1
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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024; 124:10281-10362. [PMID: 39120726 PMCID: PMC11441406 DOI: 10.1021/acs.chemrev.3c00878] [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: 11/29/2023] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB
International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A. Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
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2
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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.
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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
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3
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Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024; 124:9580-9608. [PMID: 38953775 PMCID: PMC11363022 DOI: 10.1021/acs.chemrev.4c00031] [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: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.
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Affiliation(s)
- Nikolaj G. Koch
- Department
of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Nediljko Budisa
- Biocatalysis
Group, Institute of Chemistry, Technische
Universität Berlin, 10623 Berlin, Germany
- Chemical
Synthetic Biology Chair, Department of Chemistry, University of Manitoba, Winnipeg MB R3T 2N2, Canada
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4
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [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: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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5
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [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: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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6
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [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: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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7
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Ben‐Ishay Y, Barak Y, Feintuch A, Ouari O, Pierro A, Mileo E, Su X, Goldfarb D. Exploring the dynamics and structure of PpiB in living Escherichia coli cells using electron paramagnetic resonance spectroscopy. Protein Sci 2024; 33:e4903. [PMID: 38358137 PMCID: PMC10868451 DOI: 10.1002/pro.4903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
The combined effects of the cellular environment on proteins led to the definition of a fifth level of protein structural organization termed quinary structure. To explore the implication of potential quinary structure for globular proteins, we studied the dynamics and conformations of Escherichia coli (E. coli) peptidyl-prolyl cis/trans isomerase B (PpiB) in E. coli cells. PpiB plays a major role in maturation and regulation of folded proteins by catalyzing the cis/trans isomerization of the proline imidic peptide bond. We applied electron paramagnetic resonance (EPR) techniques, utilizing both Gadolinium (Gd(III)) and nitroxide spin labels. In addition to using standard spin labeling approaches with genetically engineered cysteines, we incorporated an unnatural amino acid to achieve Gd(III)-nitroxide orthogonal labeling. We probed PpiB's residue-specific dynamics by X-band continuous wave EPR at ambient temperatures and its structure by double electron-electron resonance (DEER) on frozen samples. PpiB was delivered to E. coli cells by electroporation. We report a significant decrease in the dynamics induced by the cellular environment for two chosen labeling positions. These changes could not be reproduced by adding crowding agents and cell extracts. Concomitantly, we report a broadening of the distance distribution in E. coli, determined by Gd(III)-Gd(III) DEER measurements, as compared with solution and human HeLa cells. This suggests an increase in the number of PpiB conformations present in E. coli cells, possibly due to interactions with other cell components, which also contributes to the reduction in mobility and suggests the presence of a quinary structure.
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Affiliation(s)
- Yasmin Ben‐Ishay
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Barak
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
| | - Akiva Feintuch
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
| | - Olivier Ouari
- CNRS, ICR, Institut de Chimie RadicalaireAix‐Marseille UniversitéMarseilleFrance
| | - Annalisa Pierro
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
- Present address:
Konstanz Research School Chemical Biology, Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Elisabetta Mileo
- CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des ProtéinesAix Marseille UniversitéMarseilleFrance
| | - Xun‐Cheng Su
- State Key Laboratory of Elemento‐organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular RecognitionCollege of Chemistry, Nankai UniversityTianjinChina
| | - Daniella Goldfarb
- Department of Chemical and Biological PhysicsWeizmann Institute of ScienceRehovotIsrael
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8
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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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9
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Schloßhauer JL, Zemella A, Dondapati SK, Thoring L, Meyer M, Kubick S. Enhancing the performance of a mutant pyrrolysyl-tRNA synthetase to create a highly versatile eukaryotic cell-free protein synthesis tool. Sci Rep 2023; 13:15236. [PMID: 37709815 PMCID: PMC10502014 DOI: 10.1038/s41598-023-42198-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Modification of proteins with a broad range of chemical functionalities enables the investigation of protein structure and activity by manipulating polypeptides at single amino acid resolution. Indeed, various functional groups including bulky non-canonical amino acids like strained cyclooctenes could be introduced by the unique features of the binding pocket of the double mutant pyrrolysyl-tRNA synthetase (Y306A, Y384F), but the instable nature of the enzyme limits its application in vivo. Here, we constructed a cell-free protein production system, which increased the overall enzyme stability by combining different reaction compartments. Moreover, a co-expression approach in a one-pot reaction allowed straightforward site-specific fluorescent labeling of the functional complex membrane protein cystic fibrosis transmembrane conductance regulator. Our work provides a versatile platform for introducing various non-canonical amino acids into difficult-to-express proteins for structural and fluorescence based investigation of proteins activity.
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Affiliation(s)
- Jeffrey L Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Institute of Biotechnology,, Brandenburg University of Technology Cottbus-Senftenberg, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany.
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Manpreet Meyer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
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10
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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: 4] [Impact Index Per Article: 4.0] [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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11
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultrafast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. J Am Chem Soc 2023; 145:14608-14620. [PMID: 37364003 PMCID: PMC10440187 DOI: 10.1021/jacs.3c00967] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Site-directed spin-labeling (SDSL)─in combination with double electron-electron resonance (DEER) spectroscopy─has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. DEER combined with in situ SDSL in live cells is challenging since current bioorthogonal labeling approaches are too slow to allow for complete labeling with low concentrations of spin label prior to loss of signal from cellular reduction. Here, we overcome this limitation by genetically encoding a novel family of small, tetrazine-bearing noncanonical amino acids (Tet-v4.0) at multiple sites in proteins expressed in Escherichia coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans-cyclooctene (sTCO)-functionalized nitroxides─including a gem-diethyl-substituted nitroxide with enhanced stability in cells─with rate constants that can exceed 106 M-1 s-1. The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro. Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and support assignment of the conformational state of an MBP mutant within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification.
