.5 nm between protein sites carrying commercial gadolinium spin labels.
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Affiliation(s)
- Svetlana Kucher
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
| | - Christina Elsner
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
| | - Mariya Safonova
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
| | - Stefano Maffini
- Max Planck Institute of Molecular Physiology, Department of Mechanistic Cell Biology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Enrica Bordignon
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
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37
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Giannoulis A, Ben-Ishay Y, Goldfarb D. Characteristics of Gd(III) spin labels for the study of protein conformations. Methods Enzymol 2021; 651:235-290. [PMID: 33888206 DOI: 10.1016/bs.mie.2021.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gd(III) complexes are currently established as spin labels for structural studies of biomolecules using pulse dipolar electron paramagnetic resonance (PD-EPR) techniques. This has been achieved by the availability of medium- and high-field spectrometers, understanding the spin physics underlying the spectroscopic properties of high spin Gd(III) (S=7/2) pairs and their dipolar interaction, the design of well-defined model compounds and optimization of measurement techniques. In addition, a variety of Gd(III) chelates and labeling schemes have allowed a broad scope of applications. In this review, we provide a brief background of the spectroscopic properties of Gd(III) pertinent for effective PD-EPR measurements and focus on the various labels available to date. We report on their use in PD-EPR applications and highlight their pros and cons for particular applications. We also devote a section to recent in-cell structural studies of proteins using Gd(III), which is an exciting new direction for Gd(III) spin labeling.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Yasmin Ben-Ishay
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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38
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Ketter S, Gopinath A, Rogozhnikova O, Trukhin D, Tormyshev VM, Bagryanskaya EG, Joseph B. In Situ Labeling and Distance Measurements of Membrane Proteins in E. coli Using Finland and OX063 Trityl Labels. Chemistry 2021; 27:2299-2304. [PMID: 33197077 PMCID: PMC7898545 DOI: 10.1002/chem.202004606] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/13/2020] [Indexed: 01/03/2023]
Abstract
In situ investigation of membrane proteins is a challenging task. Previously we demonstrated that nitroxide labels combined with pulsed ESR spectroscopy is a promising tool for this purpose. However, the nitroxide labels suffer from poor stability, high background labeling, and low sensitivity. Here we show that Finland (FTAM) and OX063 based labels enable labeling of the cobalamin transporter BtuB and BamA, the central component of the β-barrel assembly machinery (BAM) complex, in E coli. Compared to the methanethiosulfonate spin label (MTSL), trityl labels eliminated the background signals and enabled specific in situ labeling of the proteins with high efficiency. The OX063 labels show a long phase memory time (TM ) of ≈5 μs. All the trityls enabled distance measurements between BtuB and an orthogonally labeled substrate with high selectivity and sensitivity down to a few μm concentration. Our data corroborate the BtuB and BamA conformations in the cellular environment of E. coli.
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Affiliation(s)
- Sophie Ketter
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Aathira Gopinath
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
| | - Olga Rogozhnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Dmitrii Trukhin
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Victor M. Tormyshev
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Elena G. Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic ChemistrySB RASPr. Lavrentieva 9Novosibirsk630090Russia
| | - Benesh Joseph
- Institute of BiophysicsDepartment of PhysicsGoethe University FrankfurtMax-von-Laue-Str. 160438Frankfurt/MainGermany
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39
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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.
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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.
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40
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Heiliger J, Matzel T, Çetiner EC, Schwalbe H, Kuenze G, Corzilius B. Site-specific dynamic nuclear polarization in a Gd(III)-labeled protein. Phys Chem Chem Phys 2020; 22:25455-25466. [PMID: 33103678 DOI: 10.1039/d0cp05021k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dynamic nuclear polarization (DNP) of a biomolecule tagged with a polarizing agent has the potential to not only increase NMR sensitivity but also to provide specificity towards the tagging site. Although the general concept has been often discussed, the observation of true site-specific DNP and its dependence on the electron-nuclear distance has been elusive. Here, we demonstrate site-specific DNP in a uniformly isotope-labeled ubiquitin. By recombinant expression of three different ubiquitin point mutants (F4C, A28C, and G75C) post-translationally modified with a Gd3+-chelator tag, localized metal-ion DNP of 13C and 15N is investigated. Effects counteracting the site-specificity of DNP such as nuclear spin-lattice relaxation and proton-driven spin diffusion have been attenuated by perdeuteration of the protein. Particularly for 15N, large DNP enhancement factors on the order of 100 and above as well as localized effects within side-chain resonances differently distributed over the protein are observed. By analyzing the experimental DNP built-up dynamics combined with structural modeling of Gd3+-tags in ubiquitin supported by paramagnetic relaxation enhancement (PRE) in solution, we provide, for the first time, quantitative information on the distance dependence of the initial DNP transfer. We show that the direct 15N DNP transfer rate indeed linearly depends on the square of the hyperfine interaction between the electron and the nucleus following Fermi's golden rule, however, below a certain distance cutoff paramagnetic signal bleaching may dramatically skew the correlation.
