1
|
Sweger SR, Cheung JC, Zha L, Pribitzer S, Stoll S. Bayesian Probabilistic Inference of Nonparametric Distance Distributions in DEER Spectroscopy. J Phys Chem A 2024. [PMID: 39365178 DOI: 10.1021/acs.jpca.4c05056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Double electron-electron resonance (DEER) spectroscopy measures distance distributions between spin labels in proteins, yielding important structural and energetic information about conformational landscapes. Analysis of an experimental DEER signal in terms of a distance distribution is a nontrivial task due to the ill-posed nature of the underlying mathematical inversion problem. This work introduces a Bayesian probabilistic inference approach to analyze DEER data, assuming a nonparametric distance distribution with a Tikhonov smoothness prior. The method uses Markov Chain Monte Carlo sampling with a compositional Gibbs sampler to determine a posterior probability distribution over the entire parameter space, including the distance distribution, given an experimental data set. This posterior contains all of the information available from the data, including a full quantification of the uncertainty about the model parameters. The corresponding uncertainty about the distance distribution is visually captured via an ensemble of posterior predictive distributions. Several examples are presented to illustrate the method. Compared with bootstrapping, it performs faster and provides slightly larger uncertainty intervals.
Collapse
Affiliation(s)
- Sarah R Sweger
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Julian C Cheung
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lukas Zha
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Stephan Pribitzer
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
2
|
Meron S, Peleg S, Shenberger Y, Hofmann L, Gevorkyan-Airapetov L, Ruthstein S. Tracking Disordered Extracellular Domains of Membrane Proteins in the Cell with Cu(II)-Based Spin Labels. J Phys Chem B 2024; 128:8908-8914. [PMID: 39231533 PMCID: PMC11421077 DOI: 10.1021/acs.jpcb.4c03676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
In-cell electron paramagnetic resonance (EPR) spectroscopy experiments provide high-resolution data about conformational changes of proteins within the cell. However, one of the limitations of EPR is the requisite of stable paramagnetic centers in a reducing environment. We recently showed that histidine-rich sites in proteins hold a high affinity to Cu(II) ions complexed with a chelator. Using a chelator prevents the reduction of Cu(II) ions. Moreover, this spin-labeling methodology can be performed within the native cellular environment on any overexpressed protein without protein purification and delivery to the cell. Herein, we use this novel methodology to gain spatial information on the extracellular domain of the human copper transporter, hCtr1. Limited structural information on the transmembrane domain of the human Ctr1 (hCtr1) was obtained using X-ray crystallography and cryo-EM. However, these structures are missing information on the disordered extracellular domains of hCtr1. Extracellular domains are sensing or interacting with the environment outside of the cell and therefore play an essential role in any transmembrane protein. Especially in hCtr1, the extracellular domain functions as a gating mechanism for copper ions. Here, we performed EPR experiments revealing structural information about the extracellular N-terminal domain of the full-length hCtr1 in vitro and in situ in insect cells and cell membrane fragments. The comparison revealed that the extracellular domains of the in situ and native membrane hCtr1 are further apart than the structure of the purified protein. These method-related differences highlight the significance of studying membrane proteins in their native environment.
Collapse
Affiliation(s)
- Shelly Meron
- The Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Shahaf Peleg
- The Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Yulia Shenberger
- The Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Lukas Hofmann
- The Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Lada Gevorkyan-Airapetov
- The Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 529002, Israel
| | - Sharon Ruthstein
- The Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 529002, Israel
| |
Collapse
|
3
|
Belyaeva J, Elgeti M. Exploring protein structural ensembles: Integration of sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling methods. eLife 2024; 13:e99770. [PMID: 39283059 PMCID: PMC11405019 DOI: 10.7554/elife.99770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/29/2024] [Indexed: 09/22/2024] Open
Abstract
Under physiological conditions, proteins continuously undergo structural fluctuations on different timescales. Some conformations are only sparsely populated, but still play a key role in protein function. Thus, meaningful structure-function frameworks must include structural ensembles rather than only the most populated protein conformations. To detail protein plasticity, modern structural biology combines complementary experimental and computational approaches. In this review, we survey available computational approaches that integrate sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling techniques to derive all-atom structural models of rare protein conformations. We also propose strategies to increase the reliability and improve efficiency using deep learning approaches, thus advancing the field of integrative structural biology.
Collapse
Affiliation(s)
- Julia Belyaeva
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
- Institute for Medical Physics and Biophysics, Leipzig University Medical School, Leipzig, Germany
| | - Matthias Elgeti
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
- Institute for Medical Physics and Biophysics, Leipzig University Medical School, Leipzig, Germany
- Integrative Center for Bioinformatics, Leipzig University, Leipzig, Germany
| |
Collapse
|
4
|
Ovcherenko SS, Raizvich AE, Rogozhnikova OY, Tormyshev VM, Trukhin DV, Koval VV, Salnikov GE, Genaev AM, Shernyukov AV, Bagryanskaya EG. Redox Transformations of the OX063 Radical in Biological Media: Oxidative Decay of Initial Trityl with Further Formation of Structurally-Modified TAM. Chemistry 2024; 30:e202400718. [PMID: 39003595 DOI: 10.1002/chem.202400718] [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: 02/22/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024]
Abstract
Being a low-toxic and hydrophilic representative of TAM, OX063 has shown its suitability for in-vivo and in-cell EPR experiments and design of spin labels. Using 13C labeling, we investigated the course of oxidative degradation of OX063 into quinone-methide (QM) under the influence of superoxide as well as further thiol-promoted reduction of QM into TAM radical, which formally corresponds to substitution of a carboxyl function by a hydroxyl group. We found these transformations being quantitative in model reactions mimicking specific features of biological media and confirmed the presence of these reactions in the blood and liver homogenate of mice in vitro. The emergence of the trityl with the hydroxyl group can be masked by an initial TAM in EPR spectra and may introduce distortions into EPR-derived oximetry data if they have been obtained for objects under hypoxia. 13C labeling allows one to detect its presence, considering its different hyperfine splitting constant on 13C1 (2.04 mT) as compared to OX063 (2.30 mT). The potential involvement of these reactions should be considered when using TAM in spin-labeling of biopolymers intended for subsequent EPR experiments, as well as in the successful application of TAM in experiments in vivo and in cell.
Collapse
Affiliation(s)
- Sergey S Ovcherenko
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
- Novosibirsk State University, 2 Pirogova Street, Novosibirsk, 630090, Russian Federation
| | - Arthur E Raizvich
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
- Novosibirsk State University, 2 Pirogova Street, Novosibirsk, 630090, Russian Federation
| | - Olga Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
| | - Victor M Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
| | - Dmitry V Trukhin
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
| | - Georgii E Salnikov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
| | - Alexander M Genaev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
| | - Andrey V Shernyukov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk, 630090, Russian Federation
| |
Collapse
|
5
|
Pierro A, Bonucci A, Magalon A, Belle V, Mileo E. Impact of Cellular Crowding on Protein Structural Dynamics Investigated by EPR Spectroscopy. Chem Rev 2024; 124:9873-9898. [PMID: 39213496 DOI: 10.1021/acs.chemrev.3c00951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The study of how the intracellular medium influences protein structural dynamics and protein-protein interactions is a captivating area of research for scientists aiming to comprehend biomolecules in their native environment. As the cellular environment can hardly be reproduced in vitro, direct investigation of biomolecules within cells has attracted growing interest in the past two decades. Among magnetic resonances, site-directed spin labeling coupled to electron paramagnetic resonance spectroscopy (SDSL-EPR) has emerged as a powerful tool for studying the structural properties of biomolecules directly in cells. Since the first in-cell EPR experiment was reported in 2010, substantial progress has been made, and this Review provides a detailed overview of the developments and applications of this spectroscopic technique. The strategies available for preparing a cellular sample and the EPR methods that can be applied to cells will be discussed. The array of spin labels available, along with their strengths and weaknesses in cellular contexts, will also be described. Several examples will illustrate how in-cell EPR can be applied to different biological systems and how the cellular environment affects the structural and dynamic properties of different proteins. Lastly, the Review will focus on the future developments expected to expand the capabilities of this promising technique.
Collapse
Affiliation(s)
- Annalisa Pierro
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Alessio Bonucci
- Aix Marseille University, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM, IM2B, Marseille, France
| | - Axel Magalon
- Aix Marseille University, CNRS, Laboratoire de Chimie Bactérienne (LCB), IMM, IM2B, Marseille, France
| | - Valérie Belle
- Aix Marseille University, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM, IM2B, Marseille, France
| | - Elisabetta Mileo
- Aix Marseille University, CNRS, Bioénergétique et Ingénierie des Protéines (BIP), IMM, IM2B, Marseille, France
| |
Collapse
|
6
|
Li S, Deng P, Chang Q, Feng M, Shang Y, Song Y, Liu Y. In Situ Generation and High Bioresistance of Trityl-based Semiquinone Methide Radicals Under Anaerobic Conditions in Cellular Systems. Chemistry 2024; 30:e202400985. [PMID: 38932665 DOI: 10.1002/chem.202400985] [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: 03/09/2024] [Revised: 06/02/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
Bioreduction of spin labels and polarizing agents (generally stable radicals) has been an obstacle limiting the in-cell applications of pulsed electron paramagnetic resonance (EPR) spectroscopy and dynamic nuclear polarization (DNP). In this work, we have demonstrated that two semiquinone methide radicals (OXQM⋅ and CTQM⋅) can be easily produced from the trityl-based quinone methides (OXQM and CTQM) via reduction by various reducing agents including biothiols and ascorbate under anaerobic conditions. Both radicals have relatively low pKa's and exhibit EPR single line signals at physiological pH. Moreover, the bioreduction of OXQM in three cell lysates enables quantitative generation of OXQM⋅ which was most likely mediated by flavoenzymes. Importantly, the resulting OXQM⋅ exhibited extremely high stability in the E.coli lysate under anaerobic conditions with 76- and 14.3-fold slower decay kinetics as compared to the trityl OX063 and a gem-diethyl pyrrolidine nitroxide, respectively. Intracellular delivery of OXQM into HeLa cells was also achieved by covalent conjugation with a cell-permeable peptide as evidenced by the stable intracellular EPR signal from the OXQM⋅ moiety. Owing to extremely high resistance of OXQM⋅ towards bioreduction, OXQM and its derivatives show great application potential in in-cell EPR and in-cell DNP studies for various cells which can endure short-term anoxic treatments.
