1
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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: 0] [Impact Index Per Article: 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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2
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Vitali V, Torricella F, Massai L, Messori L, Banci L. Enlarging the scenario of site directed 19F labeling for NMR spectroscopy of biomolecules. Sci Rep 2023; 13:22017. [PMID: 38086881 PMCID: PMC10716153 DOI: 10.1038/s41598-023-49247-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
The possibility of using selectively incorporated 19F nuclei for NMR spectroscopic studies has retrieved increasing interest in recent years. The high gyromagnetic ratio of 19F and its absence in native biomolecular systems make this nucleus an interesting alternative to standard 1H NMR spectroscopy. Here we show how we can attach a label, carrying a 19F atom, to protein tyrosines, through the use of a specific three component Mannich-type reaction. To validate the efficacy and the specificity of the approach, we tested it on two selected systems with the aid of ESI MS measurements.
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Affiliation(s)
- Valentina Vitali
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Francesco Torricella
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Lara Massai
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Luigi Messori
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy.
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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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Gerbaud G, Barbat B, Tribout M, Etienne E, Belle V, Douzi B, Voulhoux R, Bonucci A. Refining the Dynamic Network of T2SS Endopilus Tip Heterocomplex Combining cw-EPR and Nitroxide-Gd III Distance Measurements. Chembiochem 2023; 24:e202300099. [PMID: 36999435 DOI: 10.1002/cbic.202300099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 03/30/2023] [Indexed: 04/01/2023]
Abstract
The type 2 secretion system (T2SS) is a bacterial nanomachine composed of an inner membrane assembly platform, an outer membrane pore and a dynamic endopilus. T2SS endopili are organized into a homo-multimeric body formed by the major pilin capped by a heterocomplex of four minor pilins. The first model of the T2SS endopilus was recently released, even if structural dynamics insights are still required to decipher the role of each protein in the full tetrameric complex. Here, we applied continuous-wave and pulse EPR spectroscopy using nitroxide-gadolinium orthogonal labelling strategies to investigate the hetero-oligomeric assembly of the minor pilins. Overall, our data are in line with the endopilus model even if they evidenced conformational flexibility and alternative orientations at local scale of specific regions of minor pilins. The integration of different labelling strategies and EPR experiments demonstrates the pertinence of this approach to investigate protein-protein interactions in such multiprotein heterocomplexes.
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Affiliation(s)
- Guillaume Gerbaud
- BIP-Bioénérgetique et Ingénierie es Protéines, IMM, Aix Marseille Université, CNRS, 13009, Marseille, France
| | - Brice Barbat
- LCB-Laboratoire de Chimie Bactérienne, IMM, Aix Marseille Université, CNRS, 13009, Marseille, France
| | - Mathilde Tribout
- LCB-Laboratoire de Chimie Bactérienne, IMM, Aix Marseille Université, CNRS, 13009, Marseille, France
| | - Emilien Etienne
- BIP-Bioénérgetique et Ingénierie es Protéines, IMM, Aix Marseille Université, CNRS, 13009, Marseille, France
| | - Valérie Belle
- BIP-Bioénérgetique et Ingénierie es Protéines, IMM, Aix Marseille Université, CNRS, 13009, Marseille, France
| | - Badreddine Douzi
- LCB-Laboratoire de Chimie Bactérienne, IMM, Aix Marseille Université, CNRS, 13009, Marseille, France
- Present address: INRAE, DynAMic, Université de Lorraine, 54000, Nancy, France
| | - Romé Voulhoux
- LCB-Laboratoire de Chimie Bactérienne, IMM, Aix Marseille Université, CNRS, 13009, Marseille, France
| | - Alessio Bonucci
- BIP-Bioénérgetique et Ingénierie es Protéines, IMM, Aix Marseille Université, CNRS, 13009, Marseille, France
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5
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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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6
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Guidelines for the Simulations of Nitroxide X-Band cw EPR Spectra from Site-Directed Spin Labeling Experiments Using S imLabel. Molecules 2023; 28:molecules28031348. [PMID: 36771013 PMCID: PMC9919594 DOI: 10.3390/molecules28031348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the local level, the dynamics of structural transitions in proteins. Here, we consider SDSL-EPR based on the selective grafting of a nitroxide on the protein under study, followed by X-band cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give a reliable interpretation on biological system dynamics, a numerical simulation of the spectra is required. However, regardless of the numerical tool chosen to perform such simulations, the number of parameters is often too high to provide unambiguous results. In this study, we have chosen SimLabel to perform such simulations. SimLabel is a graphical user interface (GUI) of Matlab, using some functions of Easyspin. An exhaustive review of the parameters used in this GUI has enabled to define the adjustable parameters during the simulation fitting and to fix the others prior to the simulation fitting. Among them, some are set once and for all (gy, gz) and others are determined (Az, gx) thanks to a supplementary X-band spectrum recorded on a frozen solution. Finally, we propose guidelines to perform the simulation of X-band cw-EPR spectra of nitroxide labeled proteins at room temperature, with no need of uncommon higher frequency spectrometry and with the minimal number of variable parameters.