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, Washington 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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12
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Tabares LC, Daniel DT, Vázquez-Ibar JL, Kouklovsky C, Alezra V, Un S. Using the Noncanonical Metallo-Amino Acid [Cu(II)(2,2'-Bipyridin-5-yl)]-alanine to Study the Structures of Proteins. J Phys Chem Lett 2023; 14:3368-3375. [PMID: 36995079 DOI: 10.1021/acs.jpclett.3c00196] [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: 06/19/2023]
Abstract
Genetic code expansion allows modification of the physical and chemical properties of proteins by the site-directed insertion of noncanonical amino acids. Here we exploit this technology for measuring nanometer-scale distances in proteins. (2,2'-Bipyridin-5-yl)alanine was incorporated into the green fluorescent protein (GFP) and used as an anchoring point for Cu(II) to create a spin-label. The incorporation of (2,2'-bipyridin-5-yl)alanine directly into the protein resulted in a high-affinity binding site for Cu(II) capable of outcompeting other binding positions in the protein. The resulting Cu(II)-spin label is very compact and not larger than a conventional amino acid. By using 94 GHz electron paramagnetic resonance (EPR) pulse dipolar spectroscopy we have been able to determine accurately the distance between two such spin-labels. Our measurements revealed that GFP dimers can adopt different quaternary conformations. The combination of spin-labeling using a paramagnetic nonconventional amino acid with high-frequency EPR techniques resulted in a sensitive method for studying the structures of proteins.
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Affiliation(s)
- Leandro C Tabares
- Institute for Integrative Biology of the Cell, Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198, CEA-Saclay, Gif-sur-Yvette F-91198, France
| | - Davis T Daniel
- Institute for Integrative Biology of the Cell, Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198, CEA-Saclay, Gif-sur-Yvette F-91198, France
| | - José Luis Vázquez-Ibar
- Institute for Integrative Biology of the Cell, Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198, CEA-Saclay, Gif-sur-Yvette F-91198, France
| | - Cyrille Kouklovsky
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Saclay, CNRS, Orsay F-91405, Cedex France
| | - Valérie Alezra
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Saclay, CNRS, Orsay F-91405, Cedex France
| | - Sun Un
- Institute for Integrative Biology of the Cell, Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198, CEA-Saclay, Gif-sur-Yvette F-91198, France
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13
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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14
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Dunleavy R, Chandrasekaran S, Crane BR. Enzymatic Spin-Labeling of Protein N- and C-Termini for Electron Paramagnetic Resonance Spectroscopy. Bioconjug Chem 2023:10.1021/acs.bioconjchem.3c00029. [PMID: 36921260 PMCID: PMC10502183 DOI: 10.1021/acs.bioconjchem.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for investigating the structure and dynamics of proteins. The introduction of paramagnetic moieties at specific positions in a protein enables precise measurement of local structure and dynamics. This technique, termed site-directed spin-labeling, has traditionally been performed using cysteine-reactive radical-containing probes. However, large proteins are more likely to contain multiple cysteine residues and cysteine labeling at specific sites may be infeasible or impede function. To address this concern, we applied three peptide-ligating enzymes (sortase, asparaginyl endopeptidase, and inteins) for nitroxide labeling of N- and C-termini of select monomeric and dimeric proteins. Continuous wave and pulsed EPR (double electron electron resonance) experiments reveal specific attachment of nitroxide probes to ether N-termini (OaAEP1) or C-termini (sortase and intein) across three test proteins (CheY, CheA, and iLOV), thereby enabling a straightforward, highly specific, and general method for protein labeling. Importantly, the linker length (3, 5, and 9 residues for OaAEP1, intein, and sortase reactions, respectively) between the probe and the target protein has a large impact on the utility of distance measurements by pulsed EPR, with longer linkers leading to broader distributions. As these methods are only dependent on accessible N- and C-termini, we anticipate application to a wide range of protein targets for biomolecular EPR spectroscopy.
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Affiliation(s)
- Robert Dunleavy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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15
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Jana S, Evans EGB, Jang HS, Zhang S, Zhang H, Rajca A, Gordon SE, Zagotta WN, Stoll S, Mehl RA. Ultra-Fast Bioorthogonal Spin-Labeling and Distance Measurements in Mammalian Cells Using Small, Genetically Encoded Tetrazine Amino Acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525763. [PMID: 36747808 PMCID: PMC9901033 DOI: 10.1101/2023.01.26.525763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Studying protein structures and dynamics directly in the cellular environments in which they function is essential to fully understand the molecular mechanisms underlying cellular processes. Site-directed spin-labeling (SDSL)-in combination with double electron-electron resonance (DEER) spectroscopy-has emerged as a powerful technique for determining both the structural states and the conformational equilibria of biomacromolecules. In-cell DEER spectroscopy on proteins in mammalian cells has thus far not been possible due to the notable challenges of spin-labeling in live cells. In-cell SDSL requires exquisite biorthogonality, high labeling reaction rates and low background signal from unreacted residual spin label. While the bioorthogonal reaction must be highly specific and proceed under physiological conditions, many spin labels display time-dependent instability in the reducing cellular environment. Additionally, high concentrations of spin label can be toxic. Thus, an exceptionally fast bioorthogonal reaction is required that can allow for complete labeling with low concentrations of spin-label prior to loss of signal. Here we utilized genetic code expansion to site-specifically encode a novel family of small, tetrazine-bearing non-canonical amino acids (Tet-v4.0) at multiple sites in green fluorescent protein (GFP) and maltose binding protein (MBP) expressed both in E. coli and in human HEK293T cells. We achieved specific and quantitative spin-labeling of Tet-v4.0-containing proteins by developing a series of strained trans -cyclooctene (sTCO)-functionalized nitroxides-including a gem -diethyl-substituted nitroxide with enhanced stability in cells-with rate constants that can exceed 10 6 M -1 s -1 . The remarkable speed of the Tet-v4.0/sTCO reaction allowed efficient spin-labeling of proteins in live HEK293T cells within minutes, requiring only sub-micromolar concentrations of sTCO-nitroxide added directly to the culture medium. DEER recorded from intact cells revealed distance distributions in good agreement with those measured from proteins purified and labeled in vitro . Furthermore, DEER was able to resolve the maltose-dependent conformational change of Tet-v4.0-incorporated and spin-labeled MBP in vitro and successfully discerned the conformational state of MBP within HEK293T cells. We anticipate the exceptional reaction rates of this system, combined with the relatively short and rigid side chains of the resulting spin labels, will enable structure/function studies of proteins directly in cells, without any requirements for protein purification. TOC
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Affiliation(s)
- Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
- Equal contributors
| | - Eric G B Evans
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
- Equal contributors
| | - Hyo Sang Jang
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shuyang Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, United States
| | - Sharona E Gordon
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - William N Zagotta
- Department of Physiology & Biophysics, University of Washington, Seattle, WA 98195, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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16
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Pierro A, Drescher M. Dance with spins: site-directed spin labeling coupled to electron paramagnetic resonance spectroscopy directly inside cells. Chem Commun (Camb) 2023; 59:1274-1284. [PMID: 36633152 PMCID: PMC9890500 DOI: 10.1039/d2cc05907j] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023]
Abstract
Depicting how biomolecules move and interact within their physiological environment is one of the hottest topics of structural biology. This Feature Article gives an overview of the most recent advances in Site-directed Spin Labeling coupled to Electron Paramagnetic Resonance spectroscopy (SDSL-EPR) to study biomolecules in living cells. The high sensitivity, the virtual absence of background, and the versatility of spin-labeling strategies make this approach one of the most promising techniques for the study of biomolecules in physiologically relevant environments. After presenting the milestones achieved in this field, we present a summary of the future goals and ambitions of this community.