Collapse
Affiliation(s)
- Shuai Li
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Peng Deng
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Qi Chang
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Meirong Feng
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Yixuan Shang
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Yuguang Song
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Yangping Liu
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| |
Collapse
|
7
|
Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J Mol Biol 2024; 436:168546. [PMID: 38508301 PMCID: PMC11377171 DOI: 10.1016/j.jmb.2024.168546] [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: 01/23/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.
Collapse
Affiliation(s)
- Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Benjamin M Webb
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, the Quantitative Biosciences Institute (QBI), and the Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of California, San Francisco, San Francisco, CA 94157, USA
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Thomas D Goddard
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Christian A Hanke
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; Human Technopole, 20157 Milan, Italy
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, the Quantitative Biosciences Institute (QBI), and the Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of California, San Francisco, San Francisco, CA 94157, USA
| | - Jared Sagendorf
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, the Quantitative Biosciences Institute (QBI), and the Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of California, San Francisco, San Francisco, CA 94157, USA
| | - Hongsuda Tangmunarunkit
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Serban Voinea
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Monica Sekharan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jian Yu
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Alexander A M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37221, USA; Institute for Drug Discovery, Leipzig University Medical School, 04103 Leipzig, Germany
| | - Emad Tajkhorshid
- NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, c/o Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jeffrey C Hoch
- Biological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, University of Connecticut, Farmington, CT 06030-3305, USA
| | - Genji Kurisu
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kyle Morris
- Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ardan Patwardhan
- Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology & SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Carl Kesselman
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles CA 90089, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, the Quantitative Biosciences Institute (QBI), and the Research Collaboratory for Structural Bioinformatics Protein Data Bank, University of California, San Francisco, San Francisco, CA 94157, USA
| |
Collapse
|
8
|
Aupič J, Pokorná P, Ruthstein S, Magistrato A. Predicting Conformational Ensembles of Intrinsically Disordered Proteins: From Molecular Dynamics to Machine Learning. J Phys Chem Lett 2024; 15:8177-8186. [PMID: 39093570 DOI: 10.1021/acs.jpclett.4c01544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Intrinsically disordered proteins and regions (IDP/IDRs) are ubiquitous across all domains of life. Characterized by a lack of a stable tertiary structure, IDP/IDRs populate a diverse set of transiently formed structural states that can promiscuously adapt upon binding with specific interaction partners and/or certain alterations in environmental conditions. This malleability is foundational for their role as tunable interaction hubs in core cellular processes such as signaling, transcription, and translation. Tracing the conformational ensemble of an IDP/IDR and its perturbation in response to regulatory cues is thus paramount for illuminating its function. However, the conformational heterogeneity of IDP/IDRs poses several challenges. Here, we review experimental and computational methods devised to disentangle the conformational landscape of IDP/IDRs, highlighting recent computational advances that permit proteome-wide scans of IDP/IDRs conformations. We briefly evaluate selected computational methods using the disordered N-terminal of the human copper transporter 1 as a test case and outline further challenges in IDP/IDRs ensemble prediction.
Collapse
Affiliation(s)
- Jana Aupič
- CNR-IOM at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Pavlína Pokorná
- CNR-IOM at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences and the Institute for Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Alessandra Magistrato
- CNR-IOM at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
9
|
Chubarov AS, Endeward B, Kanarskaya MA, Polienko YF, Prisner TF, Lomzov AA. Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies. Biomolecules 2024; 14:887. [PMID: 39199275 PMCID: PMC11351890 DOI: 10.3390/biom14080887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 09/01/2024] Open
Abstract
Pulsed electron-electron double resonance (PELDOR) spectroscopy is a powerful method for determining nucleic acid (NA) structure and conformational dynamics. PELDOR with molecular dynamics (MD) simulations opens up unique possibilities for defining the conformational ensembles of flexible, three-dimensional, self-assembled complexes of NA. Understanding the diversity and structure of these complexes is vital for uncovering matrix and regulative biological processes in the human body and artificially influencing them for therapeutic purposes. To explore the reliability of PELDOR and MD simulations, we site-specifically attached nitroxide spin labels to oligonucleotides, which form self-assembled complexes between NA chains and exhibit significant conformational flexibility. The DNA complexes assembled from a pair of oligonucleotides with different linker sizes showed excellent agreement between the distance distributions obtained from PELDOR and calculated from MD simulations, both for the mean inter-spin distance and the distance distribution width. These results prove that PELDOR with MD simulations has significant potential for studying the structure and dynamics of conformational flexible complexes of NA.
Collapse
Affiliation(s)
- Alexey S. Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia;
| | - Burkhard Endeward
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany; (B.E.); (T.F.P.)
| | - Maria A. Kanarskaya
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia;
| | - Yuliya F. Polienko
- N.N. Vorozhtsov Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia;
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany; (B.E.); (T.F.P.)
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia;
| |
Collapse
|
10
|
Chadda R, Kaushik V, Ahmad IM, Deveryshetty J, Holehouse AS, Sigurdsson ST, Biswas G, Levy Y, Bothner B, Cooley RB, Mehl RA, Dastvan R, Origanti S, Antony E. Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic Acids Res 2024:gkae584. [PMID: 38989614 DOI: 10.1093/nar/gkae584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/30/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024] Open
Abstract
Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA-ssDNA complexes using single-molecule FRET and double electron-electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.
Collapse
Affiliation(s)
- Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Iram Munir Ahmad
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Jaigeeth Deveryshetty
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Gargi Biswas
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Sofia Origanti
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| |
Collapse
|
11
|
Syryamina VN, Aisenbrey C, Kardash M, Dzuba SA, Bechinger B. Self-assembly of spin-labeled antimicrobial peptides magainin 2 and PGLa in lipid bilayers. Biophys Chem 2024; 310:107251. [PMID: 38678820 DOI: 10.1016/j.bpc.2024.107251] [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: 01/29/2024] [Revised: 04/15/2024] [Accepted: 04/21/2024] [Indexed: 05/01/2024]
Abstract
The cationic antimicrobial peptides PGLa and magainin 2 (Mag2) are known for their antimicrobial activity and synergistic enhancement in antimicrobial and membrane leakage assays. Further use of peptides in combinatory therapy requires knowledge of the mechanisms of action of both individual peptides and their mixtures. Here, electron paramagnetic resonance (EPR), double electron-electron resonance (DEER, also known as PELDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies were applied to study self-assembly and localization of spin-labeled PGLa and Mag2 in POPE/POPG membranes with a wide range of peptide/lipid ratios (P/L) from ∼1/1500 to 1/50. EPR and DEER data showed that both peptides tend to organize in clusters, which occurs already at the lowest peptide/lipid molar ratio of 1/1500 (0.067 mol%). For individual peptides, these clusters are quite dense with intermolecular distances of the order of ∼2 nm. In the presence of a synergistic peptide partner, these homo-clusters are transformed into lipid-diluted hetero-clusters. These clusters are characterized by a local surface density that is several times higher than expected from a random distribution. ESEEM data indicate a slightly different insertion depth of peptides in hetero-clusters when compared to homo-clusters.
Collapse
Affiliation(s)
- Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation
| | - Christopher Aisenbrey
- University of Strasbourg/CNRS, UMR7177, Strasbourg Institute of Chemistry, Membrane Biophysics and NMR, 67000 Strasbourg, France
| | - Maria Kardash
- University of Strasbourg/CNRS, UMR7177, Strasbourg Institute of Chemistry, Membrane Biophysics and NMR, 67000 Strasbourg, France
| | - Sergei A Dzuba
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation; Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russian Federation.
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177, Strasbourg Institute of Chemistry, Membrane Biophysics and NMR, 67000 Strasbourg, France; Institut Universitaire de France, 75231 Paris, France.
| |
Collapse
|
12
|
Baker ZD, Rasmussen DM, Levinson NM. Exploring the conformational landscapes of protein kinases: perspectives from FRET and DEER. Biochem Soc Trans 2024; 52:1071-1083. [PMID: 38778760 PMCID: PMC11346445 DOI: 10.1042/bst20230558] [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: 02/15/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Conformational changes of catalytically-important structural elements are a key feature of the regulation mechanisms of protein kinases and are important for dictating inhibitor binding modes and affinities. The lack of widely applicable methods for tracking kinase conformational changes in solution has hindered our understanding of kinase regulation and our ability to design conformationally selective inhibitors. Here we provide an overview of two recently developed methods that detect conformational changes of the regulatory activation loop and αC-helix of kinases and that yield complementary information about allosteric mechanisms. An intramolecular Förster resonance energy transfer-based approach provides a scalable platform for detecting and classifying structural changes in high-throughput, as well as quantifying ligand binding cooperativity, shedding light on the energetics governing allostery. The pulsed electron paramagnetic resonance technique double electron-electron resonance provides lower throughput but higher resolution information on structural changes that allows for unambiguous assignment of conformational states and quantification of population shifts. Together, these methods are shedding new light on kinase regulation and drug interactions and providing new routes for the identification of novel kinase inhibitors and allosteric modulators.
