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Zhan J, Zeng D, Xiao X, Fang Z, Huang T, Zhao B, Zhu Q, Liu C, Jiang B, Zhou X, Li C, He L, Yang D, Liu M, Zhang X. Real-Time Observation of Conformational Changes and Translocation of Endogenous Cytochrome c within Intact Mitochondria. J Am Chem Soc 2024; 146:4455-4466. [PMID: 38335066 DOI: 10.1021/jacs.3c10216] [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: 02/12/2024]
Abstract
Cytochrome c (cyt c) is a multifunctional protein with varying conformations. However, the conformation of cyt c in its native environment, mitochondria, is still unclear. Here, we applied NMR spectroscopy to investigate the conformation and location of endogenous cyt c within intact mitochondria at natural isotopic abundance, mainly using widespread methyl groups as probes. By monitoring time-dependent chemical shift perturbations, we observed that most cyt c is located in the inner mitochondrial membrane and partially unfolded, which is distinct from its native conformation in solution. When suffering oxidative stress, cyt c underwent oxidative modifications due to increasing reactive oxygen species (ROS), weakening electrostatic interactions with the membrane, and gradually translocating into the inner membrane spaces of mitochondria. Meanwhile, the lethality of oxidatively modified cyt c to cells was reduced compared with normal cyt c. Our findings significantly improve the understanding of the molecular mechanisms underlying the regulation of ROS by cyt c in mitochondria. Moreover, it highlights the potential of NMR to monitor high-concentration molecules at a natural isotopic abundance within intact cells or organelles.
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Affiliation(s)
- Jianhua Zhan
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Danyun Zeng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiong Xiao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhongpei Fang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Tao Huang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Beibei Zhao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Qinjun Zhu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Caixiang Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
- Optics Valley Laboratory, Wuhan 430074, People's Republic of China
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
- Optics Valley Laboratory, Wuhan 430074, People's Republic of China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
- Optics Valley Laboratory, Wuhan 430074, People's Republic of China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, People's Republic of China
- Optics Valley Laboratory, Wuhan 430074, People's Republic of China
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2
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Pierro A, Tamburrini KC, Leguenno H, Gerbaud G, Etienne E, Guigliarelli B, Belle V, Zambelli B, Mileo E. In-cell investigation of the conformational landscape of the GTPase UreG by SDSL-EPR. iScience 2023; 26:107855. [PMID: 37766968 PMCID: PMC10520941 DOI: 10.1016/j.isci.2023.107855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/07/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
UreG is a cytosolic GTPase involved in the maturation network of urease, an Ni-containing bacterial enzyme. Previous investigations in vitro showed that UreG features a flexible tertiary organization, making this protein the first enzyme discovered to be intrinsically disordered. To determine whether this heterogeneous behavior is maintained in the protein natural environment, UreG structural dynamics was investigated directly in intact bacteria by in-cell EPR. This approach, based on site-directed spin labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy, enables the study of proteins in their native environment. The results show that UreG maintains heterogeneous structural landscape in-cell, existing in a conformational ensemble of two major conformers, showing either random coil-like or compact properties. These data support the physiological relevance of the intrinsically disordered nature of UreG and indicates a role of protein flexibility for this specific enzyme, possibly related to the regulation of promiscuous protein interactions for metal ion delivery.
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Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Ketty Concetta Tamburrini
- Aix Marseille Univ, CNRS, AFMB, 13009 Marseille, France
- INRAE, Aix Marseille Univ, BBF, 13009 Marseille, France
| | - Hugo Leguenno
- Aix Marseille Univ, CNRS, IMM, Microscopy Core Facility, 13009 Marseille, France
| | | | | | | | - Valérie Belle
- Aix Marseille Univ, CNRS, BIP, IMM, 13009 Marseille, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
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3
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Chen JL, Yang Y, Shi T, Su XC. Effective assessment of lanthanide ion delivery into live cells by paramagnetic NMR spectroscopy. Chem Commun (Camb) 2023; 59:10552-10555. [PMID: 37575089 DOI: 10.1039/d3cc03135g] [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: 08/15/2023]
Abstract
We report an effective assessment of lanthanide ion (Ln3+) delivery into live cells by paramagnetic NMR spectroscopy. Free Ln3+ ions are toxic to live cells resulting in a gradual leakage of target proteins to the extracellular media. The citrate-Ln3+ complex is an efficient and mild reagent over the free Ln3+ form for live cell delivery.