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Affiliation(s)
- Jörg Heiliger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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41
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Miao Q, Zurlo E, de Bruin D, Wondergem JAJ, Timmer M, Blok A, Heinrich D, Overhand M, Huber M, Ubbink M. A Two-Armed Probe for In-Cell DEER Measurements on Proteins*. Chemistry 2020; 26:17128-17133. [PMID: 33200852 PMCID: PMC7839491 DOI: 10.1002/chem.202002743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022]
Abstract
The application of double electron‐electron resonance (DEER) with site‐directed spin labeling (SDSL) to measure distances in proteins and protein complexes in living cells puts rigorous restraints on the spin‐label. The linkage and paramagnetic centers need to resist the reducing conditions of the cell. Rigid attachment of the probe to the protein improves precision of the measured distances. Here, three two‐armed GdIII complexes, GdIII‐CLaNP13a/b/c were synthesized. Rather than the disulfide linkage of most other CLaNP molecules, a thioether linkage was used to avoid reductive dissociation of the linker. The doubly GdIII labeled N55C/V57C/K147C/T151C variants of T4Lysozyme were measured by 95 GHz DEER. The constructs were measured in vitro, in cell lysate and in Dictyostelium discoideum cells. Measured distances were 4.5 nm, consistent with results from paramagnetic NMR. A narrow distance distribution and typical modulation depth, also in cell, indicate complete and durable labeling and probe rigidity due to the dual attachment sites.
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Affiliation(s)
- Qing Miao
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Enrico Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Donny de Bruin
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Joeri A J Wondergem
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Doris Heinrich
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands.,Fraunhofer Institute for Silicate Research ISC, 97082, Würzburg, Germany
| | - Mark Overhand
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
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42
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Collauto A, Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alberto Collauto
- 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
| | - Sören Bülow
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Dnyaneshwar B. Gophane
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Subham Saha
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Lukas S. Stelzl
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
- Institute for Biophysics Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
| | - Snorri T. Sigurdsson
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - 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
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43
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Collauto A, von Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell*. Angew Chem Int Ed Engl 2020; 59:23025-23029. [PMID: 32804430 PMCID: PMC7756485 DOI: 10.1002/anie.202009800] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 11/15/2022]
Abstract
The structure and flexibility of RNA depends sensitively on the microenvironment. Using pulsed electron-electron double-resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy combined with advanced labeling techniques, we show that the structure of double-stranded RNA (dsRNA) changes upon internalization into Xenopus laevis oocytes. Compared to dilute solution, the dsRNA A-helix is more compact in cells. We recapitulate this compaction in a densely crowded protein solution. Atomic-resolution molecular dynamics simulations of dsRNA semi-quantitatively capture the compaction, and identify non-specific electrostatic interactions between proteins and dsRNA as a possible driver of this effect.