Collapse
Affiliation(s)
- Zachary D. Baker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Damien M. Rasmussen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Nicholas M. Levinson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, U.S.A
| |
Collapse
|
13
|
Lane BJ, Ma Y, Yan N, Wang B, Ackermann K, Karamanos TK, Bode BE, Pliotas C. Monitoring the conformational ensemble and lipid environment of a mechanosensitive channel under cyclodextrin-induced membrane tension. Structure 2024; 32:739-750.e4. [PMID: 38521071 DOI: 10.1016/j.str.2024.02.020] [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: 09/14/2023] [Revised: 12/29/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Membrane forces shift the equilibria of mechanosensitive channels enabling them to convert mechanical cues into electrical signals. Molecular tools to stabilize and methods to capture their highly dynamic states are lacking. Cyclodextrins can mimic tension through the sequestering of lipids from membranes. Here we probe the conformational ensemble of MscS by EPR spectroscopy, the lipid environment with NMR, and function with electrophysiology under cyclodextrin-induced tension. We show the extent of MscS activation depends on the cyclodextrin-to-lipid ratio, and that lipids are depleted slower when MscS is present. This has implications in MscS' activation kinetics when distinct membrane scaffolds such as nanodiscs or liposomes are used. We find MscS transits from closed to sub-conducting state(s) before it desensitizes, due to the lack of lipid availability in its vicinity required for closure. Our approach allows for monitoring tension-sensitive states in membrane proteins and screening molecules capable of inducing molecular tension in bilayers.
Collapse
Affiliation(s)
- Benjamin J Lane
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yue Ma
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Nana Yan
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Bolin Wang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Theodoros K Karamanos
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK; Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
| |
Collapse
|
14
|
Gauger M, Heinz M, Halbritter ALJ, Stelzl LS, Erlenbach N, Hummer G, Sigurdsson ST, Prisner TF. Structure and Internal Dynamics of Short RNA Duplexes Determined by a Combination of Pulsed EPR Methods and MD Simulations. Angew Chem Int Ed Engl 2024; 63:e202402498. [PMID: 38530284 DOI: 10.1002/anie.202402498] [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: 02/03/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
We used EPR spectroscopy to characterize the structure of RNA duplexes and their internal twist, stretch and bending motions. We prepared eight 20-base-pair-long RNA duplexes containing the rigid spin-label Çm, a cytidine analogue, at two positions and acquired orientation-selective PELDOR/DEER data. By using different frequency bands (X-, Q-, G-band), detailed information about the distance and orientation of the labels was obtained and provided insights into the global conformational dynamics of the RNA duplex. We used 19F Mims ENDOR experiments on three singly Çm- and singly fluorine-labeled RNA duplexes to determine the exact position of the Çm spin label in the helix. In a quantitative comparison to MD simulations of RNA with and without Çm spin labels, we found that state-of-the-art force fields with explicit parameterization of the spin label were able to describe the conformational ensemble present in our experiments. The MD simulations further confirmed that the Çm spin labels are excellent mimics of cytidine inducing only small local changes in the RNA structure. Çm spin labels are thus ideally suited for high-precision EPR experiments to probe the structure and, in conjunction with MD simulations, motions of RNA.
Collapse
Affiliation(s)
- Maximilian Gauger
- 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
| | - Marcel Heinz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
| | | | - Lukas S Stelzl
- Faculty of Biology, Johannes Gutenberg University, 55128, Mainz, Germany
- KOMET 1, Institute of Physics, Johannes Gutenberg University, Staudingerweg 9, 55128, Mainz, Germany
- Institute of Quantitative and Computational Bioscience (IQCB), Johannes Gutenberg University Mainz, 55128, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Nicole Erlenbach
- 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
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue Str. 1, 60438, Frankfurt am Main, Germany
| | | | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt am Main, Germany
| |
Collapse
|
15
|
Grosskopf JD, Sidabras JW, Altenbach C, Anderson JR, Mett RR, Strangeway RA, Hyde JS, Hubbell WL, Lerch MT. A pressure-jump EPR system to monitor millisecond conformational exchange rates of spin-labeled proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.593074. [PMID: 38766191 PMCID: PMC11100676 DOI: 10.1101/2024.05.07.593074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) using nitroxide spin labels is a well-established technology for mapping site-specific secondary and tertiary structure and for monitoring conformational changes in proteins of any degree of complexity, including membrane proteins, with high sensitivity. SDSL-EPR also provides information on protein dynamics in the time scale of ps-µs using continuous wave lineshape analysis and spin lattice relaxation time methods. However, the functionally important time domain of µs-ms, corresponding to large-scale protein motions, is inaccessible to those methods. To extend SDSL-EPR to the longer time domain, the perturbation method of pressure-jump relaxation is implemented. Here, we describe a complete high-pressure EPR system at Q-band for both static pressure and millisecond-timescale pressure-jump measurements on spin-labeled proteins. The instrument enables pressure jumps both up and down from any holding pressure, ranging from atmospheric pressure to the maximum pressure capacity of the system components (~3500 bar). To demonstrate the utility of the system, we characterize a local folding-unfolding equilibrium of T4 lysozyme. The results illustrate the ability of the system to measure thermodynamic and kinetic parameters of protein conformational exchange on the millisecond timescale.
Collapse
Affiliation(s)
- Julian D Grosskopf
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jason W Sidabras
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christian Altenbach
- Department of Chemistry and Biochemistry and Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Jim R Anderson
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Richard R Mett
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Robert A Strangeway
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - James S Hyde
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wayne L Hubbell
- Department of Chemistry and Biochemistry and Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Michael T Lerch
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| |
Collapse
|
16
|
Kashnik AS, Baranov DS, Dzuba SA. Spatial Arrangement of the Drug Ibuprofen in a Model Membrane in the Presence of Lipid Rafts. J Phys Chem B 2024; 128:3652-3661. [PMID: 38576273 DOI: 10.1021/acs.jpcb.4c01507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Many pharmaceutical drugs are known to interact with lipid membranes through nonspecific molecular interactions, which affect their therapeutic effect. Ibuprofen is a nonsteroidal anti-inflammatory drug (NSAID) and one of the most commonly prescribed. In the presence of cholesterol, lipid bilayers can separate into nanoscale liquid-disordered and liquid-ordered structures, the latter known as lipid rafts. Here, we study spin-labeled ibuprofen (ibuprofen-SL) in the model membrane consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol in the molar ratio of (0.5-0.5xchol)/(0.5-0.5xchol)/xchol. Electron paramagnetic resonance (EPR) spectroscopy is employed, along with its pulsed version of double electron-electron resonance (DEER, also known as PELDOR). The data obtained indicate lateral lipid-mediated clustering of ibuprofen-SL molecules with a local surface density noticeably larger than that expected for random lateral distribution. In the absence of cholesterol, the data can be interpreted as indicating alternating clustering in two opposing leaflets of the bilayer. In the presence of cholesterol, for xchol ≥ 20 mol %, the results show that ibuprofen-SL molecules have a quasi-regular lateral distribution, with a "superlattice" parameter of ∼3.0 nm. This regularity can be explained by the entrapment of ibuprofen-SL molecules by lipid rafts known to exist in this system with the additional assumption that lipid rafts have a nanoscale substructure.
Collapse
Affiliation(s)
- Anna S Kashnik
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Denis S Baranov
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sergei A Dzuba
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| |
Collapse
|
17
|
Casiraghi M, Wang H, Brennan P, Habrian C, Hubner H, Schmidt MF, Maul L, Pani B, Bahriz SM, Xu B, White E, Sunahara RK, Xiang YK, Lefkowitz RJ, Isacoff EY, Nucci N, Gmeiner P, Lerch M, Kobilka BK. Structure and dynamics determine G protein coupling specificity at a class A GPCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587240. [PMID: 38586060 PMCID: PMC10996611 DOI: 10.1101/2024.03.28.587240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
G protein coupled receptors (GPCRs) exhibit varying degrees of selectivity for different G protein isoforms. Despite the abundant structures of GPCR-G protein complexes, little is known about the mechanism of G protein coupling specificity. The β2-adrenergic receptor is an example of GPCR with high selectivity for Gαs, the stimulatory G protein for adenylyl cyclase, and much weaker for the Gαi family of G proteins inhibiting adenylyl cyclase. By developing a new Gαi-biased agonist (LM189), we provide structural and biophysical evidence supporting that distinct conformations at ICL2 and TM6 are required for coupling of the different G protein subtypes Gαs and Gαi. These results deepen our understanding of G protein specificity and bias and can accelerate the design of ligands that select for preferred signaling pathways.
Collapse
|
18
|
Grüschow S, McQuarrie S, Ackermann K, McMahon S, Bode B, Gloster T, White M. CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23. Nucleic Acids Res 2024; 52:2761-2775. [PMID: 38471818 PMCID: PMC11014256 DOI: 10.1093/nar/gkae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
CRISPR-Cas provides adaptive immunity in prokaryotes. Type III CRISPR systems detect invading RNA and activate the catalytic Cas10 subunit, which generates a range of nucleotide second messengers to signal infection. These molecules bind and activate a diverse range of effector proteins that provide immunity by degrading viral components and/or by disturbing key aspects of cellular metabolism to slow down viral replication. Here, we focus on the uncharacterised effector Csx23, which is widespread in Vibrio cholerae. Csx23 provides immunity against plasmids and phage when expressed in Escherichia coli along with its cognate type III CRISPR system. The Csx23 protein localises in the membrane using an N-terminal transmembrane α-helical domain and has a cytoplasmic C-terminal domain that binds cyclic tetra-adenylate (cA4), activating its defence function. Structural studies reveal a tetrameric structure with a novel fold that binds cA4 specifically. Using pulse EPR, we demonstrate that cA4 binding to the cytoplasmic domain of Csx23 results in a major perturbation of the transmembrane domain, consistent with the opening of a pore and/or disruption of membrane integrity. This work reveals a new class of cyclic nucleotide binding protein and provides key mechanistic detail on a membrane-associated CRISPR effector.