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7
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Wan C, Wang Y, Lian C, Chang Q, An Y, Chen J, Sun J, Hou Z, Yang D, Guo X, Yin F, Wang R, Li Z. Histidine-specific bioconjugation via visible-light-promoted thioacetal activation. Chem Sci 2022; 13:8289-8296. [PMID: 35919717 PMCID: PMC9297702 DOI: 10.1039/d2sc02353a] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/25/2022] [Indexed: 11/21/2022] Open
Abstract
Histidine (His, H) undergoes various post-translational modifications (PTMs) and plays multiple roles in protein interactions and enzyme catalyzed reactions. However, compared with other amino acids such as Lys or Cys, His modification is much less explored. Herein we describe a novel visible-light-driven thioacetal activation reaction which enables facile modification on histidine residues. An efficient addition to histidine imidazole N3 under biocompatible conditions was achieved with an electrophilic thionium intermediate. This method allows chemo-selective modification on peptides and proteins with good conversions and efficient histidine-proteome profiling with cell lysates. 78 histidine containing proteins were for the first time found with significant enrichment, most functioning in metal accumulation in brain related diseases. This facile His modification method greatly expands the chemo-selective toolbox for histidine-targeted protein conjugation and helps to reveal histidine's role in protein functions. Functionalization of histidine residues in proteins via visible-light-promoted thioacetal activation is reported. ∼2000 proteins with reactive and exposed histidine residues from the MCF7 cell line are characterized using ABPP by this method.![]()
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Affiliation(s)
- Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, P. R. China
| | - Qi Chang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, P. R. China
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, P. R. China
| | - Jiean Chen
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, P. R. China
| | - Jinming Sun
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Zhanfeng Hou
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, P. R. China
| | - Dongyan Yang
- College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, P. R. China
| | - Xiaochun Guo
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, P. R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, P. R. China
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8
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Heaven G, Hollas MA, Tabernero L, Fielding AJ. Spin Labeling of Surface Cysteines Using a Bromoacrylaldehyde Spin Label. APPLIED MAGNETIC RESONANCE 2021; 52:959-970. [PMID: 34776648 PMCID: PMC8550513 DOI: 10.1007/s00723-021-01350-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/28/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Structural investigations of proteins and their biological complexes are now frequently complemented by distance constraints between spin labeled cysteines generated using double electron-electron resonance (DEER) spectroscopy, via site directed spin labeling (SDSL). Methanethiosulfonate spin label (MTSSL), has become ubiquitous in the SDSL of proteins, however, has limitations owing to its high number of rotamers, and reducibility. In this article we introduce the use of bromoacrylaldehyde spin label (BASL) as a cysteine spin label, demonstrating an advantage over MTSSL due to its increased selectivity for surface cysteines, eliminating the need to 'knock out' superfluous cysteine residues. Applied to the multidomain protein, His domain protein tyrosine phosphatase (HD-PTP), we show that BASL can be easily added in excess with selective labeling, whereas MTSSL causes protein precipitation. Furthermore, using DEER, we were able to measure a single cysteine pair distance in a three cysteine domain within HD-PTP. The label has a further advantage of comprising a sulfide in a three-bond tether, making it a candidate for protein binding and in-cell studies. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00723-021-01350-1.
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Affiliation(s)
- Graham Heaven
- Department of Chemistry, The University of Manchester, Manchester, M13 9PL UK
| | - Michael A. Hollas
- Department of Chemistry, The University of Manchester, Manchester, M13 9PL UK
| | - Lydia Tabernero
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PL UK
| | - Alistair J. Fielding
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF UK
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9
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Groves P, Huang J, Heise A, Marsh J, Chechik V. Molecular environment and reactivity in gels and colloidal solutions under identical conditions. Phys Chem Chem Phys 2020; 22:12267-12272. [PMID: 32432245 DOI: 10.1039/d0cp01956a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A PEG-Tyr block copolymer forms a kinetically stable colloidal solution in water at room temperature which undergoes an irreversible conversion to a gel phase upon heating. A micellar solution and a gel can therefore be studied under identical experimental conditions. This made it possible to compare physical properties and chemical reactivity of micelles and gels in identical chemical environments and under identical conditions. EPR spectra of the spin-labelled copolymer showed that tyrosine mobility in gels was slightly reduced compared to micelles. Chemical reactivity was studied using photochemical degradation of tyrosine and tyrosine dimerization, in the absence and in the presence of an Fe(iii) salt. The reactivity trends were explained by reduced tyrosine mobility in the gel environment. The largest reactivity difference in gels and micelles was observed for bimolecular dityrosine formation which was also attributed to the reduction in molecular mobility.