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Affiliation(s)
- Annalisa Pierro
- Department of Chemistry, University of Konstanz, and Konstanz Research School Chemical Biology, Universitätsstraße 10, 78457 Konstanz, Germany.
| | - Malte Drescher
- Department of Chemistry, University of Konstanz, and Konstanz Research School Chemical Biology, Universitätsstraße 10, 78457 Konstanz, Germany.
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17
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Berkeley RF, Debelouchina GT. Chemical tools for study and modulation of biomolecular phase transitions. Chem Sci 2022; 13:14226-14245. [PMID: 36545140 PMCID: PMC9749140 DOI: 10.1039/d2sc04907d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
Biomolecular phase transitions play an important role in organizing cellular processes in space and time. Methods and tools for studying these transitions, and the intrinsically disordered proteins (IDPs) that often drive them, are typically less developed than tools for studying their folded protein counterparts. In this perspective, we assess the current landscape of chemical tools for studying IDPs, with a specific focus on protein liquid-liquid phase separation (LLPS). We highlight methodologies that enable imaging and spectroscopic studies of these systems, including site-specific labeling with small molecules and the diverse range of capabilities offered by inteins and protein semisynthesis. We discuss strategies for introducing post-translational modifications that are central to IDP and LLPS function and regulation. We also investigate the nascent field of noncovalent small-molecule modulators of LLPS. We hope that this review of the state-of-the-art in chemical tools for interrogating IDPs and LLPS, along with an associated perspective on areas of unmet need, can serve as a valuable and timely resource for these rapidly expanding fields of study.
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Affiliation(s)
- Raymond F. Berkeley
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
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18
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Pierro A, Bonucci A, Normanno D, Ansaldi M, Pilet E, Ouari O, Guigliarelli B, Etienne E, Gerbaud G, Magalon A, Belle V, Mileo E. Probing the Structural Dynamics of a Bacterial Chaperone in Its Native Environment by Nitroxide‐Based EPR Spectroscopy. Chemistry 2022; 28:e202202249. [DOI: 10.1002/chem.202202249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
- Department of Chemistry University of Konstanz, and Konstanz Research School Chemical Biology 78457 Konstanz Germany
| | - Alessio Bonucci
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Davide Normanno
- Aix Marseille Univ CNRS, Inserm Institut Paoli-Calmettes, CRCM Centre de Recherche en Cancérologie de Marseille 13273 Marseille France
- Univ Montpellier CNRS, IGH Institut de Génétique Humaine 34396 Montpellier France
| | - Mireille Ansaldi
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Eric Pilet
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Olivier Ouari
- Aix Marseille Univ CNRS, ICR Institut de Chimie Radicalaire 13397 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Emilien Etienne
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Axel Magalon
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
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19
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Peter MF, Gebhardt C, Mächtel R, Muñoz GGM, Glaenzer J, Narducci A, Thomas GH, Cordes T, Hagelueken G. Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET. Nat Commun 2022; 13:4396. [PMID: 35906222 PMCID: PMC9338047 DOI: 10.1038/s41467-022-31945-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are frequently used to determine conformational changes, structural heterogeneity, and inter probe distances in biological macromolecules. They provide qualitative information that facilitates mechanistic understanding of biochemical processes and quantitative data for structural modelling. To provide a comprehensive comparison of the accuracy of PELDOR/DEER and smFRET, we use a library of double cysteine variants of four proteins that undergo large-scale conformational changes upon ligand binding. With either method, we use established standard experimental protocols and data analysis routines to determine inter-probe distances in the presence and absence of ligands. The results are compared to distance predictions from structural models. Despite an overall satisfying and similar distance accuracy, some inconsistencies are identified, which we attribute to the use of cryoprotectants for PELDOR/DEER and label-protein interactions for smFRET. This large-scale cross-validation of PELDOR/DEER and smFRET highlights the strengths, weaknesses, and synergies of these two important and complementary tools in integrative structural biology.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gabriel G Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Janin Glaenzer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, UK
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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20
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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: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/20/2022] [Accepted: 04/30/2022] [Indexed: 11/18/2022]
Abstract
The electron-electron double resonance (DEER) method, which provides distance distributions between two spin labels, attached site specifically to biomolecules (proteins and nucleic acids), is currently a well-recognized biophysical tool in structural biology. The most commonly used spin labels are based on nitroxide stable radicals, conjugated to the proteins primarily via native or engineered cysteine residues. However, in recent years, new spin labels, along with different labeling chemistries, have been introduced, driven in part by the desire to study structural and dynamical properties of biomolecules in their native environment, the cell. This mini-review focuses on these new spin labels, which allow for DEER on orthogonal spin labels, and on the state of the art methods for in-cell DEER distance measurements.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 761001, Israel
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21
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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22
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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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23
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Vatansever EC, Yang KS, Geng ZZ, Qiao Y, Li P, Xu S, Liu WR. A Designed, Highly Efficient Pyrrolysyl-tRNA Synthetase Mutant Binds o-Chlorophenylalanine Using Two Halogen Bonds. J Mol Biol 2022; 434:167534. [PMID: 35278475 PMCID: PMC9018553 DOI: 10.1016/j.jmb.2022.167534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/28/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
As one of the most valuable tools for genetic code expansion, pyrrolysyl-tRNA synthetase (PylRS) is structurally related to phenylalanyl-tRNA synthetase (PheRS). By introducing mutations that mimic ligand interactions in PheRS into PylRS, we designed a PylRS mutant. This mutant, designated as oClFRS, recognizes a number of o-substituted phenylalanines for their genetic incorporation at amber codon. Its efficiency in catalyzing genetic incorporation of o-chlorophenylalanine (o-ClF) is better than that for Nε-tert-butyloxycarbonyl-lysine catalyzed by PylRS. The crystal structure of oClFRS bound with o-ClF shows that o-ClF binds deeply into a hydrophobic but catalytically inactive pocket in the active site and involves two halogen bonds to achieve strong interactions. The shift of o-ClF to a catalytically active position in the oClFRS active site will be necessary for its activation. This is the first reported aminoacyl-tRNA synthetase that involves two halogen bonds for ligation recognition and might represent an alternative route to develop aminoacyl-tRNA synthetase mutants that are selective for noncanonical amino acids over native amino acids.