Collapse
Affiliation(s)
- Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Stephen McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| |
Collapse
|
19
|
Dantu SC, Khalil M, Bria M, Saint-Pierre C, Orio M, Gasparutto D, Sicoli G. Cleaving DNA with DNA: Cooperative Tuning of Structure and Reactivity Driven by Copper Ions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306710. [PMID: 38419268 DOI: 10.1002/advs.202306710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/15/2024] [Indexed: 03/02/2024]
Abstract
A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.
Collapse
Affiliation(s)
- Sarath Chandra Dantu
- Department of Computer Science, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Mahdi Khalil
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Marc Bria
- Michle-Eugène Chevreul Institute, FR 2638, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Christine Saint-Pierre
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Maylis Orio
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, UMR CNRS 7313, Marseille, 13397, France
| | - Didier Gasparutto
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Giuseppe Sicoli
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| |
Collapse
|
20
|
Vallat B, Berman HM. Structural highlights of macromolecular complexes and assemblies. Curr Opin Struct Biol 2024; 85:102773. [PMID: 38271778 DOI: 10.1016/j.sbi.2023.102773] [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: 10/05/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024]
Abstract
The structures of macromolecular assemblies have given us deep insights into cellular processes and have profoundly impacted biological research and drug discovery. We highlight the structures of macromolecular assemblies that have been modeled using integrative and computational methods and describe how open access to these structures from structural archives has empowered the research community. The arsenal of experimental and computational methods for structure determination ensures a future where whole organelles and cells can be modeled.
Collapse
Affiliation(s)
- Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank and the Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles CA 90089, USA
| |
Collapse
|
21
|
Chadda R, Kaushik V, Ahmad IM, Deveryshetty J, Holehouse A, Sigurdsson ST, Bothner B, Dastvan R, Origanti S, Antony E. Wrapping of single-stranded DNA by Replication Protein A and modulation through phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587234. [PMID: 38585962 PMCID: PMC10996701 DOI: 10.1101/2024.03.28.587234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Single-stranded DNA (ssDNA) intermediates, which emerge during DNA metabolic processes are shielded by Replication Protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper, directing the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent specificity requires a comprehensive understanding of the structural conformation of ssDNA when bound to RPA. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA-ssDNA complexes using single-molecule FRET and Double Electron-Electron Resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.
Collapse
Affiliation(s)
- Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Iram Munir Ahmad
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Jaigeeth Deveryshetty
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Alex Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Snorri Th.d Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Sofia Origanti
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| |
Collapse
|
22
|
Esteban-Hofer L, Emmanouilidis L, Yulikov M, Allain FHT, Jeschke G. Ensemble structure of the N-terminal domain (1-267) of FUS in a biomolecular condensate. Biophys J 2024; 123:538-554. [PMID: 38279531 PMCID: PMC10938082 DOI: 10.1016/j.bpj.2024.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/06/2023] [Accepted: 01/22/2024] [Indexed: 01/28/2024] Open
Abstract
Solutions of some proteins phase separate into a condensed state of high protein concentration and a dispersed state of low concentration. Such behavior is observed in living cells for a number of RNA-binding proteins that feature intrinsically disordered domains. It is relevant for cell function via the formation of membraneless organelles and transcriptional condensates. On a basic level, the process can be studied in vitro on protein domains that are necessary and sufficient for liquid-liquid phase separation (LLPS). We have performed distance distribution measurements by electron paramagnetic resonance for 13 sections in an N-terminal domain (NTD) construct of the protein fused in sarcoma (FUS), consisting of the QGSY-rich domain and the RGG1 domain, in the denatured, dispersed, and condensed state. Using 10 distance distribution restraints for ensemble modeling and three such restraints for model validation, we have found that FUS NTD behaves as a random-coil polymer under good-solvent conditions in both the dispersed and condensed state. Conformation distribution in the biomolecular condensate is virtually indistinguishable from the one in an unrestrained ensemble, with the latter one being based on only residue-specific Ramachandran angle distributions. Over its whole length, FUS NTD is slightly more compact in the condensed than in the dispersed state, which is in line with the theory for random coils in good solvent proposed by de Gennes, Daoud, and Jannink. The estimated concentration in the condensate exceeds the overlap concentration resulting from this theory. The QGSY-rich domain is slightly more extended, slightly more hydrated, and has slightly higher propensity for LLPS than the RGG1 domain. Our results support previous suggestions that LLPS of FUS is driven by multiple transient nonspecific hydrogen bonding and π-sp2 interactions.
Collapse
Affiliation(s)
- Laura Esteban-Hofer
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | | | - Maxim Yulikov
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
| | | | - Gunnar Jeschke
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland.
| |
Collapse
|
23
|
Jeschke G. Protein ensemble modeling and analysis with MMMx. Protein Sci 2024; 33:e4906. [PMID: 38358120 PMCID: PMC10868441 DOI: 10.1002/pro.4906] [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: 08/04/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 02/16/2024]
Abstract
Proteins, especially of eukaryotes, often have disordered domains and may contain multiple folded domains whose relative spatial arrangement is distributed. The MMMx ensemble modeling and analysis toolbox (https://github.com/gjeschke/MMMx) can support the design of experiments to characterize the distributed structure of such proteins, starting from AlphaFold2 predictions or folded domain structures. Weak order can be analyzed with reference to a random coil model or to peptide chains that match the residue-specific Ramachandran angle distribution of the loop regions and are otherwise unrestrained. The deviation of the mean square end-to-end distance of chain sections from their average over sections of the same sequence length reveals localized compaction or expansion of the chain. The shape sampled by disordered chains is visualized by superposition in the principal axes frame of their inertia tensor. Ensembles of different sizes and with weighted conformers can be compared based on a similarity parameter that abstracts from the ensemble width.
Collapse
Affiliation(s)
- Gunnar Jeschke
- Department of Chemistry and Applied BiosciencesETH ZürichZürichSwitzerland
| |
Collapse
|
24
|
Kopp K, Westhofen L, Hett T, Felix Schwering-Sohnrey M, Mayländer M, Richert S, Schiemann O. Synthesis and dark state EPR properties of PDI-trityl dyads and triads. Chemistry 2024; 30:e202303635. [PMID: 38055217 DOI: 10.1002/chem.202303635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/07/2023]
Abstract
Covalently-linked chromophore-radical systems with their unique optical and magnetic properties are useful for applications in, e. g., quantum information science. To expand the catalog of molecular systems, we synthesized and characterized six novel chromophore-radical and radical-chromophore-radical systems employing derivatives of perylene diimide (PDI) as the chromophore and trityl as the radical. The EPR properties of these compounds were evaluated in solution at cryogenic and room temperatures. In addition, the electron spin-spin coupling in the two bistrityl systems was investigated using DQC measurements. The presented results serve as a basis for further spectroscopic investigations under photoexcitation of the PDI core.
Collapse
Affiliation(s)
- Kevin Kopp
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Lars Westhofen
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Tobias Hett
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | | | - Maximilian Mayländer
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Sabine Richert
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| |
Collapse
|
25
|
Sicoli G, Sieme D, Overkamp K, Khalil M, Backer R, Griesinger C, Willbold D, Rezaei-Ghaleh N. Large dynamics of a phase separating arginine-glycine-rich domain revealed via nuclear and electron spins. Nat Commun 2024; 15:1610. [PMID: 38383529 PMCID: PMC10881997 DOI: 10.1038/s41467-024-45788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Liquid-liquid phase separation is the key process underlying formation of membrane-less compartments in cells. A highly dynamic cellular body with rapid component exchange is Cajal body (CB), which supports the extensive compositional dynamics of the RNA splicing machinery, spliceosome. Here, we select an arginine-glycine (RG)-rich segment of coilin, the major component of CB, establish its RNA-induced phase separation, and through combined use of nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) probes, interrogate its dynamics within the crowded interior of formed droplets. Taking advantage of glycine-based singlet-states, we show that glycines retain a large level of sub-nanoseconds dynamics inside the coilin droplets. Furthermore, the continuous-wave (CW) and electron-electron dipolar (PELDOR) and electron-nucleus hyperfine coupling EPR data (HYSCORE) support the RNA-induced formation of dynamic coilin droplets with high coilin peptide concentrations. The combined NMR and EPR data reveal the high dynamics of the RG-rich coilin within droplets and suggest its potential role in the large dynamics of CBs.
Collapse
Affiliation(s)
- Giuseppe Sicoli
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Daniel Sieme
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Kerstin Overkamp
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Mahdi Khalil
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Robin Backer
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Dieter Willbold
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany
| | - Nasrollah Rezaei-Ghaleh
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany.