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Affiliation(s)
- Philip Groves
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
| | - Jin Huang
- School of Chemical Sciences, Dublin City University, Dublin 9, Ireland
| | - Andreas Heise
- Department of Chemistry, Royal College of Surgeons in Ireland, 123 St. Stephens Green, Dublin 2, Ireland
| | - Jennifer Marsh
- The Procter & Gamble Company, Mason Business Center, 8700 Mason-Montgomery Road, Mason, 45040, USA
| | - Victor Chechik
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
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10
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Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:1-78. [PMID: 32828463 PMCID: PMC7129803 DOI: 10.1016/bs.pmbts.2020.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess the property of inherent flexibility and can be distinguished from other proteins in terms of lack of any fixed structure. Such dynamic behavior of IDPs earned the name "Dancing Proteins." The exploration of these dancing proteins in viruses has just started and crucial details such as correlation of rapid evolution, high rate of mutation and accumulation of disordered contents in viral proteome at least understood partially. In order to gain a complete understanding of this correlation, there is a need to decipher the complexity of viral mediated cell hijacking and pathogenesis in the host organism. Further there is necessity to identify the specific patterns within viral and host IDPs such as aggregation; Molecular recognition features (MoRFs) and their association to virulence, host range and rate of evolution of viruses in order to tackle the viral-mediated diseases. The current book chapter summarizes the aforementioned details and suggests the novel opportunities for further research of IDPs senses in viruses.
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Kugele A, Silkenath B, Langer J, Wittmann V, Drescher M. Protein Spin Labeling with a Photocaged Nitroxide Using Diels-Alder Chemistry. Chembiochem 2019; 20:2479-2484. [PMID: 31090999 PMCID: PMC6790680 DOI: 10.1002/cbic.201900318] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 12/31/2022]
Abstract
EPR spectroscopy of diamagnetic bio-macromolecules is based on site-directed spin labeling (SDSL). Herein, a novel labeling strategy for proteins is presented. A nitroxide-based spin label has been developed and synthesized that can be ligated to proteins by an inverse-electron-demand Diels-Alder (DAinv ) cycloaddition to genetically encoded noncanonical amino acids. The nitroxide moiety is shielded by a photoremovable protecting group with an attached tetra(ethylene glycol) unit to achieve water solubility. SDSL is demonstrated on two model proteins with the photoactivatable nitroxide for DAinv reaction (PaNDA) label. The strategy features high reaction rates, combined with high selectivity, and the possibility to deprotect the nitroxide in Escherichia coli lysate.
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Affiliation(s)
- Anandi Kugele
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Bjarne Silkenath
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Jakob Langer
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Valentin Wittmann
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Malte Drescher
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
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12
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Bonucci A, Ouari O, Guigliarelli B, Belle V, Mileo E. In‐Cell EPR: Progress towards Structural Studies Inside Cells. Chembiochem 2019; 21:451-460. [DOI: 10.1002/cbic.201900291] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alessio Bonucci
- Magnetic Resonance CenterCERMUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Olivier Ouari
- Aix Marseille UnivCNRSICRInstitut de Chimie Radicalaire 13013 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
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13
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Brodrecht M, Herr K, Bothe S, de Oliveira M, Gutmann T, Buntkowsky G. Efficient Building Blocks for Solid-Phase Peptide Synthesis of Spin Labeled Peptides for Electron Paramagnetic Resonance and Dynamic Nuclear Polarization Applications. Chemphyschem 2019; 20:1475-1487. [PMID: 30950574 DOI: 10.1002/cphc.201900211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/22/2019] [Indexed: 11/11/2022]
Abstract
Specific spin labeling allows the site-selective investigation of biomolecules by EPR and DNP enhanced NMR spectroscopy. A novel spin labeling strategy for commercially available Fmoc-amino acids is developed. In this approach, the PROXYL spin label is covalently attached to the hydroxyl side chain of three amino acids hydroxyproline (Hyp), serine (Ser) and tyrosine (Tyr) by a simple three-step synthesis route. The obtained PROXYL containing building-blocks are N-terminally protected by the Fmoc-protection group, which makes them applicable for the use in solid-phase peptide synthesis (SPPS). This approach allows the insertion of the spin label at any desired position during SPPS, which makes it more versatile than the widely used post synthetic spin labeling strategies. For the final building-blocks, the radical activity is proven by EPR. DNP enhanced solid-state NMR experiments employing these building-blocks in a TCE solution show enhancement factors of up to 26 for 1 H and 13 C (1 H→13 C cross-polarization). To proof the viability of the presented building-blocks for insertion of the spin label during SPPS the penta-peptide Acetyl-Gly-Ser(PROXYL)-Gly-Gly-Gly was synthesized employing the spin labeled Ser building-block. This peptide could successfully be isolated and the spin label activity proved by EPR and DNP NMR measurements, showing enhancement factors of 12.1±0.1 for 1 H and 13.9±0.5 for 13 C (direct polarization).