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Affiliation(s)
- Jia-Liang Chen
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang, Shandong, 277160, China.
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - 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.
| | - Tiesheng Shi
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang, Shandong, 277160, China.
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China.
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4
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Shenberger Y, Gevorkyan-Airapetov L, Hirsch M, Hofmann L, Ruthstein S. An in-cell spin-labelling methodology provides structural information on cytoplasmic proteins in bacteria. Chem Commun (Camb) 2023; 59:10524-10527. [PMID: 37563959 DOI: 10.1039/d3cc03047d] [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: 08/12/2023]
Abstract
EPR in-cell spin-labeling was applied to CueR in E. coli. The methodology employed a Cu(II)-NTA complexed with dHis. High resolved in-cell distance distributions were obtained revealing minor differences between in vitro and in-cell data. This methodology allows study of structural changes of any protein in-cell, independent of size or cellular system.
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Affiliation(s)
- Yulia Shenberger
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Melanie Hirsch
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Lukas Hofmann
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
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5
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Teucher M, Kucher S, Timachi MH, Wilson CB, Śmiłowicz D, Stoll R, Metzler-Nolte N, Sherwin MS, Han S, Bordignon E. Spectroscopically Orthogonal Spin Labels in Structural Biology at Physiological Temperatures. J Phys Chem B 2023; 127:6668-6674. [PMID: 37490415 PMCID: PMC10405217 DOI: 10.1021/acs.jpcb.3c04497] [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: 07/04/2023] [Revised: 07/08/2023] [Indexed: 07/27/2023]
Abstract
Electron paramagnetic resonance spectroscopy (EPR) is mostly used in structural biology in conjunction with pulsed dipolar spectroscopy (PDS) methods to monitor interspin distances in biomacromolecules at cryogenic temperatures both in vitro and in cells. In this context, spectroscopically orthogonal spin labels were shown to increase the information content that can be gained per sample. Here, we exploit the characteristic properties of gadolinium and nitroxide spin labels at physiological temperatures to study side chain dynamics via continuous wave (cw) EPR at X band, surface water dynamics via Overhauser dynamic nuclear polarization at X band and short-range distances via cw EPR at high fields. The presented approaches further increase the accessible information content on biomolecules tagged with orthogonal labels providing insights into molecular interactions and dynamic equilibria that are only revealed under physiological conditions.
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Affiliation(s)
- Markus Teucher
- Faculty
of Chemistry and Biochemistry, Ruhr University
of Bochum, Bochum 44801, Germany
| | - Svetlana Kucher
- Faculty
of Chemistry and Biochemistry, Ruhr University
of Bochum, Bochum 44801, Germany
- Department
of Physical Chemistry, University of Geneva, Genève 1211, Switzerland
| | - M. Hadi Timachi
- Faculty
of Chemistry and Biochemistry, Ruhr University
of Bochum, Bochum 44801, Germany
| | - C. Blake Wilson
- Department
of Physics, University of California, Santa
Barbara, Santa
Barbara, California 93106, United States
- Institute
for Terahertz Science and Technology, University
of California, Santa Barbara, Santa
Barbara, California 93106, United States
| | - Dariusz Śmiłowicz
- Faculty
of Chemistry and Biochemistry, Ruhr University
of Bochum, Bochum 44801, Germany
| | - Raphael Stoll
- Faculty
of Chemistry and Biochemistry, Ruhr University
of Bochum, Bochum 44801, Germany
| | - Nils Metzler-Nolte
- Faculty
of Chemistry and Biochemistry, Ruhr University
of Bochum, Bochum 44801, Germany
| | - Mark S. Sherwin
- Department
of Physics, University of California, Santa
Barbara, Santa
Barbara, California 93106, United States
- Institute
for Terahertz Science and Technology, University
of California, Santa Barbara, Santa
Barbara, California 93106, United States
| | - Songi Han
- Institute
for Terahertz Science and Technology, University
of California, Santa Barbara, Santa
Barbara, California 93106, United States
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Enrica Bordignon
- Faculty
of Chemistry and Biochemistry, Ruhr University
of Bochum, Bochum 44801, Germany
- Department
of Physical Chemistry, University of Geneva, Genève 1211, Switzerland
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6
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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7
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Pierro A, Drescher M. Dance with spins: site-directed spin labeling coupled to electron paramagnetic resonance spectroscopy directly inside cells. Chem Commun (Camb) 2023; 59:1274-1284. [PMID: 36633152 PMCID: PMC9890500 DOI: 10.1039/d2cc05907j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023]
Abstract
Depicting how biomolecules move and interact within their physiological environment is one of the hottest topics of structural biology. This Feature Article gives an overview of the most recent advances in Site-directed Spin Labeling coupled to Electron Paramagnetic Resonance spectroscopy (SDSL-EPR) to study biomolecules in living cells. The high sensitivity, the virtual absence of background, and the versatility of spin-labeling strategies make this approach one of the most promising techniques for the study of biomolecules in physiologically relevant environments. After presenting the milestones achieved in this field, we present a summary of the future goals and ambitions of this community.