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Affiliation(s)
- Erol C Vatansever
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Kai S Yang
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Zhi Zachary Geng
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Yuchen Qiao
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA.
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24
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Tracking protein domain movements by EPR distance determination and multilateration. Methods Enzymol 2022; 666:121-144. [DOI: 10.1016/bs.mie.2022.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Meichsner SL, Kutin Y, Kasanmascheff M. In‐Cell Characterization of the Stable Tyrosyl Radical in
E. coli
Ribonucleotide Reductase Using Advanced EPR Spectroscopy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shari L. Meichsner
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Yury Kutin
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Strasse 6 44227 Dortmund Germany
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26
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Meichsner SL, Kutin Y, Kasanmascheff M. In-Cell Characterization of the Stable Tyrosyl Radical in E. coli Ribonucleotide Reductase Using Advanced EPR Spectroscopy. Angew Chem Int Ed Engl 2021; 60:19155-19161. [PMID: 33844392 PMCID: PMC8453577 DOI: 10.1002/anie.202102914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/11/2021] [Indexed: 12/21/2022]
Abstract
The E. coli ribonucleotide reductase (RNR), a paradigm for class Ia enzymes including human RNR, catalyzes the biosynthesis of DNA building blocks and requires a di‐iron tyrosyl radical (Y122.) cofactor for activity. The knowledge on the in vitro Y122. structure and its radical distribution within the β2 subunit has accumulated over the years; yet little information exists on the in vivo Y122.. Here, we characterize this essential radical in whole cells. Multi‐frequency EPR and electron‐nuclear double resonance (ENDOR) demonstrate that the structure and electrostatic environment of Y122. are identical under in vivo and in vitro conditions. Pulsed dipolar EPR experiments shed light on a distinct in vivo Y122. per β2 distribution, supporting the key role of Y. concentrations in regulating RNR activity. Additionally, we spectroscopically verify the generation of an unnatural amino acid radical, F3Y122., in whole cells, providing a crucial step towards unique insights into the RNR catalysis under physiological conditions.
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Affiliation(s)
- Shari L Meichsner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Yury Kutin
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
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27
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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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28
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Wort JL, Ackermann K, Norman DG, Bode BE. A general model to optimise Cu II labelling efficiency of double-histidine motifs for pulse dipolar EPR applications. Phys Chem Chem Phys 2021; 23:3810-3819. [PMID: 33533341 DOI: 10.1039/d0cp06196d] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to studies of biomolecules underpinning health and disease by providing highly accurate and precise geometric constraints. Combining double-histidine (dH) motifs with CuII spin labels shows promise for further increasing the precision of distance measurements, and for investigating subtle conformational changes. However, non-covalent coordination-based spin labelling is vulnerable to low binding affinity. Dissociation constants of dH motifs for CuII-nitrilotriacetic acid were previously investigated via relaxation induced dipolar modulation enhancement (RIDME), and demonstrated the feasibility of exploiting the dH motif for EPR applications at sub-μM protein concentrations. Herein, the feasibility of using modulation depth quantitation in CuII-CuII RIDME to simultaneously estimate a pair of non-identical independent KD values in such a tetra-histidine model protein is addressed. Furthermore, we develop a general speciation model to optimise CuII labelling efficiency, depending upon pairs of identical or disparate KD values and total CuII label concentration. We find the dissociation constant estimates are in excellent agreement with previously determined values, and empirical modulation depths support the proposed model.
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Affiliation(s)
- Joshua L Wort
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, UK.
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, UK.
| | - David G Norman
- School of Life Sciences, University of Dundee, Medical Sciences Institute, Dundee, DD1 5EH, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, UK.
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29
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Torricella F, Pierro A, Mileo E, Belle V, Bonucci A. Nitroxide spin labels and EPR spectroscopy: A powerful association for protein dynamics studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140653. [PMID: 33757896 DOI: 10.1016/j.bbapap.2021.140653] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/01/2023]
Abstract
Site-Directed Spin Labelling (SDSL) technique is based on the attachment of a paramagnetic label onto a specific position of a protein (or other bio-molecules) and the subsequent study by Electron Paramagnetic Resonance (EPR) spectroscopy. In particular, continuous-wave EPR (cw-EPR) spectra can detect the local conformational dynamics for proteins under various conditions. Moreover, pulse-EPR experiments on doubly spin-labelled proteins allow measuring distances between spin centres in the 1.5-8 nm range, providing information about structures and functions. This review focuses on SDSL-EPR spectroscopy as a structural biology tool to investigate proteins using nitroxide labels. The versatility of this spectroscopic approach for protein structural characterization has been demonstrated through the choice of recent studies. The main aim is to provide a general overview of the technique, particularly for non-experts, to spread the applicability of this technique in various fields of structural biology.
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Affiliation(s)
- F Torricella
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - A Pierro
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - E Mileo
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - V Belle
- Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France
| | - A Bonucci
- CERM-Magnetic Resonance Center, Department of Chemistry, University of Florence, via L.Sacconi 6, 50019 Sesto Fiorentino, Italy; Aix Marseille Univ, CNRS, BIP, Bioénergétique et Ingénierie des Protéines, IMM, Marseille, France.