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Affiliation(s)
- Martin Brodrecht
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Kevin Herr
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Sarah Bothe
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Marcos de Oliveira
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Torsten Gutmann
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.,University Kassel, Institute for Chemistry, Heinrich-Plett-Straße 40, D-34132, Kassel
| | - Gerd Buntkowsky
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
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Le Breton N, Longhi S, Rockenbauer A, Guigliarelli B, Marque SRA, Belle V, Martinho M. Probing the dynamic properties of two sites simultaneously in a protein–protein interaction process: a SDSL-EPR study. Phys Chem Chem Phys 2019; 21:22584-22588. [DOI: 10.1039/c9cp04660g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Probing two sites simultaneously in a protein–protein interaction process combining spin labels of different EPR signatures.
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Affiliation(s)
| | - S. Longhi
- Aix Marseille Univ
- CNRS
- AFMB
- Marseille
- France
| | - A. Rockenbauer
- Research Center of Natural Sciences
- Budapest University of Technology and Economics
- Budapest
- Hungary
| | | | | | - V. Belle
- Aix Marseille Univ., CNRS, BIP
- Marseille
- France
| | - M. Martinho
- Aix Marseille Univ., CNRS, BIP
- Marseille
- France
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15
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Balo AR, Lee J, Ernst OP. Stationary Phase EPR Spectroscopy for Monitoring Membrane Protein Refolding by Conformational Response. Anal Chem 2018; 91:1071-1079. [DOI: 10.1021/acs.analchem.8b04542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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16
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New limits of sensitivity of site-directed spin labeling electron paramagnetic resonance for membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:841-853. [DOI: 10.1016/j.bbamem.2017.12.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/27/2017] [Accepted: 12/09/2017] [Indexed: 01/27/2023]
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17
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Karthikeyan G, Bonucci A, Casano G, Gerbaud G, Abel S, Thomé V, Kodjabachian L, Magalon A, Guigliarelli B, Belle V, Ouari O, Mileo E. A Bioresistant Nitroxide Spin Label for In-Cell EPR Spectroscopy: In Vitro and In Oocytes Protein Structural Dynamics Studies. Angew Chem Int Ed Engl 2018; 57:1366-1370. [DOI: 10.1002/anie.201710184] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/07/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Ganesan Karthikeyan
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Gilles Casano
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Sébastien Abel
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Virginie Thomé
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Axel Magalon
- Aix Marseille Univ, CNRS, LCB; Laboratoire de Chimie Bactérienne; Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
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Karthikeyan G, Bonucci A, Casano G, Gerbaud G, Abel S, Thomé V, Kodjabachian L, Magalon A, Guigliarelli B, Belle V, Ouari O, Mileo E. A Bioresistant Nitroxide Spin Label for In-Cell EPR Spectroscopy: In Vitro and In Oocytes Protein Structural Dynamics Studies. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710184] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ganesan Karthikeyan
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Alessio Bonucci
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Gilles Casano
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Sébastien Abel
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Virginie Thomé
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Laurent Kodjabachian
- Aix Marseille Univ, CNRS, IBDM; Institut de Biologie du Développement de Marseille; Marseille France
| | - Axel Magalon
- Aix Marseille Univ, CNRS, LCB; Laboratoire de Chimie Bactérienne; Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, ICR; Institut de Chimie Radicalaire; Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ, CNRS, BIP; Laboratoire de Bioénergétique et Ingénierie des Protéines; Marseille France
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M. Dunleavy K, Milshteyn E, Sorrentino Z, L. Pirman N, Liu Z, B. Chandler M, W. D’Amore P, E. Fanucci G. Spin-label scanning reveals conformational sensitivity of the bound helical interfaces of IA<sub>3</sub>. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.3.166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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20
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Gmeiner C, Klose D, Mileo E, Belle V, Marque SRA, Dorn G, Allain FHT, Guigliarelli B, Jeschke G, Yulikov M. Orthogonal Tyrosine and Cysteine Site-Directed Spin Labeling for Dipolar Pulse EPR Spectroscopy on Proteins. J Phys Chem Lett 2017; 8:4852-4857. [PMID: 28933855 DOI: 10.1021/acs.jpclett.7b02220] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Site-directed spin labeling of native tyrosine residues in isolated domains of the protein PTBP1, using a Mannich-type reaction, was combined with conventional spin labeling of cysteine residues. Double electron-electron resonance (DEER) EPR measurements were performed for both the nitroxide-nitroxide and Gd(III)-nitroxide label combinations within the same protein molecule. For the prediction of distance distributions from a structure model, rotamer libraries were generated for the two linker forms of the tyrosine-reactive isoindoline-based nitroxide radical Nox. Only moderate differences exist between the spatial spin distributions for the two linker forms of Nox. This strongly simplifies DEER data analysis, in particular, if only mean distances need to be predicted.