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Affiliation(s)
- Annalisa Pierro
- Department of Chemistry, University of Konstanz, and Konstanz Research School Chemical Biology, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Malte Drescher
- Department of Chemistry, University of Konstanz, and Konstanz Research School Chemical Biology, Universitätsstraße 10, 78457 Konstanz, Germany.
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8
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Scherer A, Yao X, Qi M, Wiedmaier M, Godt A, Drescher M. Increasing the Modulation Depth of Gd III-Based Pulsed Dipolar EPR Spectroscopy (PDS) with Porphyrin-Gd III Laser-Induced Magnetic Dipole Spectroscopy. J Phys Chem Lett 2022; 13:10958-10964. [PMID: 36399541 PMCID: PMC9720741 DOI: 10.1021/acs.jpclett.2c02138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Distance determination with pulsed EPR has become an important technique for the structural investigation of biomacromolecules, with double electron-electron resonance spectroscopy (DEER) as the most important method. GdIII-based spin labels are one of the most frequently used spin labels for DEER owing to their stability against reduction, high magnetic moment, and absence of orientation selection. A disadvantage of GdIII-GdIII DEER is the low modulation depth due to the broad EPR spectrum of GdIII. Here, we introduce laser-induced magnetic dipole spectroscopy (LaserIMD) with a spin pair consisting of GdIII(PymiMTA) and a photoexcited porphyrin as an alternative technique. We show that the excited state of the porphyrin is not disturbed by the presence of the GdIII complex and that herewith modulation depths of almost 40% are possible. This is significantly higher than the value of 7.2% that was achieved with GdIII-GdIII DEER.
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Affiliation(s)
- Andreas Scherer
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Xuemei Yao
- Faculty
of Chemistry and Center of Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Mian Qi
- Faculty
of Chemistry and Center of Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Max Wiedmaier
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Adelheid Godt
- Faculty
of Chemistry and Center of Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Malte Drescher
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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9
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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10
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Goldfarb D. Exploring protein conformations in vitro and in cell with EPR distance measurements. Curr Opin Struct Biol 2022; 75:102398. [PMID: 35667279 DOI: 10.1016/j.sbi.2022.102398] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/20/2022] [Accepted: 04/30/2022] [Indexed: 11/18/2022]
Abstract
The electron-electron double resonance (DEER) method, which provides distance distributions between two spin labels, attached site specifically to biomolecules (proteins and nucleic acids), is currently a well-recognized biophysical tool in structural biology. The most commonly used spin labels are based on nitroxide stable radicals, conjugated to the proteins primarily via native or engineered cysteine residues. However, in recent years, new spin labels, along with different labeling chemistries, have been introduced, driven in part by the desire to study structural and dynamical properties of biomolecules in their native environment, the cell. This mini-review focuses on these new spin labels, which allow for DEER on orthogonal spin labels, and on the state of the art methods for in-cell DEER distance measurements.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 761001, Israel
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11
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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12