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30
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Welegedara AP, Maleckis A, Bandara R, Mahawaththa MC, Dilhani Herath I, Jiun Tan Y, Giannoulis A, Goldfarb D, Otting G, Huber T. Cell-Free Synthesis of Selenoproteins in High Yield and Purity for Selective Protein Tagging. Chembiochem 2021; 22:1480-1486. [PMID: 33319405 DOI: 10.1002/cbic.202000785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Indexed: 01/10/2023]
Abstract
The selenol group of selenocysteine is much more nucleophilic than the thiol group of cysteine. Selenocysteine residues in proteins thus offer reactive points for rapid post-translational modification. Herein, we show that selenoproteins can be expressed in high yield and purity by cell-free protein synthesis by global substitution of cysteine by selenocysteine. Complete alkylation of solvent-exposed selenocysteine residues was achieved in 10 minutes with 4-chloromethylene dipicolinic acid (4Cl-MDPA) under conditions that left cysteine residues unchanged even after overnight incubation. GdIII -GdIII distances measured by double electron-electron resonance (DEER) experiments of maltose binding protein (MBP) containing two selenocysteine residues tagged with 4Cl-MDPA-GdIII were indistinguishable from GdIII -GdIII distances measured of MBP containing cysteine reacted with 4Br-MDPA tags.
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Affiliation(s)
- Adarshi P Welegedara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.,Department of Chemistry, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, 1006, Riga, Latvia
| | - Ruchira Bandara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Mithun C Mahawaththa
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Iresha Dilhani Herath
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Yi Jiun Tan
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Angeliki Giannoulis
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
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31
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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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32
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Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
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33
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Liu J, Cheng R, Van Eps N, Wang N, Morizumi T, Ou WL, Klauser PC, Rozovsky S, Ernst OP, Wang L. Genetically Encoded Quinone Methides Enabling Rapid, Site-Specific, and Photocontrolled Protein Modification with Amine Reagents. J Am Chem Soc 2020; 142:17057-17068. [PMID: 32915556 DOI: 10.1021/jacs.0c06820] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Site-specific modification of proteins with functional molecules provides powerful tools for researching and engineering proteins. Here we report a new chemical conjugation method which photocages highly reactive but chemically selective moieties, enabling the use of protein-inert amines for selective protein modification. New amino acids FnbY and FmnbY, bearing photocaged quinone methides (QMs), were genetically incorporated into proteins. Upon light activation, they generated highly reactive QM, which rapidly reacted with amine derivatives. This method features a rare combination of desired properties including fast kinetics, small and stable linkage, compatibility with low temperature, photocontrollability, and widely available reagents. Moreover, labeling via FnbY occurs on the β-carbon, affording the shortest linkage to protein backbone which is essential for advanced studies involving orientation and distance. We installed various functionalities onto proteins and attached a spin label as close as possible to the protein backbone, achieving high resolution in double electron-electron paramagnetic resonance distance measurements.
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Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Rujin Cheng
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nanxi Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Paul C Klauser
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
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34
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Softley CA, Bostock MJ, Popowicz GM, Sattler M. Paramagnetic NMR in drug discovery. JOURNAL OF BIOMOLECULAR NMR 2020; 74:287-309. [PMID: 32524233 PMCID: PMC7311382 DOI: 10.1007/s10858-020-00322-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/26/2020] [Indexed: 05/05/2023]
Abstract
The presence of an unpaired electron in paramagnetic molecules generates significant effects in NMR spectra, which can be exploited to provide restraints complementary to those used in standard structure-calculation protocols. NMR already occupies a central position in drug discovery for its use in fragment screening, structural biology and validation of ligand-target interactions. Paramagnetic restraints provide unique opportunities, for example, for more sensitive screening to identify weaker-binding fragments. A key application of paramagnetic NMR in drug discovery, however, is to provide new structural restraints in cases where crystallography proves intractable. This is particularly important at early stages in drug-discovery programs where crystal structures of weakly-binding fragments are difficult to obtain and crystallization artefacts are probable, but structural information about ligand poses is crucial to guide medicinal chemistry. Numerous applications show the value of paramagnetic restraints to filter computational docking poses and to generate interaction models. Paramagnetic relaxation enhancements (PREs) generate a distance-dependent effect, while pseudo-contact shift (PCS) restraints provide both distance and angular information. Here, we review strategies for introducing paramagnetic centers and discuss examples that illustrate the utility of paramagnetic restraints in drug discovery. Combined with standard approaches, such as chemical shift perturbation and NOE-derived distance information, paramagnetic NMR promises a valuable source of information for many challenging drug-discovery programs.
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Affiliation(s)
- Charlotte A Softley
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mark J Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
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35
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Müller D, Trucks S, Schwalbe H, Hengesbach M. Genetic Code Expansion Facilitates Position-Selective Modification of Nucleic Acids and Proteins. Chempluschem 2020; 85:1233-1243. [PMID: 32515171 DOI: 10.1002/cplu.202000150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Transcription and translation obey to the genetic code of four nucleobases and 21 amino acids evolved over billions of years. Both these processes have been engineered to facilitate the use of non-natural building blocks in both nucleic acids and proteins, enabling researchers with a decent toolbox for structural and functional analyses. Here, we review the most common approaches for how labeling of both nucleic acids as well as proteins in a site-selective fashion with either modifiable building blocks or spectroscopic probes can be facilitated by genetic code expansion. We emphasize methodological approaches and how these can be adapted for specific modifications, both during as well as after biomolecule synthesis. These modifications can facilitate, for example, a number of different spectroscopic analysis techniques and can under specific circumstances even be used in combination.
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Affiliation(s)
- Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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36
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EPR of site-directed spin-labeled proteins: A powerful tool to study structural flexibility. Arch Biochem Biophys 2020; 684:108323. [DOI: 10.1016/j.abb.2020.108323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022]
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37
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Braun TS, Widder P, Osswald U, Groß L, Williams L, Schmidt M, Helmle I, Summerer D, Drescher M. Isoindoline-Based Nitroxides as Bioresistant Spin Labels for Protein Labeling through Cysteines and Alkyne-Bearing Noncanonical Amino Acids. Chembiochem 2020; 21:958-962. [PMID: 31657498 PMCID: PMC7187341 DOI: 10.1002/cbic.201900537] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/18/2019] [Indexed: 12/15/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy in combination with site-directed spin labeling (SDSL) is a powerful tool in protein structural research. Nitroxides are highly suitable spin labeling reagents, but suffer from limited stability, particularly in the cellular environment. Herein we present the synthesis of a maleimide- and an azide-modified tetraethyl-shielded isoindoline-based nitroxide (M- and Az-TEIO) for labeling of cysteines or the noncanonical amino acid para-ethynyl-l-phenylalanine (pENF). We demonstrate the high stability of TEIO site-specifically attached to the protein thioredoxin (TRX) against reduction in prokaryotic and eukaryotic environments, and conduct double electron-electron resonance (DEER) measurements. We further generate a rotamer library for the new residue pENF-Az-TEIO that affords a distance distribution that is in agreement with the measured distribution.