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Affiliation(s)
- Christoph Gmeiner
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Elisabetta Mileo
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Valérie Belle
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Sylvain R A Marque
- Aix Marseille Univ , CNRS, ICR, Institut de Chimie Radicalaire, Marseille 13397, France
- N. N. Vorozhtsov Novosibirsk Insititute of Organic Chemistry , 630090 Novosibirsk, Russia
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, ETH Zurich , Zurich 8093, Switzerland
| | - Frédéric H T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich , Zurich 8093, Switzerland
| | - Bruno Guigliarelli
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
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21
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Etienne E, Le Breton N, Martinho M, Mileo E, Belle V. SimLabel: a graphical user interface to simulate continuous wave EPR spectra from site-directed spin labeling experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:714-719. [PMID: 28078740 DOI: 10.1002/mrc.4578] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 05/24/2023]
Abstract
Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the residue level, structural transitions in proteins. SDSL-EPR is based on the selective grafting of a paramagnetic label on the protein under study, followed by cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give reliable interpretation on biological system dynamics, numerical simulations of the spectra are required. Such spectral simulations can be carried out by coding in MATLAB using functions from the EasySpin toolbox. For non-expert users of MATLAB, this could be a complex task or even impede the use of such simulation tool. We developed a graphical user interface called SimLabel dedicated to run cw EPR spectra simulations particularly coming from SDSL-EPR experiments. Simlabel provides an intuitive way to visualize, simulate, and fit such cw EPR spectra. An example of SDSL-EPR spectra simulation concerning the study of an intrinsically disordered region undergoing a local induced folding is described and discussed. We believe that this new tool will help the users to rapidly obtain reliable simulated spectra and hence facilitate the interpretation of their results. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- E Etienne
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
| | - N Le Breton
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
- Queen Mary University of London, School of Biological and Chemical Sciences, UK
| | - M Martinho
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
| | - E Mileo
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
| | - V Belle
- Aix Marseille Univ, CNRS, BIP (UMR 7281), IMM (FR 3479), Marseille, France
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22
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Basak S, Chatterjee S, Chakrapani S. Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels. J Vis Exp 2016. [PMID: 27403967 DOI: 10.3791/54127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Ion channel gating is a stimulus-driven orchestration of protein motions that leads to transitions between closed, open, and desensitized states. Fundamental to these transitions is the intrinsic flexibility of the protein, which is critically modulated by membrane lipid-composition. To better understand the structural basis of channel function, it is necessary to study protein dynamics in a physiological membrane environment. Electron Paramagnetic Resonance (EPR) spectroscopy is an important tool to characterize conformational transitions between functional states. In comparison to NMR and X-ray crystallography, the information obtained from EPR is intrinsically of lower resolution. However, unlike in other techniques, in EPR there is no upper-limit to the molecular weight of the protein, the sample requirements are significantly lower, and more importantly the protein is not constrained by the crystal lattice forces. Therefore, EPR is uniquely suited for studying large protein complexes and proteins in reconstituted systems. In this article, we will discuss general protocols for site-directed spin labeling and membrane reconstitution using a prokaryotic proton-gated pentameric Ligand-Gated Ion Channel (pLGIC) from Gloeobacter violaceus (GLIC) as an example. A combination of steady-state Continuous Wave (CW) and Pulsed (Double Electron Electron Resonance-DEER) EPR approaches will be described that will enable a complete quantitative characterization of channel dynamics.
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Affiliation(s)
- Sandip Basak
- Department of Physiology and Biophysics, Case Western Reserve University
| | - Soumili Chatterjee
- Department of Physiology and Biophysics, Case Western Reserve University
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University; School of Medicine, Case Western Reserve University;
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23
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Gölz JP, NejatyJahromy Y, Bauer M, Muhammad A, Schnakenburg G, Grimme S, Schiemann O, Menche D. Design, Synthesis, EPR-Studies and Conformational Bias of Novel Spin-Labeled DCC-Analogues for the Highly Regioselective Labeling of Aliphatic and Aromatic Carboxylic Acids. Chemistry 2016; 22:9591-8. [PMID: 27272435 DOI: 10.1002/chem.201600528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 01/17/2023]
Abstract
Novel types of spin-labeled N,N'-dicyclohexylcarbodiimides (DCC) are reported that bear a 2,2,6,6-tetramethylpiperidinyloxyl (TEMPO) residue on one side and different aromatic and aliphatic cyclohexyl analogues on the other side of the diimide core. These readily available novel reagents add efficiently to aliphatic and aromatic carboxylic acids, forming two possible spin-labeled amide derivatives with different radical distances of the resulting amide. The addition of aromatic DCC analogues proceeds with excellent selectivity, giving amides where the carboxylic acid is exclusively connected to the aromatic residue, while little or no selectivity was observed for the aliphatic congeners. The usefulness of these adducts in structural studies was demonstrated by EPR (electron paramagnetic resonance) measurements of biradical adducts of biphenyl-4,4'-dicarboxylic acids. These analyses also reveal high degrees of conformational bias for aromatic DCC derivatives, which further underlines the powerfulness of these novel reagents. This observation was further corroborated by quantum chemical calculations, giving a detailed understanding of the structural dynamics, while detailed information on the solid state structure of all novel reagents was obtained by X-ray structure analyses.
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Affiliation(s)
- Jan Philipp Gölz
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Yaser NejatyJahromy
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Mirko Bauer
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Ashraf Muhammad
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Gregor Schnakenburg
- Institut für Anorganische Chemie, Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Olav Schiemann
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany.