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Soto J, Algarra M, Peláez D. Nitrene formation is the first step of the thermal and photochemical decomposition reactions of organic azides. Phys Chem Chem Phys 2022; 24:5109-5115. [PMID: 35156109 DOI: 10.1039/d1cp05785e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this work, the decomposition of a prototypical azide, isopropyl azide, both in the ground and excited states, has been investigated through the use of multiconfigurational CASSCF and MS-CASPT2 electronic structure approaches. Particular emphasis has been placed on the thermal reaction starting at the S0 ground state surface. It has been found that the azide thermally decomposes via a stepwise mechanism, whose rate-determining step is the formation of isopropyl nitrene, which is, in turn, the first step of the global mechanism. After that, the nitrene isomerizes to the corresponding imine derivative. Two routes are possible for such a decomposition: (i) a spin-allowed path involving a transition state; and (ii) a spin-forbidden one via a S0/T0 intersystem crossing. Both intermediates have been determined and characterised. Their associated relative energies have been found to be quite similar, 45.75 and 45.52 kcal mol-1, respectively. To complete this study, the kinetics of the singlet and triplet channels are modeled with the MESMER (Master Equation Solver for Multi-Energy Well Reactions) code by applying the RRKM and Landau-Zener (with WKB tunnelling correction) theories, respectively. It is found that the canonical rate-coefficients of the singlet path are 2-orders of magnitude higher than the rate-coefficients of the forbidden reaction. In addition, the concerted mechanism has been investigated that would lead to the formation of the imine derivative and nitrogen extrusion in the first step of the decomposition. After a careful analysis of CASSCF calculations with different active spaces and their comparison with single electronic configuration methods (MP2 and B3LYP), the concerted mechanism is discarded.
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Affiliation(s)
- Juan Soto
- Department of Physical Chemistry, Faculty of Science, University of Málaga, E-29071 Málaga, Spain.
| | - Manuel Algarra
- INAMAT2 Institute for Advanced Materials and Mathematics, Department of Sciences, Campus de Arrosadia, 31006 Pamplona, Spain
| | - Daniel Peláez
- Institut des Sciences Moléculaires d'Orsay (ISMO) - UMR 8214, Université Paris-Saclay, 91405 Orsay Cedex, Spain
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Kugele A, Ketter S, Silkenath B, Wittmann V, Joseph B, Drescher M. In situ EPR spectroscopy of a bacterial membrane transporter using an expanded genetic code. Chem Commun (Camb) 2021; 57:12980-12983. [PMID: 34792069 PMCID: PMC8640571 DOI: 10.1039/d1cc04612h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022]
Abstract
The membrane transporter BtuB is site-directedly spin labelled on the surface of living Escherichia coli via Diels-Alder click chemistry of the genetically encoded amino acid SCO-L-lysine. The previously introduced photoactivatable nitroxide PaNDA prevents off-target labelling, is used for distance measurements, and the temporally shifted activation of the nitroxide allows for advanced experimental setups. This study describes significant evolution of Diels-Alder-mediated spin labelling on cellular surfaces and opens up new vistas for the the study of membrane proteins.
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Affiliation(s)
- Anandi Kugele
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Sophie Ketter
- Institute of Biophysics, Department of Physics & The Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany.
| | - Bjarne Silkenath
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Benesh Joseph
- Institute of Biophysics, Department of Physics & The Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany.
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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Torricella F, Bonucci A, Polykretis P, Cencetti F, Banci L. Rapid protein delivery to living cells for biomolecular investigation. Biochem Biophys Res Commun 2021; 570:82-88. [PMID: 34274850 DOI: 10.1016/j.bbrc.2021.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 12/24/2022]
Abstract
The lack of a simple, fast and efficient method for protein delivery is limiting the widespread application of in-cell experiments, which are crucial for understanding the cellular function. We present here an innovative strategy to deliver proteins into both prokaryotic and eukaryotic cells, exploiting thermal vesiculation. This method allows to internalize substantial amounts of proteins, with different molecular weight and conformation, without compromising the structural properties and cell viability. Characterizing proteins in a physiological environment is essential as the environment can dramatically affect the conformation and dynamics of biomolecules as shown by in-cell EPR spectra vs those acquired in buffer solution. Considering its versatility, this method opens the possibility to scientists to study proteins directly in living cells through a wide range of techniques.