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany.
| |
Collapse
|
26
|
Ackermann K, Heubach CA, Schiemann O, Bode BE. Pulse Dipolar Electron Paramagnetic Resonance Spectroscopy Distance Measurements at Low Nanomolar Concentrations: The Cu II-Trityl Case. J Phys Chem Lett 2024; 15:1455-1461. [PMID: 38294197 PMCID: PMC10860127 DOI: 10.1021/acs.jpclett.3c03311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Recent sensitivity enhancements in pulse dipolar electron paramagnetic resonance spectroscopy (PDS) have afforded distance measurements at submicromolar spin concentrations. This development opens the path for new science as more biomolecular systems can be investigated at their respective physiological concentrations. Here, we demonstrate that the combination of orthogonal spin-labeling using CuII ions and trityl yields a >3-fold increase in sensitivity compared to that of the established CuII-nitroxide labeling strategy. Application of the recently developed variable-time relaxation-induced dipolar modulation enhancement (RIDME) method yields a further ∼2.5-fold increase compared to the commonly used constant-time RIDME. This overall increase in sensitivity of almost an order of magnitude makes distance measurements in the range of 3 nm with protein concentrations as low as 10 nM feasible, >2 times lower than the previously reported concentration. We expect that experiments at single-digit nanomolar concentrations are imminent, which have the potential to transform biological PDS applications.
Collapse
Affiliation(s)
- Katrin Ackermann
- EaStCHEM
School of Chemistry and Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St Andrews KY16 9ST, U.K.
| | - Caspar A. Heubach
- Clausius-Institute
of Physical and Theoretical Chemistry, University
of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Clausius-Institute
of Physical and Theoretical Chemistry, University
of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Bela E. Bode
- EaStCHEM
School of Chemistry and Biomedical Sciences Research Complex, Centre
of Magnetic Resonance, University of St
Andrews, North Haugh, St Andrews KY16 9ST, U.K.
| |
Collapse
|
27
|
Syryamina VN, Matveeva AG, Bowman MK. Confidence limits in pulse dipolar EPR spectroscopy: estimates for individual measurements. Phys Chem Chem Phys 2024; 26:5537-5547. [PMID: 38284165 DOI: 10.1039/d3cp05797f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
The distribution of inter-label distances obtained by electron paramagnetic resonance (EPR) pulse dipolar spectroscopies (PDS), such as DEER aka PELDOR, gives a valuable characterization of structure on the nanometer scale. The impact of random experimental noise on such experiments is examined for three independent methods for analysing PDS data: the model-free method with Tikhonov regularization, model-free with Mellin-transformation, and a model-based method. All three methods show negative bias for the mean distance and positive bias for the distribution width. Both biases grow with increasing noise levels. The estimated confidence bands and the uncertainties obtained from a single experimental measurement by the standard bootstrapping or χ2-surface scanning approaches are inconsistent and can exclude the true distance distribution. Yet, both approaches can provide quite valuable support for hypothesis testing in PDS studies.
Collapse
Affiliation(s)
- Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk, 630090, Russian Federation.
| | - Anna G Matveeva
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk, 630090, Russian Federation.
| | - Michael K Bowman
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL 35487, USA
| |
Collapse
|
28
|
Lasorsa A, Merzougui H, Cantrelle FX, Sicoli G, Dupré E, Hanoulle X, Belle V, Smet-Nocca C, Landrieu I. Magnetic resonance investigation of conformational responses of tau protein to specific phosphorylation. Biophys Chem 2024; 305:107155. [PMID: 38100856 DOI: 10.1016/j.bpc.2023.107155] [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: 07/23/2023] [Revised: 09/27/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
Intrinsically disordered proteins (IDPs) are known to adopt many rapidly interconverting structures, making it difficult to pinpoint the specific conformational states that are relevant for their function. Tau is an important IDP, and its conformation is known to be affected by post-translational modifications (PTMs), such as phosphorylation. To investigate the effect of specific phosphorylation on full-length Tau's dynamic global conformation, we employed a combination of nuclear magnetic resonance-based paramagnetic relaxation interference methods and electron paramagnetic resonance spectroscopy. By reproducing the AT8 epitope, comprising exclusive phosphorylation at residues S202 and T205, we were able to identify conformations specific to phosphorylated Tau, which exhibited a tendency towards less compact states. These mechanistic details are of significance to understand the path leading from soluble Tau to the ordered structure of Tau fibers. This approach proved to be successful for studying the conformational changes of (phosphorylated) full-length Tau and can potentially be extended to the study of other IDPs that undergo various PTMs.
Collapse
Affiliation(s)
- Alessia Lasorsa
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.; CNRS EMR9002 - BSI - Integrative Structural Biology, F-59000 Lille, France.; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Hamida Merzougui
- CNRS EMR9002 - BSI - Integrative Structural Biology, F-59000 Lille, France.; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - François-Xavier Cantrelle
- CNRS EMR9002 - BSI - Integrative Structural Biology, F-59000 Lille, France.; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Giuseppe Sicoli
- Univ. Lille, CNRS UMR 8516 - LASIRE - Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, F-59000 Lille, France
| | - Elian Dupré
- CNRS EMR9002 - BSI - Integrative Structural Biology, F-59000 Lille, France.; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Xavier Hanoulle
- CNRS EMR9002 - BSI - Integrative Structural Biology, F-59000 Lille, France.; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP - Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - Caroline Smet-Nocca
- CNRS EMR9002 - BSI - Integrative Structural Biology, F-59000 Lille, France.; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Isabelle Landrieu
- CNRS EMR9002 - BSI - Integrative Structural Biology, F-59000 Lille, France.; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France.
| |
Collapse
|
29
|
Gopinath A, Rath T, Morgner N, Joseph B. Lateral gating mechanism and plasticity of the β-barrel assembly machinery complex in micelles and Escherichia coli. PNAS NEXUS 2024; 3:pgae019. [PMID: 38312222 PMCID: PMC10833450 DOI: 10.1093/pnasnexus/pgae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024]
Abstract
The β-barrel assembly machinery (BAM) mediates the folding and insertion of the majority of outer membrane proteins (OMPs) in gram-negative bacteria. BAM is a penta-heterooligomeric complex consisting of the central β-barrel BamA and four interacting lipoproteins BamB, C, D, and E. The conformational switching of BamA between inward-open (IO) and lateral-open (LO) conformations is required for substrate recognition and folding. However, the mechanism for the lateral gating or how the structural details observed in vitro correspond with the cellular environment remains elusive. In this study, we addressed these questions by characterizing the conformational heterogeneity of BamAB, BamACDE, and BamABCDE complexes in detergent micelles and/or Escherichia coli using pulsed dipolar electron spin resonance spectroscopy (PDS). We show that the binding of BamB does not induce any visible changes in BamA, and the BamAB complex exists in the IO conformation. The BamCDE complex induces an IO to LO transition through a coordinated movement along the BamA barrel. However, the extracellular loop 6 (L6) is unaffected by the presence of lipoproteins and exhibits large segmental dynamics extending to the exit pore. PDS experiments with the BamABCDE complex in intact E. coli confirmed the dynamic behavior of both the lateral gate and the L6 in the native environment. Our results demonstrate that the BamCDE complex plays a key role in the function by regulating lateral gating in BamA.
Collapse
Affiliation(s)
- Aathira Gopinath
- Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany
- Institute of Biophysics, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Tobias Rath
- Institute of Physical and Theoretical Chemistry, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe Universität Frankfurt, Frankfurt, 60438, Germany
| | - Benesh Joseph
- Department of Physics, Freie Universität Berlin, Berlin, 14195, Germany
| |
Collapse
|
30
|
Bertran A, De Zotti M, Timmel CR, Di Valentin M, Bowen AM. Determining and controlling conformational information from orientationally selective light-induced triplet-triplet electron resonance spectroscopy for a set of bis-porphyrin rulers. Phys Chem Chem Phys 2024; 26:2589-2602. [PMID: 38170870 PMCID: PMC10793979 DOI: 10.1039/d3cp03454b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/31/2023] [Indexed: 01/05/2024]
Abstract
We recently reported a new technique, light-induced triplet-triplet electron resonance (LITTER) spectroscopy, which allows quantification of the dipolar interaction between the photogenerated triplet states of two chromophores. Here we carry out a systematic LITTER study, considering orientation selection by the detection pulses, of a series of bis-porphyrin model peptides with different porphyrin-porphyrin distances and relative orientations. Orientation-dependent analysis of the dipolar datasets yields conformational information of the molecules in frozen solution which is in good agreement with density functional theory predictions. Additionally, a fast partial orientational-averaging treatment produces distance distributions with minimized orientational artefacts. Finally, by direct comparison of LITTER data to double electron-electron resonance (DEER) measured on a system with Cu(II) coordinated into the porphyrins, we demonstrate the advantages of the LITTER technique over the standard DEER methodology. This is due to the remarkable spectroscopic properties of the photogenerated porphyrin triplet state. This work sets the basis for the use of LITTER in structural investigations of unmodified complex biological macromolecules, which could be combined with Förster resonance energy transfer and microscopy inside cells.
Collapse
Affiliation(s)
- Arnau Bertran
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca "Centro Studi di Economia e Tecnica dell'energia Giorgio Levi Cases", 35131 Padova, Italy.
| | - Christiane R Timmel
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK.