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24
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Gölz JP, Bockelmann S, Mayer K, Steinhoff HJ, Wieczorek H, Huss M, Klare JP, Menche D. EPR Studies of V-ATPase with Spin-Labeled Inhibitors DCC and Archazolid: Interaction Dynamics with Proton Translocating Subunit c. ChemMedChem 2015; 11:420-8. [DOI: 10.1002/cmdc.201500500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Jan Philipp Gölz
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Svenja Bockelmann
- Fachbereich Biologie/Chemie; Universität Osnabrück; 49069 Osnabrück Germany
| | - Kerstin Mayer
- Institut für Organische Chemie; Ruprecht-Karls-Universität Heidelberg; INF 270; 69120 Heidelberg Germany
| | | | - Helmut Wieczorek
- Fachbereich Biologie/Chemie; Universität Osnabrück; 49069 Osnabrück Germany
| | - Markus Huss
- Fachbereich Biologie/Chemie; Universität Osnabrück; 49069 Osnabrück Germany
| | - Johann P. Klare
- Fachbereich Physik; Universität Osnabrück; 49069 Osnabrück Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Str. 1 53121 Bonn Germany
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Le Breton N, Martinho M, Mileo E, Etienne E, Gerbaud G, Guigliarelli B, Belle V. Exploring intrinsically disordered proteins using site-directed spin labeling electron paramagnetic resonance spectroscopy. Front Mol Biosci 2015; 2:21. [PMID: 26042221 PMCID: PMC4436889 DOI: 10.3389/fmolb.2015.00021] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/03/2015] [Indexed: 11/15/2022] Open
Abstract
Proteins are highly variable biological systems, not only in their structures but also in their dynamics. The most extreme example of dynamics is encountered within the family of Intrinsically Disordered Proteins (IDPs), which are proteins lacking a well-defined 3D structure under physiological conditions. Among the biophysical techniques well-suited to study such highly flexible proteins, Site-Directed Spin Labeling combined with EPR spectroscopy (SDSL-EPR) is one of the most powerful, being able to reveal, at the residue level, structural transitions such as folding events. SDSL-EPR is based on selective grafting of a paramagnetic label on the protein under study and is limited neither by the size nor by the complexity of the system. The objective of this mini-review is to describe the basic strategy of SDSL-EPR and to illustrate how it can be successfully applied to characterize the structural behavior of IDPs. Recent developments aimed at enlarging the panoply of SDSL-EPR approaches are presented in particular newly synthesized spin labels that allow the limitations of the classical ones to be overcome. The potentialities of these new spin labels will be demonstrated on different examples of IDPs.
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Affiliation(s)
- Nolwenn Le Breton
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Marlène Martinho
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Elisabetta Mileo
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Emilien Etienne
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Guillaume Gerbaud
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Bruno Guigliarelli
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
| | - Valérie Belle
- Bioénergétique et Ingénierie des Protéines Laboratory, UMR 7281, Aix-Marseille Université and Centre National de la Recherche Scientifique Marseille, France
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Affiliation(s)
- Omar Boutureira
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili , C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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Bagryanskaya EG, Krumkacheva OA, Fedin MV, Marque SR. Development and Application of Spin Traps, Spin Probes, and Spin Labels. Methods Enzymol 2015; 563:365-96. [DOI: 10.1016/bs.mie.2015.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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New developments in spin labels for pulsed dipolar EPR. Molecules 2014; 19:16998-7025. [PMID: 25342554 PMCID: PMC6271499 DOI: 10.3390/molecules191016998] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
Spin labelling is a chemical technique that enables the integration of a molecule containing an unpaired electron into another framework for study. Given the need to understand the structure, dynamics, and conformational changes of biomacromolecules, spin labelling provides a relatively non-intrusive technique and has certain advantages over X-ray crystallography; which requires high quality crystals. The technique relies on the design of binding probes that target a functional group, for example, the thiol group of a cysteine residue within a protein. The unpaired electron is typically supplied through a nitroxide radical and sterically shielded to preserve stability. Pulsed electron paramagnetic resonance (EPR) techniques allow small magnetic couplings to be measured (e.g., <50 MHz) providing information on single label probes or the dipolar coupling between multiple labels. In particular, distances between spin labels pairs can be derived which has led to many protein/enzymes and nucleotides being studied. Here, we summarise recent examples of spin labels used for pulse EPR that serve to illustrate the contribution of chemistry to advancing discoveries in this field.