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Affiliation(s)
- Theresa Sophie Braun
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Konstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Pia Widder
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Konstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Uwe Osswald
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Lina Groß
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Lara Williams
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Moritz Schmidt
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Irina Helmle
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Present address: Faculty of ScienceDepartment of Pharmaceutical BiologyUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical BiologyTU DortmundOtto-Hahn-Strasse 4a44227DortmundGermany
| | - Malte Drescher
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Konstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
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38
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Tang B, Zhao J, Xu JF, Zhang X. Tuning the stability of organic radicals: from covalent approaches to non-covalent approaches. Chem Sci 2020; 11:1192-1204. [PMID: 34123243 PMCID: PMC8148027 DOI: 10.1039/c9sc06143f] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/26/2019] [Indexed: 12/22/2022] Open
Abstract
Organic radicals are important species with single electrons. Because of their open-shell structure, they are widely used in functional materials, such as spin probes, magnetic materials and optoelectronic materials. Owing to the high reactivity of single electrons, they often serve as a key intermediate in organic synthesis. Therefore, tuning the stability of radicals is crucial for their functions. Herein, we summarize covalent and non-covalent approaches to tune the stability of organic radicals through steric effects and tuning the delocalization of spin density. Covalent approaches can tune the stability of radicals effectively and non-covalent approaches benefit from dynamicity and reversibility. It is anticipated that the further development of covalent and non-covalent approaches, as well as the interplay between them, may push the fields forward by enriching new radical materials and radical mediated reactions.
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Affiliation(s)
- Bohan Tang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Jiantao Zhao
- Key Laboratory of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Jiang-Fei Xu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Xi Zhang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University Beijing 100084 China
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39
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Kucher S, Korneev S, Klare JP, Klose D, Steinhoff HJ. In cell Gd3+-based site-directed spin labeling and EPR spectroscopy of eGFP. Phys Chem Chem Phys 2020; 22:13358-13362. [DOI: 10.1039/d0cp01930e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A newly synthesized Gd3+ chelate complex allows in cell spin labeling and detection of eGFP by EPR spectroscopy.
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Affiliation(s)
| | - Sergej Korneev
- Department of Biology
- Osnabrück University
- Osnabrück
- Germany
| | | | - Daniel Klose
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- Zurich
- Switzerland
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40
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Vuong W, Mosquera-Guagua F, Sanichar R, McDonald TR, Ernst OP, Wang L, Vederas JC. Synthesis of Chiral Spin-Labeled Amino Acids. Org Lett 2019; 21:10149-10153. [DOI: 10.1021/acs.orglett.9b04216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | | | - Randy Sanichar
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Tyler R. McDonald
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Oliver P. Ernst
- Departments of Biochemistry & Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Lei Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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41
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Kugele A, Silkenath B, Langer J, Wittmann V, Drescher M. Protein Spin Labeling with a Photocaged Nitroxide Using Diels-Alder Chemistry. Chembiochem 2019; 20:2479-2484. [PMID: 31090999 PMCID: PMC6790680 DOI: 10.1002/cbic.201900318] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 12/31/2022]
Abstract
EPR spectroscopy of diamagnetic bio-macromolecules is based on site-directed spin labeling (SDSL). Herein, a novel labeling strategy for proteins is presented. A nitroxide-based spin label has been developed and synthesized that can be ligated to proteins by an inverse-electron-demand Diels-Alder (DAinv ) cycloaddition to genetically encoded noncanonical amino acids. The nitroxide moiety is shielded by a photoremovable protecting group with an attached tetra(ethylene glycol) unit to achieve water solubility. SDSL is demonstrated on two model proteins with the photoactivatable nitroxide for DAinv reaction (PaNDA) label. The strategy features high reaction rates, combined with high selectivity, and the possibility to deprotect the nitroxide in Escherichia coli lysate.
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Affiliation(s)
- Anandi Kugele
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Bjarne Silkenath
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Jakob Langer
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Valentin Wittmann
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Malte Drescher
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
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42
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Bonucci A, Ouari O, Guigliarelli B, Belle V, Mileo E. In‐Cell EPR: Progress towards Structural Studies Inside Cells. Chembiochem 2019; 21:451-460. [DOI: 10.1002/cbic.201900291] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alessio Bonucci
- Magnetic Resonance CenterCERMUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Olivier Ouari
- Aix Marseille UnivCNRSICRInstitut de Chimie Radicalaire 13013 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
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43
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Goldfarb D. Pulse EPR in biological systems - Beyond the expert's courtyard. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:102-108. [PMID: 31337564 DOI: 10.1016/j.jmr.2019.07.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/07/2019] [Accepted: 07/08/2019] [Indexed: 05/14/2023]
Abstract
Application of EPR to biological systems includes many techniques and applications. In this short perspective, which dares to look into the future, I focus on pulse EPR, which is my field of expertise. Generally, pulse EPR techniques can be divided into two main groups: (1) hyperfine spectroscopy, which explores electron-nuclear interactions, and (2) pulse-dipolar (PD) EPR spectroscopy, which is based on electron-electron spin interactions. Here I focus on PD-EPR because it has a better chance of becoming a widely applied, easy-to-use table-top method to study the structural and dynamic aspects of bio-molecules. I will briefly introduce this technique, its current state of the art, the challenges it is facing, and finally I will describe futuristic scenarios of low-cost PD-EPR approaches that can cross the diffusion barrier from the core of experts to the bulk of the scientific community.