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca "Centro Studi di Economia e Tecnica dell'energia Giorgio Levi Cases", 35131 Padova, Italy.
| | - Alice M Bowen
- The National Research Facility for Electron Paramagnetic Resonance, Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
| |
Collapse
|
31
|
Oranges M, Giannoulis A, Vanyushkina A, Sirkis YF, Dalaloyan A, Unger T, Su XC, Sharon M, Goldfarb D. C-terminal domain dimerization in yeast Hsp90 is moderately modulated by the other domains. Biophys J 2024; 123:172-183. [PMID: 38071428 PMCID: PMC10808039 DOI: 10.1016/j.bpj.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/26/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Heat shock protein 90 (Hsp90) serves as a crucial regulator of cellular proteostasis by stabilizing and regulating the activity of numerous substrates, many of which are oncogenic proteins. Therefore, Hsp90 is a drug target for cancer therapy. Hsp90 comprises three structural domains, a highly conserved amino-terminal domain (NTD), a middle domain (MD), and a carboxyl-terminal domain (CTD). The CTD is responsible for protein dimerization, is crucial for Hsp90's activity, and has therefore been targeted for inhibiting Hsp90. Here we addressed the question of whether the CTD dimerization in Hsp90, in the absence of bound nucleotides, is modulated by allosteric effects from the other domains. We studied full length (FL) and isolated CTD (isoC) yeast Hsp90 spin-labeled with a Gd(III) tag by double electron-electron resonance measurements to track structural differences and to determine the apparent dissociation constant (Kd). We found the distance distributions for both the FL and isoC to be similar, indicating that the removal of the NTD and MD does not significantly affect the structure of the CTD dimer. The low-temperature double electron-electron resonance-derived Kd values, as well as those obtained at room temperature using microscale thermophoresis and native mass spectrometry, collectively suggested the presence of some allosteric effects from the NTDs and MDs on the CTD dimerization stability in the apo state. This was evidenced by a moderate increase in the Kd for the isoC compared with the FL mutants. Our results reveal a fine regulation of the CTD dimerization by allosteric modulation, which may have implications for drug targeting strategies in cancer therapy.
Collapse
Affiliation(s)
- Maria Oranges
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Vanyushkina
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Fridmann Sirkis
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Arina Dalaloyan
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin, China
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
32
|
Abdullin D, Rauh Corro P, Hett T, Schiemann O. PDSFit: PDS data analysis in the presence of orientation selectivity, g-anisotropy, and exchange coupling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:37-60. [PMID: 38130168 DOI: 10.1002/mrc.5415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS), encompassing techniques such as pulsed electron-electron double resonance (PELDOR or DEER) and relaxation-induced dipolar modulation enhancement (RIDME), is a valuable method in structural biology and materials science for obtaining nanometer-scale distance distributions between electron spin centers. An important aspect of PDS is the extraction of distance distributions from the measured time traces. Most software used for this PDS data analysis relies on simplifying assumptions, such as assuming isotropic g-factors of ~2 and neglecting orientation selectivity and exchange coupling. Here, the program PDSFit is introduced, which enables the analysis of PELDOR and RIDME time traces with or without orientation selectivity. It can be applied to spin systems consisting of up to two spin centers with anisotropic g-factors and to spin systems with exchange coupling. It employs a model-based fitting of the time traces using parametrized distance and angular distributions, and parametrized PDS background functions. The fitting procedure is followed by an error analysis for the optimized parameters of the distributions and backgrounds. Using five different experimental data sets published previously, the performance of PDSFit is tested and found to provide reliable solutions.
Collapse
Affiliation(s)
- Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Pablo Rauh Corro
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Tobias Hett
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| |
Collapse
|
33
|
Heubach CA, Hasanbasri Z, Abdullin D, Reuter A, Korzekwa B, Saxena S, Schiemann O. Differentiating between Label and Protein Conformers in Pulsed Dipolar EPR Spectroscopy with the dHis-Cu 2+ (NTA) Motif. Chemistry 2023; 29:e202302541. [PMID: 37755452 DOI: 10.1002/chem.202302541] [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: 08/04/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 09/28/2023]
Abstract
Pulsed dipolar EPR spectroscopy (PDS) in combination with site-directed spin labeling is a powerful tool in structural biology. However, the commonly used spin labels are conjugated to biomolecules via rather long and flexible linkers, which hampers the translation of distance distributions into biomolecular conformations. In contrast, the spin label copper(II)-nitrilotriacetic acid [Cu2+ (NTA)] bound to two histidines (dHis) is rigid and yields narrow distance distributions, which can be more easily translated into biomolecular conformations. Here, we use this label on the 71 kDa Yersinia outer protein O (YopO) to decipher whether a previously experimentally observed bimodal distance distribution is due to two conformations of the biomolecule or of the flexible spin labels. Two different PDS experiments, that is, pulsed electron-electron double resonance (PELDOR aka DEER) and relaxation-induced dipolar modulation enhancement (RIDME), yield unimodal distance distribution with the dHis-Cu2+ (NTA) motif; this result suggests that the α-helical backbone of YopO adopts a single conformation in frozen solution. In addition, we show that the Cu2+ (NTA) label preferentially binds to the target double histidine (dHis) sites even in the presence of 22 competing native histidine residues. Our results therefore suggest that the generation of a His-null background is not required for this spin labeling methodology. Together these results highlight the value of the dHis-Cu2+ (NTA) motif in PDS experiments.
Collapse
Affiliation(s)
- Caspar A Heubach
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Zikri Hasanbasri
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Arne Reuter
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| | - Benedict Korzekwa
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
- Leibniz-Center for Diabetes Research, University of Düsseldorf, Auf'm Hennekamp 65, 40225, Düsseldorf, Germany
| | - Sunil Saxena
- Department of Chemistry, Chevron Science Center, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany
| |
Collapse
|
34
|
Shi J, Xu W, Yu H, Wang X, Jin F, Zhang Q, Zhang H, Peng Q, Abdurahman A, Wang M. A Highly Luminescent Metallo-Supramolecular Radical Cage. J Am Chem Soc 2023; 145:24081-24088. [PMID: 37796113 DOI: 10.1021/jacs.3c07477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Luminescent metal-radicals have recently received increasing attention due to their unique properties and promising applications in materials science. However, the luminescence of metal-radicals tends to be quenched after formation of metallo-complexes. It is challenging to construct metal-radicals with highly luminescent properties. Herein, we report a highly luminescent metallo-supramolecular radical cage (LMRC) constructed by the assembly of a tritopic terpyridinyl ligand RL with tris(2,4,6-trichlorophenyl)methyl (TTM) radical and Zn2+. Electrospray ionization-mass spectrometry (ESI-MS), traveling-wave ion mobility-mass spectrometry (TWIM-MS), X-ray crystallography, electron paramagnetic resonance (EPR) spectroscopy, and superconducting quantum interference device (SQUID) confirm the formation of a prism-like supramolecular radical cage. LMRC exhibits a remarkable photoluminescence quantum yield (PLQY) of 65%, which is 5 times that of RL; meanwhile, LMRC also shows high photostability. Notably, significant magnetoluminescence can be observed for the high-concentration LMRC (15 wt % doped in PMMA film); however, the magnetoluminescence of 0.1 wt % doped LMRC film vanishes, revealing negligible spin-spin interactions between two radical centers in LMRC.
Collapse
Affiliation(s)
- Junjuan Shi
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Wei Xu
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Hao Yu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Xing Wang
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM) & School of Flexible Electronics (Future Technologies), Nanjing Tech University (Nanjing Tech), Nanjing, Jiangsu 211816, China
| | - Feng Jin
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qingming Zhang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Houyu Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Qiming Peng
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM) & School of Flexible Electronics (Future Technologies), Nanjing Tech University (Nanjing Tech), Nanjing, Jiangsu 211816, China
| | - Alim Abdurahman
- State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Changchun, Jilin 130012, China
| | - Ming Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| |
Collapse
|
35
|
Syryamina VN, Wu X, Boulos S, Nyström L, Yulikov M. Pulse EPR spectroscopy and molecular modeling reveal the origins of the local heterogeneity of dietary fibers. Carbohydr Polym 2023; 319:121167. [PMID: 37567691 DOI: 10.1016/j.carbpol.2023.121167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 08/13/2023]
Abstract
Optimizing human diet by including dietary fibers would be more efficient when the fibers' chain interactions with other molecules are understood in depth. Thereby, it is important to develop methods for characterizing the fiber chain to be able to monitor its structural alterations upon intermolecular interactions. Here, we demonstrate the utility of the electron paramagnetic resonance (EPR) spectroscopy, complemented by simulations in probing the atomistic details of the chain conformations for spin-labeled fibers. Barley β-glucan, a native polysaccharide with linear chain, was utilized as a test fiber system to demonstrate the technique's capabilities. Pulse dipolar EPR data show good agreement with results of the fiber chain modeling, revealing sinuous chain conformations and providing polymer shape descriptors: the gyration tensor, spin-spin distance distribution function, and information about proton density near the spin probe. Results from EPR measurements point to the fiber aggregation in aqueous solution, which agrees with the results of the dynamic light scattering. We propose that the combination of pulse EPR measurements with modeling can be a perfect experimental tool for in-depth structural investigation of dietary fibers and their interaction under such conditions, and that the presented methodology can be extended to other weakly ordered or disordered macromolecules.
Collapse
Affiliation(s)
- Victoria N Syryamina
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland; Voevodsky Institute of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation.
| | - Xiaowen Wu
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland.
| | - Samy Boulos
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland.
| | - Laura Nyström
- Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland.
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg, 2, 8093 Zürich, Switzerland.
| |
Collapse
|
36
|
Bobylev EO, Passerini L, de Zwart FJ, Poole DA, Mathew S, Huber M, de Bruin B, Reek JNH. Pd 12M nL 24 (for n = 6, 8, 12) nanospheres by post-assembly modification of Pd 12L 24 spheres. Chem Sci 2023; 14:11840-11849. [PMID: 37920352 PMCID: PMC10619623 DOI: 10.1039/d3sc03745b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/15/2023] [Indexed: 11/04/2023] Open
Abstract
In this contribution, we describe a post-assembly modification approach to selectively coordinate transition metals in Pd12L24 cuboctahedra. The herein reported approach involves the preparation of Pd12L24 nanospheres with protonated nitrogen donor ligands that are covalently linked at the interior. The so obtained Pd12(LH+)24 nanospheres are shown to be suitable for coordinative post-modification after deprotection by deprotonation. Selective formation of tetra-coordinated MB in Pd12MB6L24, tri-coordinated MB in Pd12MB8L24 nanospheres and two-coordinated MB in Pd12MB12L24 nanospheres is achieved as a result of different nitrogen donor ligands. A combination of pulsed EPR spectroscopy (DEER) to measure Cu-Cu distances in the different spheres, NMR studies and computational investigations, support the presence of the complexes at precise locations of the Pd12MB6L24 nanosphere. The general post-assembly modification methodology can be extended using other transition metal precursors or supramolecular systems and can guide precise formation and investigation of novel transition metal-complex containing nanospheres with well-defined composition.