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Affiliation(s)
- Johnny Habchi
- Aix-Marseille Université , Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
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30
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Mileo E, Lorenzi M, Erales J, Lignon S, Puppo C, Le Breton N, Etienne E, Marque SRA, Guigliarelli B, Gontero B, Belle V. Dynamics of the intrinsically disordered protein CP12 in its association with GAPDH in the green alga Chlamydomonas reinhardtii: a fuzzy complex. MOLECULAR BIOSYSTEMS 2014; 9:2869-76. [PMID: 24056937 DOI: 10.1039/c3mb70190e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CP12 is a widespread regulatory protein of oxygenic photosynthetic organisms that contributes to the regulation of the Calvin cycle by forming a supra-molecular complex with at least two enzymes: glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK). CP12 shares some similarities with intrinsically disordered proteins (IDPs) depending on its redox state. In this study, site-directed spin labeling (SDSL) combined with EPR spectroscopy was used to probe the dynamic behavior of CP12 from Chlamydomonas reinhardtii upon binding to GAPDH, the first step towards ternary complex formation. The two N-terminal cysteine residues were labeled using the classical approach while the tyrosine located at the C-terminal end of CP12 was modified following an original procedure. The results show that the label grafted at the C-terminal extremity is in the vicinity of the interaction site whereas the N-terminal region remains fully disordered upon binding to GAPDH. In conclusion, GAPDH-CP12 is a fuzzy complex, in which the N-terminal region of CP12 keeps a conformational freedom in the bound form. This fuzziness could be one of the keys to facilitate binding of PRK to CP12-GAPDH and to form the ternary supra-molecular complex.
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Affiliation(s)
- Elisabetta Mileo
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France.
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31
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Breton NL, Martinho M, Kabytaev K, Topin J, Mileo E, Blocquel D, Habchi J, Longhi S, Rockenbauer A, Golebiowski J, Guigliarelli B, Marque SRA, Belle V. Diversification of EPR signatures in site directed spin labeling using a β-phosphorylated nitroxide. Phys Chem Chem Phys 2014; 16:4202-9. [DOI: 10.1039/c3cp54816c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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32
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Cornish-Bowden A. Understanding allosteric and cooperative interactions in enzymes. FEBS J 2013; 281:621-32. [DOI: 10.1111/febs.12469] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/24/2013] [Accepted: 07/30/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Athel Cornish-Bowden
- Unité de Bioénergétique et Ingénierie des Protéines; Institut de Microbiologie de la Méditerranée; Centre National de la Recherche Scientifique and Aix-Marseille Université; France
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An intrinsically disordered protein, CP12: jack of all trades and master of the Calvin cycle. Biochem Soc Trans 2013; 40:995-9. [PMID: 22988853 DOI: 10.1042/bst20120097] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many proteins contain disordered regions under physiological conditions and lack specific three-dimensional structure. These are referred to as IDPs (intrinsically disordered proteins). CP12 is a chloroplast protein of approximately 80 amino acids and has a molecular mass of approximately 8.2-8.5 kDa. It is enriched in charged amino acids and has a small number of hydrophobic residues. It has a high proportion of disorder-promoting residues, but has at least two (often four) cysteine residues forming one (or two) disulfide bridge(s) under oxidizing conditions that confers some order. However, CP12 behaves like an IDP. It appears to be universally distributed in oxygenic photosynthetic organisms and has recently been detected in a cyanophage. The best studied role of CP12 is its regulation of the Calvin cycle responsible for CO2 assimilation. Oxidized CP12 forms a supramolecular complex with two key Calvin cycle enzymes, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and PRK (phosphoribulokinase), down-regulating their activity. Association-dissociation of this complex, induced by the redox state of CP12, allows the Calvin cycle to be inactive in the dark and active in the light. CP12 is promiscuous and interacts with other enzymes such as aldolase and malate dehydrogenase. It also plays other roles in plant metabolism such as protecting GAPDH from inactivation and scavenging metal ions such as copper and nickel, and it is also linked to stress responses. Thus CP12 seems to be involved in many functions in photosynthetic cells and behaves like a jack of all trades as well as being a master of the Calvin cycle.
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Gavrilyuk J, Ban H, Nagano M, Hakamata W, Barbas CF. Formylbenzene diazonium hexafluorophosphate reagent for tyrosine-selective modification of proteins and the introduction of a bioorthogonal aldehyde. Bioconjug Chem 2012. [PMID: 23181702 DOI: 10.1021/bc300410p] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
4-Formylbenzene diazonium hexafluorophosphate (FBDP) is a novel bench-stable crystalline diazonium salt that reacts selectively with tyrosine to install a bioorthogonal aldehyde functionality. Model studies with N-acyl-tyrosine methylamide allowed us to identify conditions optimal for tyrosine ligation reactions with small peptides and proteins. FBDP-based conjugation was used for the facile introduction of small molecule tags, poly(ethylene glycol) chains (PEGylation), and functional small molecules onto model proteins and to label the surface of living cells.