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Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
| | - Sören von Bülow
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Dnyaneshwar B. Gophane
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Subham Saha
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Lukas S. Stelzl
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Gerhard Hummer
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
- Institute for BiophysicsGoethe University FrankfurtMax-von-Laue-Str. 960438Frankfurt am MainGermany
| | - Snorri T. Sigurdsson
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
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44
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EL Mkami H, Hunter R, Cruickshank P, Taylor M, Lovett J, Feintuch A, Qi M, Godt A, Smith G. High-sensitivity Gd 3+-Gd 3+ EPR distance measurements that eliminate artefacts seen at short distances. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:301-313. [PMID: 37904818 PMCID: PMC10500690 DOI: 10.5194/mr-1-301-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/18/2020] [Indexed: 11/01/2023]
Abstract
Gadolinium complexes are attracting increasing attention as spin labels for EPR dipolar distance measurements in biomolecules and particularly for in-cell measurements. It has been shown that flip-flop transitions within the central transition of the high-spin Gd3 + ion can introduce artefacts in dipolar distance measurements, particularly when measuring distances less than 3 nm. Previous work has shown some reduction of these artefacts through increasing the frequency separation between the two frequencies required for the double electron-electron resonance (DEER) experiment. Here we use a high-power (1 kW), wideband, non-resonant system operating at 94 GHz to evaluate DEER measurement protocols using two stiff Gd(III) rulers, consisting of two b i s -Gd3 + -PyMTA complexes, with separations of 2.1 nm and 6.0 nm, respectively. We show that by avoiding the - 1 2 → 1 2 central transition completely, and placing both the pump and the observer pulses on either side of the central transition, we can now observe apparently artefact-free spectra and narrow distance distributions, even for a Gd-Gd distance of 2.1 nm. Importantly we still maintain excellent signal-to-noise ratio and relatively high modulation depths. These results have implications for in-cell EPR measurements at naturally occurring biomolecule concentrations.
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Affiliation(s)
- Hassane EL Mkami
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Robert I. Hunter
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Paul A. S. Cruickshank
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Michael J. Taylor
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Janet E. Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science,
Rehovot, Israel
| | - Mian Qi
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Graham M. Smith
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
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45
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Bordignon E, Seeger MA, Galazzo L, Meier G. From in vitro towards in situ: structure-based investigation of ABC exporters by electron paramagnetic resonance spectroscopy. FEBS Lett 2020; 594:3839-3856. [PMID: 33219535 DOI: 10.1002/1873-3468.14004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/30/2020] [Accepted: 11/15/2020] [Indexed: 12/12/2022]
Abstract
ATP-binding cassette (ABC) exporters have been studied now for more than four decades, and recent structural investigation has produced a large number of protein database entries. Yet, important questions about how ABC exporters function at the molecular level remain debated, such as which are the molecular recognition hotspots and the allosteric couplings dynamically regulating the communication between the catalytic cycle and the export of substrates. This conundrum mainly arises from technical limitations confining all research to in vitro analysis of ABC transporters in detergent solutions or embedded in membrane-mimicking environments. Therefore, a largely unanswered question is how ABC exporters operate in situ, namely in the native membrane context of a metabolically active cell. This review focuses on novel mechanistic insights into type I ABC exporters gained through a unique combination of structure determination, biochemical characterization, generation of conformation-specific nanobodies/sybodies and double electron-electron resonance.
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Affiliation(s)
- Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Switzerland
| | - Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Switzerland
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46
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Goett-Zink L, Klocke JL, Bögeholz LAK, Kottke T. In-cell infrared difference spectroscopy of LOV photoreceptors reveals structural responses to light altered in living cells. J Biol Chem 2020; 295:11729-11741. [PMID: 32580943 PMCID: PMC7450117 DOI: 10.1074/jbc.ra120.013091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/21/2020] [Indexed: 12/19/2022] Open
Abstract
Proteins are usually studied in well-defined buffer conditions, which differ substantially from those within a host cell. In some cases, the intracellular environment has an impact on the mechanism, which might be missed by in vitro experiments. IR difference spectroscopy previously has been applied to study the light-induced response of photoreceptors and photoenzymes in vitro Here, we established the in-cell IR difference (ICIRD) spectroscopy in the transmission and attenuated total reflection configuration to investigate the light-induced response of soluble proteins in living bacterial cells. ICIRD spectroscopy on the light, oxygen, or voltage (LOV) domains of the blue light receptors aureochrome and phototropin revealed a suppression of the response of specific secondary structure elements, indicating that the intracellular environment affects LOV photoreceptor mechanisms in general. Moreover, in-cell fluorescence spectroscopy disclosed that the intracellular environment slows down the recovery of the light-induced flavin adduct. Segment-resolved ICIRD spectroscopy on basic-region leucine zipper (bZIP)-LOV of aureochrome 1a from the diatom Phaeodactylum tricornutum indicated a signal progression from the LOV sensor to the bZIP effector independent of unfolding of the connecting A'α-helix, an observation that stood in contrast to in vitro results. This deviation was recapitulated in vitro by emulating the intracellular environment through the addition of the crowding agent BSA, but not by sucrose polymers. We conclude that ICIRD spectroscopy is a noninvasive, label-free approach for assessing conformational changes in receptors in living cells at ambient conditions. As demonstrated, these near-native responses may deviate from the mechanisms established under in vitro conditions.