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Affiliation(s)
- Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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44
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Akakuru OU, Iqbal MZ, Saeed M, Liu C, Paunesku T, Woloschak G, Hosmane NS, Wu A. The Transition from Metal-Based to Metal-Free Contrast Agents for T1 Magnetic Resonance Imaging Enhancement. Bioconjug Chem 2019; 30:2264-2286. [PMID: 31380621 DOI: 10.1021/acs.bioconjchem.9b00499] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Magnetic resonance imaging (MRI) has received significant attention as the noninvasive diagnostic technique for complex diseases. Image-guided therapeutic strategy for diseases such as cancer has also been at the front line of biomedical research, thanks to the innovative MRI, enhanced by the prior delivery of contrast agents (CAs) into patients' bodies through injection. These CAs have contributed a great deal to the clinical utility of MRI but have been based on metal-containing compounds such as gadolinium, manganese, and iron oxide. Some of these CAs have led to cytotoxicities such as the incurable Nephrogenic Systemic Fibrosis (NSF), resulting in their removal from the market. On the other hand, CAs based on organic nitroxide radicals, by virtue of their structural composition, are metal free and without the aforementioned drawbacks. They also have improved biocompatibility, ease of functionalization, and long blood circulation times, and have been proven to offer tissue contrast enhancement with longitudinal relaxivities comparable with those for the metal-containing CAs. Thus, this Review highlights the recent progress in metal-based CAs and their shortcomings. In addition, the remarkable goals achieved by the organic nitroxide radical CAs in the enhancement of MR images have also been discussed extensively. The focal point of this Review is to emphasize or demonstrate the crucial need for transition into the use of organic nitroxide radicals-metal-free CAs-as against the metal-containing CAs, with the aim of achieving safer application of MRI for early disease diagnosis and image-guided therapy.
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Affiliation(s)
- Ozioma Udochukwu Akakuru
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China.,University of Chinese Academy of Sciences , No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , P.R. China
| | - M Zubair Iqbal
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China.,Department of Materials Engineering, College of Materials and Textiles , Zhejiang Sci-Tech University , No. 2 Road of Xiasha , Hangzhou 310018 , P.R. China
| | - Madiha Saeed
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China.,University of Chinese Academy of Sciences , No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , P.R. China
| | - Chuang Liu
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China.,University of Chinese Academy of Sciences , No. 19(A) Yuquan Road , Shijingshan District, Beijing 100049 , P.R. China
| | - Tatjana Paunesku
- Department of Radiation Oncology , Northwestern University , Chicago , Illinois 60611 , United States
| | - Gayle Woloschak
- Department of Radiation Oncology , Northwestern University , Chicago , Illinois 60611 , United States
| | - Narayan S Hosmane
- Department of Chemistry and Biochemistry , Northern Illinois University , DeKalb , Illinois 60115 , United States
| | - Aiguo Wu
- Cixi Institute of Biomedical Engineering, CAS Key Laboratory of Magnetic Materials and Devices, & Key Laboratory of Additive Manufacturing Materials of Zhejiang Province , Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , Ningbo 315201 , P.R. China
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45
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Wort JL, Ackermann K, Giannoulis A, Stewart AJ, Norman DG, Bode BE. Sub-Micromolar Pulse Dipolar EPR Spectroscopy Reveals Increasing Cu II -labelling of Double-Histidine Motifs with Lower Temperature. Angew Chem Int Ed Engl 2019; 58:11681-11685. [PMID: 31218813 PMCID: PMC6771633 DOI: 10.1002/anie.201904848] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/03/2019] [Indexed: 12/20/2022]
Abstract
Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to the studies of biomolecules by providing highly accurate geometric constraints. Combining double-histidine motifs with CuII spin labels can further increase the precision of distance measurements. It is also useful for proteins containing essential cysteines that can interfere with thiol-specific labelling. However, the non-covalent CuII coordination approach is vulnerable to low binding-affinity. Herein, dissociation constants (KD ) are investigated directly from the modulation depths of relaxation-induced dipolar modulation enhancement (RIDME) EPR experiments. This reveals low- to sub-μm CuII KD s under EPR distance measurement conditions at cryogenic temperatures. We show the feasibility of exploiting the double-histidine motif for EPR applications even at sub-μm protein concentrations in orthogonally labelled CuII -nitroxide systems using a commercial Q-band EPR instrument.
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Affiliation(s)
- Joshua L. Wort
- EaStCHEM School of ChemistryBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Katrin Ackermann
- EaStCHEM School of ChemistryBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Angeliki Giannoulis
- EaStCHEM School of ChemistryBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9STUK
| | - Alan J. Stewart
- School of MedicineBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9TFUK
| | - David G. Norman
- School of Life SciencesUniversity of Dundee, Medical Sciences InstituteDundeeDD1 5EHUK
| | - Bela E. Bode
- EaStCHEM School of ChemistryBiomedical Sciences Research Complex, and Centre of Magnetic ResonanceUniversity of St AndrewsNorth HaughSt AndrewsKY16 9STUK
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46
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Bleicken S, Assafa TE, Zhang H, Elsner C, Ritsch I, Pink M, Rajca S, Jeschke G, Rajca A, Bordignon E. gem-Diethyl Pyrroline Nitroxide Spin Labels: Synthesis, EPR Characterization, Rotamer Libraries and Biocompatibility. ChemistryOpen 2019; 8:1057-1065. [PMID: 31463171 PMCID: PMC6709561 DOI: 10.1002/open.201900119] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Indexed: 12/29/2022] Open
Abstract
The availability of bioresistant spin labels is crucial for the optimization of site-directed spin labeling protocols for EPR structural studies of biomolecules in a cellular context. As labeling can affect proteins' fold and/or function, having the possibility to choose between different spin labels will increase the probability to produce spin-labeled functional proteins. Here, we report the synthesis and characterization of iodoacetamide- and maleimide-functionalized spin labels based on the gem-diethyl pyrroline structure. The two nitroxide labels are compared to conventional gem-dimethyl analogs by site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy, using two water soluble proteins: T4 lysozyme and Bid. To foster their use for structural studies, we also present rotamer libraries for these labels, compatible with the MMM software. Finally, we investigate the "true" biocompatibility of the gem-diethyl probes comparing the resistance towards chemical reduction of the NO group in ascorbate solutions and E. coli cytosol at different spin concentrations.