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Affiliation(s)
- Julia Gavrilyuk
- Departments of Chemistry and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA
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Han S, Kim D, Han SH, Kim NH, Kim SH, Lim YB. Structural and Conformational Dynamics of Self-Assembling Bioactive β-Sheet Peptide Nanostructures Decorated with Multivalent RNA-Binding Peptides. J Am Chem Soc 2012; 134:16047-53. [DOI: 10.1021/ja307493t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sanghun Han
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Donghun Kim
- Division of Materials
Science, Korea Basic Science Institute (KBSI), Daejeon 305-333,
Korea
| | - So-hee Han
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Nam Hee Kim
- Division of Materials
Science, Korea Basic Science Institute (KBSI), Daejeon 305-333,
Korea
| | - Sun Hee Kim
- Division of Materials
Science, Korea Basic Science Institute (KBSI), Daejeon 305-333,
Korea
| | - Yong-beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
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Martinho M, Habchi J, El Habre Z, Nesme L, Guigliarelli B, Belle V, Longhi S. Assessing induced folding within the intrinsically disordered C-terminal domain of the Henipavirus nucleoproteins by site-directed spin labeling EPR spectroscopy. J Biomol Struct Dyn 2012; 31:453-71. [PMID: 22881220 DOI: 10.1080/07391102.2012.706068] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
This work aims at characterizing structural transitions within the intrinsically disordered C-terminal domain of the nucleoprotein (NTAIL) from the Nipah and Hendra viruses, two recently emerged pathogens gathered within the Henipavirus genus. To this end, we used site-directed spin labeling combined with electron paramagnetic resonance spectroscopy to investigate the α-helical-induced folding that Henipavirus NTAIL domains undergo in the presence of the C-terminal X domain of the phosphoprotein (PXD). For each NTAIL protein, six positions located within four previously proposed molecular recognition elements (MoREs) were targeted for spin labeling, with three of these positions (475, 481, and 487) falling within the MoRE responsible for binding to PXD (Box3). A detailed analysis of the impact of the partner protein on the labeled NTAIL variants revealed a dramatic modification in the environment of the spin labels grafted within Box3, with the observed modifications supporting the formation of an induced α-helix within this region. In the free state, the slightly lower mobility of the spin labels grafted within Box3 as compared to the other positions suggests the existence of a transiently populated α-helix, as already reported for measles virus (MeV) NTAIL. Comparison with the well-characterized MeV NTAIL-PXD system, allowed us to validate the structural models of Henipavirus NTAIL-PXD complexes that we previously proposed. In addition, this study highlighted a few notable differences between the Nipah and Hendra viruses. In particular, the observation of composite spectra for the free form of the Nipah virus NTAIL variants spin labeled in Box3 supports conformational heterogeneity of this partly pre-configured α-helix, with the pre-existence of stable α-helical segments. Altogether these results provide insights into the molecular mechanisms of the Henipavirus NTAIL-PXD binding reaction.
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Affiliation(s)
- Marlène Martinho
- CNRS, Aix Marseille Université, IMM FR 3479, BIP UMR 7281, 13402 Marseille, France
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Audran G, Brémond P, Marque SRA, Obame G. Hyperfine Coupling Constants of β-Phosphorylated Nitroxides: A Tool to Probe the Cybotactic Effect by Electron Paramagnetic Resonance. Chemphyschem 2012; 13:3542-8. [DOI: 10.1002/cphc.201200420] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Indexed: 11/10/2022]
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Delaittre G, Dietrich M, Blinco JP, Hirschbiel A, Bruns M, Barner L, Barner-Kowollik C. Photo-Induced Macromolecular Functionalization of Cellulose via Nitroxide Spin Trapping. Biomacromolecules 2012; 13:1700-5. [DOI: 10.1021/bm3001364] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guillaume Delaittre
- Preparative Macromolecular
Chemistry, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr.
18, 76128 Karlsruhe, Germany
- Zoologisches Institut,
Zell- und Neurobiologie, Karlsruhe Institute of Technology (KIT), Haid-und-Neu-Str. 9, 76131 Karlsruhe,
Germany
| | - Mathias Dietrich
- Preparative Macromolecular
Chemistry, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr.
18, 76128 Karlsruhe, Germany
- Environmental
Engineering
Group, Fraunhofer Institute of Chemical Technology, Joseph-von-Fraunhofer-Str. 7, 76327 Pfinztal,
Germany
| | - James P. Blinco
- Preparative Macromolecular
Chemistry, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr.
18, 76128 Karlsruhe, Germany
- ARC
Centre of Excellence
for Free Radical Chemistry and Biotechnology, Queensland University of Technology (QUT), Brisbane,
4001, Australia
| | - Astrid Hirschbiel
- Preparative Macromolecular
Chemistry, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr.
18, 76128 Karlsruhe, Germany
| | - Michael Bruns
- Institute for Applied
Materials (IAM-WPT) and Karlsruhe Nano Micro Facility
(KNMF), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen,
Germany
| | - Leonie Barner
- Soft Matter Synthesis
Laboratory, Institut für Biologische Grenzflächen
I (IBG I), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen,
Germany
| | - Christopher Barner-Kowollik
- Preparative Macromolecular
Chemistry, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr.
18, 76128 Karlsruhe, Germany
- Soft Matter Synthesis
Laboratory, Institut für Biologische Grenzflächen
I (IBG I), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen,
Germany
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