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Affiliation(s)
- Lukas Goett-Zink
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Jessica L Klocke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Lena A K Bögeholz
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, Germany
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47
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In-cell destabilization of a homodimeric protein complex detected by DEER spectroscopy. Proc Natl Acad Sci U S A 2020; 117:20566-20575. [PMID: 32788347 DOI: 10.1073/pnas.2005779117] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The complexity of the cellular medium can affect proteins' properties, and, therefore, in-cell characterization of proteins is essential. We explored the stability and conformation of the first baculoviral IAP repeat (BIR) domain of X chromosome-linked inhibitor of apoptosis (XIAP), BIR1, as a model for a homodimer protein in human HeLa cells. We employed double electron-electron resonance (DEER) spectroscopy and labeling with redox stable and rigid Gd3+ spin labels at three representative protein residues, C12 (flexible region), E22C, and N28C (part of helical residues 26 to 31) in the N-terminal region. In contrast to predictions by excluded-volume crowding theory, the dimer-monomer dissociation constant K D was markedly higher in cells than in solution and dilute cell lysate. As expected, this increase was partially recapitulated under conditions of high salt concentrations, given that conserved salt bridges at the dimer interface are critically required for association. Unexpectedly, however, also the addition of the crowding agent Ficoll destabilized the dimer while the addition of bovine serum albumin (BSA) and lysozyme, often used to represent interaction with charged macromolecules, had no effect. Our results highlight the potential of DEER for in-cell study of proteins as well as the complexities of the effects of the cellular milieu on protein structures and stability.
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48
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Fleck N, Heubach CA, Hett T, Haege FR, Bawol PP, Baltruschat H, Schiemann O. SLIM: A Short-Linked, Highly Redox-Stable Trityl Label for High-Sensitivity In-Cell EPR Distance Measurements. Angew Chem Int Ed Engl 2020; 59:9767-9772. [PMID: 32329172 PMCID: PMC7318235 DOI: 10.1002/anie.202004452] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 12/15/2022]
Abstract
The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site-directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in-cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide-functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm, and shows high stability against reduction. Using this label, the guanine-nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.
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Affiliation(s)
- Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Caspar A. Heubach
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Tobias Hett
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Florian R. Haege
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
| | - Pawel P. Bawol
- Institute of Physical and Theoretical ChemistryUniversity of BonnRömerstr. 16453117BonnGermany
| | - Helmut Baltruschat
- Institute of Physical and Theoretical ChemistryUniversity of BonnRömerstr. 16453117BonnGermany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of BonnWegelerstr. 1253115BonnGermany
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49
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Kong F, Zhao P, Yu P, Qin Z, Huang Z, Wang Z, Wang M, Shi F, Du J. Kilohertz electron paramagnetic resonance spectroscopy of single nitrogen centers at zero magnetic field. SCIENCE ADVANCES 2020; 6:eaaz8244. [PMID: 32766444 PMCID: PMC7385428 DOI: 10.1126/sciadv.aaz8244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/20/2020] [Indexed: 06/01/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is among the most important analytical tools in physics, chemistry, and biology. The emergence of nitrogen-vacancy (NV) centers in diamond, serving as an atomic-sized magnetometer, has promoted this technique to single-spin level, even under ambient conditions. Despite the enormous progress in spatial resolution, the current megahertz spectral resolution is still insufficient to resolve key heterogeneous molecular information. A major challenge is the short coherence times of the sample electron spins. Here, we address this challenge by using a magnetic noise-insensitive transition between states of different symmetry. We demonstrate a 27-fold narrower spectrum of single substitutional nitrogen (P1) centers in diamond with a linewidth of several kilohertz, and then some weak couplings can be resolved. Those results show both spatial and spectral advances of NV center-based EPR and provide a route toward analytical (EPR) spectroscopy at the single-molecule level.
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Affiliation(s)
- Fei Kong
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Pengju Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Pei Yu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhuoyang Qin
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhehua Huang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Zhecheng Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Mengqi Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Fazhan Shi
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
| | - Jiangfeng Du
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei 230026, China
- Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, China
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50
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EPR of site-directed spin-labeled proteins: A powerful tool to study structural flexibility. Arch Biochem Biophys 2020; 684:108323. [DOI: 10.1016/j.abb.2020.108323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022]
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