Collapse
Affiliation(s)
- Eduard O Bobylev
- van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Leonardo Passerini
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Felix J de Zwart
- van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - David A Poole
- van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Simon Mathew
- van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Bas de Bruin
- van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Joost N H Reek
- van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| |
Collapse
|
37
|
Denysenkov V, Prisner TF, Neugebauer P, Stoll S, Marko A. Macroscopic sample shape effect on pulse electron double resonance (PELDOR) signal. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 356:107564. [PMID: 37852111 DOI: 10.1016/j.jmr.2023.107564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023]
Abstract
Pulse electron double resonance (PELDOR), also called double electron-electron resonance (DEER), is a technique capable of measuring the strength of electron spin dipolar interactions, revealing spin-spin distance distributions in ordered and disordered solid materials. Previous work has shown that PELDOR signals acquire an out-of-phase component under conditions of high electron spin polarization, such as at low temperatures and high fields. In this paper, we show theoretically and experimentally that the size and sign of this effect depends on the macroscopic shape of the sample and its orientation in the external magnetic field. This effect is caused by dipolar interactions between distant spins and provides new insights into the fundamental physics of PELDOR.
Collapse
Affiliation(s)
- Vasyl Denysenkov
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60437, Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60437, Frankfurt am Main, Germany
| | - Petr Neugebauer
- Central European Institute of Technology and Brno University of Technology, Purkynova 123, Brno, 61200, Czech Republic
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
| | - Andriy Marko
- Central European Institute of Technology and Brno University of Technology, Purkynova 123, Brno, 61200, Czech Republic.
| |
Collapse
|
38
|
McQuarrie S, Athukoralage JS, McMahon SA, Graham S, Ackermann K, Bode BE, White MF, Gloster TM. Activation of Csm6 ribonuclease by cyclic nucleotide binding: in an emergency, twist to open. Nucleic Acids Res 2023; 51:10590-10605. [PMID: 37747760 DOI: 10.1093/nar/gkad739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023] Open
Abstract
Type III CRISPR systems synthesize cyclic oligoadenylate (cOA) second messengers as part of a multi-faceted immune response against invading mobile genetic elements (MGEs). cOA activates non-specific CRISPR ancillary defence nucleases to create a hostile environment for MGE replication. Csm6 ribonucleases bind cOA using a CARF (CRISPR-associated Rossmann Fold) domain, resulting in activation of a fused HEPN (Higher Eukaryotes and Prokaryotes Nucleotide binding) ribonuclease domain. Csm6 enzymes are widely used in a new generation of diagnostic assays for the detection of specific nucleic acid species. However, the activation mechanism is not fully understood. Here we characterised the cyclic hexa-adenylate (cA6) activated Csm6' ribonuclease from the industrially important bacterium Streptococcus thermophilus. Crystal structures of Csm6' in the inactive and cA6 bound active states illuminate the conformational changes which trigger mRNA destruction. Upon binding of cA6, there is a close to 60° rotation between the CARF and HEPN domains, which causes the 'jaws' of the HEPN domain to open and reposition active site residues. Key to this transition is the 6H domain, a right-handed solenoid domain connecting the CARF and HEPN domains, which transmits the conformational changes for activation.
Collapse
Affiliation(s)
- Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Januka S Athukoralage
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| |
Collapse
|
39
|
Bertran A, Morbiato L, Sawyer J, Dalla Torre C, Heyes DJ, Hay S, Timmel CR, Di Valentin M, De Zotti M, Bowen AM. Direct Comparison between Förster Resonance Energy Transfer and Light-Induced Triplet-Triplet Electron Resonance Spectroscopy. J Am Chem Soc 2023; 145:22859-22865. [PMID: 37839071 PMCID: PMC10603778 DOI: 10.1021/jacs.3c04685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 10/17/2023]
Abstract
To carry out reliable and comprehensive structural investigations, the exploitation of different complementary techniques is required. Here, we report that dual triplet-spin/fluorescent labels enable the first parallel distance measurements by electron spin resonance (ESR) and Förster resonance energy transfer (FRET) on exactly the same molecules with orthogonal chromophores, allowing for direct comparison. An improved light-induced triplet-triplet electron resonance method with 2-color excitation is used, improving the signal-to-noise ratio of the data and yielding a distance distribution that provides greater insight than the single distance resulting from FRET.
Collapse
Affiliation(s)
- Arnau Bertran
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Laura Morbiato
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Jack Sawyer
- The
National Research Facility for Electron Paramagnetic Resonance, Department
of Chemistry, Manchester Institute of Biotechnology and Photon Science
Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Chiara Dalla Torre
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Derren J. Heyes
- The
National Research Facility for Electron Paramagnetic Resonance, Department
of Chemistry, Manchester Institute of Biotechnology and Photon Science
Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam Hay
- The
National Research Facility for Electron Paramagnetic Resonance, Department
of Chemistry, Manchester Institute of Biotechnology and Photon Science
Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Christiane R. Timmel
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Marilena Di Valentin
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
- Centro
Interdipartimentale di Ricerca “Centro Studi di Economia e
Tecnica dell’energia Giorgio Levi Cases”, 35131 Padova, Italy
| | - Marta De Zotti
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
- Centro
Interdipartimentale di Ricerca “Centro Studi di Economia e
Tecnica dell’energia Giorgio Levi Cases”, 35131 Padova, Italy
| | - Alice M. Bowen
- The
National Research Facility for Electron Paramagnetic Resonance, Department
of Chemistry, Manchester Institute of Biotechnology and Photon Science
Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| |
Collapse
|
40
|
Yeh PS, Li CC, Lu YS, Chiang YW. Structural Insights into the Binding and Degradation Mechanisms of Protoporphyrin IX by the Translocator Protein TSPO. JACS AU 2023; 3:2918-2929. [PMID: 37885593 PMCID: PMC10598825 DOI: 10.1021/jacsau.3c00514] [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] [Received: 08/30/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
The 18 kDa translocator protein (TSPO) has gained considerable attention as a clinical biomarker for neuroinflammation and a potential therapeutic target. However, the mechanisms by which TSPO associates with ligands, particularly the endogenous porphyrin ligand protoporphyrin IX (PpIX), remain poorly understood. In this study, we employed mutagenesis- and spectroscopy-based functional assays to investigate TSPO-mediated photo-oxidative degradation of PpIX and identify key residues involved in the reaction. We provide structural evidence using electron spin resonance, which sheds light on the highly conserved intracellular loop (LP1) connecting transmembrane 1 (TM1) and TM2. Our findings show that LP1 does not act as a lid to regulate ligand binding; instead, it interacts strongly with the TM3-TM4 linker (LP3) to stabilize the local structure of LP3. This LP1-LP3 interaction is crucial for maintaining the binding pocket structure, which is essential for proper ligand binding. Our results also demonstrate that PpIX accesses the pocket through the lipid bilayer without requiring conformational changes in TSPO. This study provides an improved understanding of TSPO-mediated PpIX degradation, highlighting potential therapeutic strategies to regulate the reaction.
Collapse
Affiliation(s)
- Pei-Shan Yeh
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Chieh-Chin Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yi-Shan Lu
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan
| |
Collapse
|
41
|
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.
Collapse
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
| | | |
Collapse
|
42
|
Dorn G, Gmeiner C, de Vries T, Dedic E, Novakovic M, Damberger FF, Maris C, Finol E, Sarnowski CP, Kohlbrecher J, Welsh TJ, Bolisetty S, Mezzenga R, Aebersold R, Leitner A, Yulikov M, Jeschke G, Allain FHT. Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility. Nat Commun 2023; 14:6429. [PMID: 37833274 PMCID: PMC10576089 DOI: 10.1038/s41467-023-42012-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.
Collapse
Affiliation(s)
- Georg Dorn
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christoph Gmeiner
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tebbe de Vries
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Mihajlo Novakovic
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Fred F Damberger
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Christophe Maris
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Esteban Finol
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, Villigen, Switzerland
| | - Timothy J Welsh
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Sreenath Bolisetty
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Raffaele Mezzenga
- Laboratory of Food & Soft Materials, Institute of Food, Nutrition and Health, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland.
| | - Frédéric H-T Allain
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
43
|
Mandato A, Hasanbasri Z, Saxena S. Double Quantum Coherence ESR at Q-Band Enhances the Sensitivity of Distance Measurements at Submicromolar Concentrations. J Phys Chem Lett 2023; 14:8909-8915. [PMID: 37768093 PMCID: PMC10577775 DOI: 10.1021/acs.jpclett.3c02372] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Recently, there have been remarkable improvements in pulsed ESR sensitivity, paving the way for broader applicability of ESR in the measurement of biological distance constraints, for instance, at physiological concentrations and in more complex systems. Nevertheless, submicromolar distance measurements with the commonly used nitroxide spin label take multiple days. Therefore, there remains a need for rapid and reliable methods of measuring distances between spins at nanomolar concentrations. In this work, we demonstrate the power of double quantum coherence (DQC) experiments at Q-band frequencies. With the help of short and intense pulses, we showcase DQC signals on nitroxide-labeled proteins with modulation depths close to 100%. We show that the deep dipolar modulations aid in the resolution of bimodal distance distributions. Finally, we establish that distance measurements with protein concentrations as low as 25 nM are feasible. This limit is approximately 4-fold lower than previously possible. We anticipate that nanomolar concentration measurements will lead to further advancements in the use of ESR, especially in cellular contexts.