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Affiliation(s)
- Stephanie Bleicken
- Faculty of Chemistry and BiochemistryRuhr University Bochum, Universitaetsstrasse 15044801BochumGermany
- ZEMOSRuhr University BochumUniversitaetsstrasse 150, 44801BochumGermany
| | - Tufa E. Assafa
- Faculty of Chemistry and BiochemistryRuhr University Bochum, Universitaetsstrasse 15044801BochumGermany
| | - Hui Zhang
- Department of ChemistryUniversity of Nebraska, LincolnNebraska68588-0304USA
| | - Christina Elsner
- Faculty of Chemistry and BiochemistryRuhr University Bochum, Universitaetsstrasse 15044801BochumGermany
| | - Irina Ritsch
- ETH ZurichLaboratory of Physical ChemistryVladimir-Prelog-Weg 2CH-8093ZurichSwitzerland.
| | - Maren Pink
- IUMSC, Department of ChemistryIndiana UniversityBloomington, Indiana47405-7102USA
| | - Suchada Rajca
- Department of ChemistryUniversity of Nebraska, LincolnNebraska68588-0304USA
| | - Gunnar Jeschke
- ETH ZurichLaboratory of Physical ChemistryVladimir-Prelog-Weg 2CH-8093ZurichSwitzerland.
| | - Andrzej Rajca
- Department of ChemistryUniversity of Nebraska, LincolnNebraska68588-0304USA
| | - Enrica Bordignon
- Faculty of Chemistry and BiochemistryRuhr University Bochum, Universitaetsstrasse 15044801BochumGermany
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47
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Wort JL, Ackermann K, Giannoulis A, Stewart AJ, Norman DG, Bode BE. Sub‐Micromolar Pulse Dipolar EPR Spectroscopy Reveals Increasing Cu
II
‐labelling of Double‐Histidine Motifs with Lower Temperature. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904848] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Joshua L. Wort
- EaStCHEM School of Chemistry Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9ST UK
| | - Katrin Ackermann
- EaStCHEM School of Chemistry Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9ST UK
| | - Angeliki Giannoulis
- EaStCHEM School of Chemistry Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9ST UK
| | - Alan J. Stewart
- School of Medicine Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9TF UK
| | - David G. Norman
- School of Life Sciences University of Dundee, Medical Sciences Institute Dundee DD1 5EH UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry Biomedical Sciences Research Complex, and Centre of Magnetic Resonance University of St Andrews North Haugh St Andrews KY16 9ST UK
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48
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Joseph B, Jaumann EA, Sikora A, Barth K, Prisner TF, Cafiso DS. In situ observation of conformational dynamics and protein ligand-substrate interactions in outer-membrane proteins with DEER/PELDOR spectroscopy. Nat Protoc 2019; 14:2344-2369. [PMID: 31278399 PMCID: PMC6886689 DOI: 10.1038/s41596-019-0182-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 04/18/2019] [Indexed: 12/01/2022]
Abstract
Observing structure and conformational dynamics of membrane proteins at high-resolution in their native environments is challenging because of the lack of suitable techniques. We have developed an approach for high-precision distance measurements in the nanometer range for outer membrane proteins (OMPs) in intact E. coli and native membranes. OMPs in Gram-negative bacteria rarely have reactive cysteines. This enables in-situ labeling of engineered cysteines with a methanethiosulfonate functionalized nitroxide spin label (MTSL) with minimal background signals. Following overexpression of the target protein, spin labeling is performed with E. coli or isolated outer membranes (OM) under selective conditions. The interspin distances are measured in-situ using pulsed electron-electron double resonance spectroscopy (PELDOR or DEER). The residual background signals, which are problematic for in-situ structural biology, contributes specifically to the intermolecular part of the signal and can be selectively removed to extract the desired interspin distance distribution. The initial cloning stage can take 5–7 d and the subsequent protein expression, OM isolation, spin labeling, PELDOR experiment, and the data analysis typically take 4–5 d. The described protocol provides a general strategy for observing protein-ligand/substrate interactions, oligomerization, and conformational dynamics of OMPs in the native OM and intact E. coli. EDITORIAL SUMMARY This protocol describes how to label bacterial outer membrane proteins with spin labels to study conformational changes and their interaction with ligands and substrates in native membranes and cells using Pulsed Electron-Electron Double Resonance (PELDOR or DEER) spectroscopy. TWEET A new protocol for studying conformational changes and ligand/substrate interactions of bacterial outer membrane proteins in-situ. COVER TEASER Studying membrane protein conformations in-situ
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Affiliation(s)
- Benesh Joseph
- Institute of Biophysics, Department of Physics, University of Frankfurt, Frankfurt am Main, Germany. .,Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany.
| | - Eva A Jaumann
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Arthur Sikora
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, VA, USA
| | - Katja Barth
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, University of Frankfurt, Frankfurt am Main, Germany
| | - David S Cafiso
- Department of Chemistry and Center for Membrane Biology, University of Virginia, Charlottesville, VA, USA
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49
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Miao H, Yu C, Yao A, Xuan W. Rational design of a function-based selection method for genetically encoding acylated lysine derivatives. Org Biomol Chem 2019; 17:6127-6130. [PMID: 31172146 DOI: 10.1039/c9ob00992b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A foundation of genetic code expansion is the evolution of orthogonal aminoacyl-tRNA synthetase to recognize a non-canonical amino acid, which typically involves read-through of amber stop codon in the genes used in selection. The process is time-consuming, labor-intensive, and susceptible to certain bias. As a complementation, herein, we rationally designed a function-based method to directed evolution of aminoacyl-tRNA synthetase for acylated lysine derivatives.
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Affiliation(s)
- Hui Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
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50
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Widder P, Berner F, Summerer D, Drescher M. Double Nitroxide Labeling by Copper-Catalyzed Azide-Alkyne Cycloadditions with Noncanonical Amino Acids for Electron Paramagnetic Resonance Spectroscopy. ACS Chem Biol 2019; 14:839-844. [PMID: 30998314 PMCID: PMC6534342 DOI: 10.1021/acschembio.8b01111] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 01/17/2023]
Abstract
Electron paramagnetic resonance spectroscopy in combination with site-directed spin labeling (SDSL) is an important tool to obtain long-range distance restraints for protein structural research. We here study a variety of azide- and alkyne-bearing noncanonical amino acids (ncAA) in terms of protein single- and double-incorporation efficiency via nonsense suppression, metabolic stability, yields of nitroxide labeling via copper-catalyzed [3 + 2] azide-alkyne cycloadditions (CuAAC), and spectroscopic properties in continuous-wave and double electron-electron resonance measurements. We identify para-ethynyl-l-phenylalanine and para-propargyloxy-l-phenylalanine as suitable ncAA for CuAAC-based SDSL that will complement current SDSL approaches, particularly in cases in which essential cysteines of a target protein prevent the use of sulfhydryl-reactive spin labels.
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Affiliation(s)
- Pia Widder
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Frederic Berner
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Daniel Summerer
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Dortmund, Germany
| | - Malte Drescher
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
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