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Affiliation(s)
- Francesco Torricella
- Magnetic Resonance Center - CERM, University of Florence, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Alessio Bonucci
- Aix Marseille, Univ, CNRS, BIP, Laboratoire de Bioénergétique et Ingégnerie des protéines, Marseille, France
| | - Panagis Polykretis
- Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Francesca Cencetti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, v.le GB Morgagni 50, 50134, Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Florence, Italy.
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Kucher S, Elsner C, Safonova M, Maffini S, Bordignon E. In-Cell Double Electron-Electron Resonance at Nanomolar Protein Concentrations. J Phys Chem Lett 2021; 12:3679-3684. [PMID: 33829785 DOI: 10.1021/acs.jpclett.1c00048] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is an established technique to site-specifically monitor conformational changes of spin-labeled biomolecules. Emerging in-cell EPR approaches aiming to address spin-labeled proteins in their native environment still struggle to reach a broad applicability and to target physiologically relevant protein concentrations. Here, we present a comparative in vitro and in-cell double electron-electron resonance (DEER) study demonstrating that nanomolar protein concentrations are at reach to measure distances up to 4.5 nm between protein sites carrying commercial gadolinium spin labels.
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Affiliation(s)
- Svetlana Kucher
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
| | - Christina Elsner
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
| | - Mariya Safonova
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
| | - Stefano Maffini
- Max Planck Institute of Molecular Physiology, Department of Mechanistic Cell Biology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Enrica Bordignon
- Ruhr University Bochum, Faculty of Chemistry and Biochemistry, Universitaetsstr. 150, 44801 Bochum, Germany
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Giannoulis A, Ben-Ishay Y, Goldfarb D. Characteristics of Gd(III) spin labels for the study of protein conformations. Methods Enzymol 2021; 651:235-290. [PMID: 33888206 DOI: 10.1016/bs.mie.2021.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gd(III) complexes are currently established as spin labels for structural studies of biomolecules using pulse dipolar electron paramagnetic resonance (PD-EPR) techniques. This has been achieved by the availability of medium- and high-field spectrometers, understanding the spin physics underlying the spectroscopic properties of high spin Gd(III) (S=7/2) pairs and their dipolar interaction, the design of well-defined model compounds and optimization of measurement techniques. In addition, a variety of Gd(III) chelates and labeling schemes have allowed a broad scope of applications. In this review, we provide a brief background of the spectroscopic properties of Gd(III) pertinent for effective PD-EPR measurements and focus on the various labels available to date. We report on their use in PD-EPR applications and highlight their pros and cons for particular applications. We also devote a section to recent in-cell structural studies of proteins using Gd(III), which is an exciting new direction for Gd(III) spin labeling.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Yasmin Ben-Ishay
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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Bordignon E, Seeger MA, Galazzo L, Meier G. From in vitro towards in situ: structure-based investigation of ABC exporters by electron paramagnetic resonance spectroscopy. FEBS Lett 2020; 594:3839-3856. [PMID: 33219535 DOI: 10.1002/1873-3468.14004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/30/2020] [Accepted: 11/15/2020] [Indexed: 12/12/2022]
Abstract
ATP-binding cassette (ABC) exporters have been studied now for more than four decades, and recent structural investigation has produced a large number of protein database entries. Yet, important questions about how ABC exporters function at the molecular level remain debated, such as which are the molecular recognition hotspots and the allosteric couplings dynamically regulating the communication between the catalytic cycle and the export of substrates. This conundrum mainly arises from technical limitations confining all research to in vitro analysis of ABC transporters in detergent solutions or embedded in membrane-mimicking environments. Therefore, a largely unanswered question is how ABC exporters operate in situ, namely in the native membrane context of a metabolically active cell. This review focuses on novel mechanistic insights into type I ABC exporters gained through a unique combination of structure determination, biochemical characterization, generation of conformation-specific nanobodies/sybodies and double electron-electron resonance.
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Affiliation(s)
- Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Switzerland
| | - Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Switzerland
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