Collapse
Affiliation(s)
- Alysia Mandato
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
44
|
Uvarov MN, Kulik LV, Dzuba SA. Assembly of galvinoxyl doped in polymer-fullerene photovoltaic blends. Phys Chem Chem Phys 2023; 25:26219-26224. [PMID: 37740340 DOI: 10.1039/d3cp02513f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Galvinoxyl (Gx) is a stable free radical used as a dopant in active layers of organic solar cells. Here, the nanoscale arrangement of Gx molecules in a composite of the PCDTBT polymer and modified C60 fullerene, PCBM, was studied using a two-pulse electron spin echo (ESE) technique. The results show that the Gx molecules assemble into clusters, which can be described by the model of 8 molecules on the surface of a sphere with a radius of 2.0 nm. Such a structure can arise due to the octahedral packing of 6 PCBM molecules surrounded by 8 Gx molecules. ESE decays also indicate that these clusters repel each other, forming a quasi-regular nanostructure in the matrix. The Gx concentration of 2 wt% at which clusters appear correlates with the literature data on the Gx-induced enhancement of photocurrent, which provides structural insight into the possible molecular mechanism of this enhancement.
Collapse
Affiliation(s)
- Mikhail N Uvarov
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
| | - Leonid V Kulik
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
| | - Sergei A Dzuba
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russian Federation
| |
Collapse
|
45
|
Stehle J, Fleming JR, Bauer PM, Mayans O, Drescher M. Titin UN2A Acts as a Stable, Non-Polymorphic Scaffold in its Binding to CARP. Chembiochem 2023; 24:e202300408. [PMID: 37503755 DOI: 10.1002/cbic.202300408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
The N2A segment of titin functions as a pivotal hub for signal transduction and interacts with various proteins involved in structural support, chaperone activities, and transcriptional regulation. Notably, the "unique N2A" (UN2A) subdomain has been shown to interact with the stress-regulated cardiac ankyrin repeat protein (CARP), which contributes to the regulation of sarcomeric stiffness. Previously, the UN2A domain's three-dimensional structure was modelled based on its secondary structure content identified by NMR spectroscopy, considering the domain in isolation. In this study, we report experimental long-range distance distributions by electron paramagnetic resonance (EPR) spectroscopy between the three helixes within the UN2A domain linked to the immunoglobulin domain I81 in the presence and absence of CARP. The data confirm the central three-helix bundle fold of UN2A and show that this adopts a compact and stable conformation in absence of CARP. After binding to CARP, no significant conformational change was observed, suggesting that the UN2A domain retains its structure upon binding to CARP thereby, mediating the interaction approximately as a rigid-body.
Collapse
Affiliation(s)
- Juliane Stehle
- Department of Chemistry and Konstanz Research School of Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Jennifer R Fleming
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Piera-Maria Bauer
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Olga Mayans
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School of Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| |
Collapse
|
46
|
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.
Collapse
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
| |
Collapse
|
47
|
Asanbaeva NB, Novopashina DS, Rogozhnikova OY, Tormyshev VM, Kehl A, Sukhanov AA, Shernyukov AV, Genaev AM, Lomzov AA, Bennati M, Meyer A, Bagryanskaya EG. 19F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes. Phys Chem Chem Phys 2023; 25:23454-23466. [PMID: 37609874 DOI: 10.1039/d3cp02969g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The combination of fluorine labeling and pulsed electron-nuclear double resonance (ENDOR) is emerging as a powerful technique for obtaining structural information about proteins and nucleic acids. In this work, we explored the capability of Mims 19F ENDOR experiments on reporting intermolecular distances in trityl- and 19F-labeled DNA duplexes at three electron paramagnetic resonance (EPR) frequencies (34, 94, and 263 GHz). For spin labeling, we used the hydrophobic Finland trityl radical and hydrophilic OX063 trityl radical. Fluorine labels were introduced into two positions of a DNA oligonucleotide. The results indicated that hyperfine splittings visible in the ENDOR spectra are consistent with the most populated interspin distances between 19F and the trityl radical predicted from molecular dynamic (MD) simulations. Moreover, for some cases, ENDOR spectral simulations based on MD results were able to reproduce the conformational distribution reflected in the experimental ENDOR line broadening. Additionally, MD simulations provided more detailed information about the melting of terminal base pairs of the oligonucleotides and about the configuration of the trityls relative to a DNA end.
Collapse
Affiliation(s)
- N B Asanbaeva
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia
| | - O Yu Rogozhnikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - V M Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - A Kehl
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - A A Sukhanov
- Zavoisky Physical-Technical Institute, FRC Kazan Scientific Center of RAS, 10/7 Sibirsky Tract, Kazan 420029, Russia
| | - A V Shernyukov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - A M Genaev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia
| | - M Bennati
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
- Institute of Physical Chemistry, Department of Chemistry, Georg August University of Göttingen, Tammannstr.6, Göttingen, Germany
| | - A Meyer
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
- Institute of Physical Chemistry, Department of Chemistry, Georg August University of Göttingen, Tammannstr.6, Göttingen, Germany
| | - E G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Pr. Ak. Lavrentjeva, Novosibirsk 630090, Russia.
| |
Collapse
|
48
|
Rudolph M, Tampé R, Joseph B. Time-Resolved Mn 2+ -NO and NO-NO Distance Measurements Reveal That Catalytic Asymmetry Regulates Alternating Access in an ABC Transporter. Angew Chem Int Ed Engl 2023; 62:e202307091. [PMID: 37459565 DOI: 10.1002/anie.202307091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
ATP-binding cassette (ABC) transporters shuttle diverse substrates across biological membranes. Transport is often achieved through a transition between an inward-facing (IF) and an outward-facing (OF) conformation of the transmembrane domains (TMDs). Asymmetric nucleotide-binding sites (NBSs) are present among several ABC subfamilies and their functional role remains elusive. Here we addressed this question using concomitant NO-NO, Mn2+ -NO, and Mn2+ -Mn2+ pulsed electron-electron double-resonance spectroscopy of TmrAB in a time-resolved manner. This type-IV ABC transporter undergoes a reversible transition in the presence of ATP with a significantly faster forward transition. The impaired degenerate NBS stably binds Mn2+ -ATP, and Mn2+ is preferentially released at the active consensus NBS. ATP hydrolysis at the consensus NBS considerably accelerates the reverse transition. Both NBSs fully open during each conformational cycle and the degenerate NBS may regulate the kinetics of this process.
Collapse
Affiliation(s)
- Michael Rudolph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Benesh Joseph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| |
Collapse
|
49
|
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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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
| |
Collapse
|
50
|
Schäfter D, Wischnat J, Tesi L, De Sousa JA, Little E, McGuire J, Mas-Torrent M, Rovira C, Veciana J, Tuna F, Crivillers N, van Slageren J. Molecular One- and Two-Qubit Systems with Very Long Coherence Times. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302114. [PMID: 37289574 DOI: 10.1002/adma.202302114] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/06/2023] [Indexed: 06/10/2023]
Abstract
General-purpose quantum computation and quantum simulation require multi-qubit architectures with precisely defined, robust interqubit interactions, coupled with local addressability. This is an unsolved challenge, primarily due to scalability issues. These issues often derive from poor control over interqubit interactions. Molecular systems are promising materials for the realization of large-scale quantum architectures, due to their high degree of positionability and the possibility to precisely tailor interqubit interactions. The simplest quantum architecture is the two-qubit system, with which quantum gate operations can be implemented. To be viable, a two-qubit system must possess long coherence times, the interqubit interaction must be well defined and the two qubits must also be addressable individually within the same quantum manipulation sequence. Here results are presented on the investigation of the spin dynamics of chlorinated triphenylmethyl organic radicals, in particular the perchlorotriphenylmethyl (PTM) radical, a mono-functionalized PTM, and a biradical PTM dimer. Extraordinarily long ensemble coherence times up to 148 µs are found at all temperatures below 100 K. Two-qubit and, importantly, individual qubit addressability in the biradical system are demonstrated. These results underline the potential of molecular materials for the development of quantum architectures.
Collapse
Affiliation(s)
- Dennis Schäfter
- Institute of Physical Chemistry and Center for Integrated Quantum Science and Technology, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Jonathan Wischnat
- Institute of Physical Chemistry and Center for Integrated Quantum Science and Technology, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Lorenzo Tesi
- Institute of Physical Chemistry and Center for Integrated Quantum Science and Technology, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - J Alejandro De Sousa
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Networking Research Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), Campus de la UAB, Bellaterra, 08193, Spain
- Laboratorio de Electroquímica, Departamento de Química, Facultad de Ciencias, Universidad de los Andes, Mérida, 5101, Venezuela
| | - Edmund Little
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Jake McGuire
- Institute of Physical Chemistry and Center for Integrated Quantum Science and Technology, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Marta Mas-Torrent
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Networking Research Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), Campus de la UAB, Bellaterra, 08193, Spain
| | - Concepció Rovira
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Networking Research Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), Campus de la UAB, Bellaterra, 08193, Spain
| | - Jaume Veciana
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Networking Research Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), Campus de la UAB, Bellaterra, 08193, Spain
| | - Floriana Tuna
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Núria Crivillers
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Networking Research Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN), Campus de la UAB, Bellaterra, 08193, Spain
| | - Joris van Slageren
- Institute of Physical Chemistry and Center for Integrated Quantum Science and Technology, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| |
Collapse
|