1
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Infield D, Schene ME, Galpin JD, Ahern CA. Genetic Code Expansion for Mechanistic Studies in Ion Channels: An (Un)natural Union of Chemistry and Biology. Chem Rev 2024; 124:11523-11543. [PMID: 39207057 PMCID: PMC11503617 DOI: 10.1021/acs.chemrev.4c00306] [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: 04/24/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Ion channels play central roles in biology and human health by catalyzing the transmembrane flow of electrical charge. These proteins are ideal targets for genetic code expansion (GCE) methods because it is feasible to measure ion channel activity from miniscule amounts of protein and to analyze the resulting data via rigorous, established biophysical methods. In an ideal scenario, the encoding of synthetic, noncanonical amino acids via GCE allows the experimenter to ask questions inaccessible to traditional methods. For this reason, GCE has been successfully applied to a variety of ligand- and voltage-gated channels wherein extensive structural, functional, and pharmacological data exist. Here, we provide a comprehensive summary of GCE as applied to ion channels. We begin with an overview of the methods used to encode noncanonical amino acids in channels and then describe mechanistic studies wherein GCE was used for photochemistry (cross-linking; caged amino acids) and atomic mutagenesis (isosteric manipulation of charge and aromaticity; backbone mutation). Lastly, we cover recent advances in the encoding of fluorescent amino acids for the real-time study of protein conformational dynamics.
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Affiliation(s)
- Daniel
T. Infield
- Department of Molecular Physiology
and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Miranda E. Schene
- Department of Molecular Physiology
and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jason D. Galpin
- Department of Molecular Physiology
and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Christopher A. Ahern
- Department of Molecular Physiology
and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
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2
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Kuru E, Rittichier J, de Puig H, Flores A, Rout S, Han I, Reese AE, Bartlett TM, De Moliner F, Bernier SG, Galpin JD, Marchand J, Bedell W, Robinson-McCarthy L, Ahern CA, Bernhardt TG, Rudner DZ, Collins JJ, Vendrell M, Church GM. Rapid discovery and evolution of nanosensors containing fluorogenic amino acids. Nat Commun 2024; 15:7531. [PMID: 39237489 PMCID: PMC11377706 DOI: 10.1038/s41467-024-50956-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/24/2024] [Indexed: 09/07/2024] Open
Abstract
Binding-activated optical sensors are powerful tools for imaging, diagnostics, and biomolecular sensing. However, biosensor discovery is slow and requires tedious steps in rational design, screening, and characterization. Here we report on a platform that streamlines biosensor discovery and unlocks directed nanosensor evolution through genetically encodable fluorogenic amino acids (FgAAs). Building on the classical knowledge-based semisynthetic approach, we engineer ~15 kDa nanosensors that recognize specific proteins, peptides, and small molecules with up to 100-fold fluorescence increases and subsecond kinetics, allowing real-time and wash-free target sensing and live-cell bioimaging. An optimized genetic code expansion chemistry with FgAAs further enables rapid (~3 h) ribosomal nanosensor discovery via the cell-free translation of hundreds of candidates in parallel and directed nanosensor evolution with improved variant-specific sensitivities (up to ~250-fold) for SARS-CoV-2 antigens. Altogether, this platform could accelerate the discovery of fluorogenic nanosensors and pave the way to modify proteins with other non-standard functionalities for diverse applications.
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Affiliation(s)
- Erkin Kuru
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| | - Jonathan Rittichier
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- EnPlusOne Biosciences Inc., Watertown, MA, USA
| | - Helena de Puig
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Allison Flores
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Subhrajit Rout
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Isaac Han
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Abigail E Reese
- IRR Chemistry Hub and Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Thomas M Bartlett
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Fabio De Moliner
- IRR Chemistry Hub and Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Sylvie G Bernier
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Jorge Marchand
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - William Bedell
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | | | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Marc Vendrell
- IRR Chemistry Hub and Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK.
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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3
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Leisle L, Lam K, Dehghani-Ghahnaviyeh S, Fortea E, Galpin JD, Ahern CA, Tajkhorshid E, Accardi A. Backbone amides are determinants of Cl - selectivity in CLC ion channels. Nat Commun 2022; 13:7508. [PMID: 36473856 PMCID: PMC9726985 DOI: 10.1038/s41467-022-35279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Chloride homeostasis is regulated in all cellular compartments. CLC-type channels selectively transport Cl- across biological membranes. It is proposed that side-chains of pore-lining residues determine Cl- selectivity in CLC-type channels, but their spatial orientation and contributions to selectivity are not conserved. This suggests a possible role for mainchain amides in selectivity. We use nonsense suppression to insert α-hydroxy acids at pore-lining positions in two CLC-type channels, CLC-0 and bCLC-k, thus exchanging peptide-bond amides with ester-bond oxygens which are incapable of hydrogen-bonding. Backbone substitutions functionally degrade inter-anion discrimination in a site-specific manner. The presence of a pore-occupying glutamate side chain modulates these effects. Molecular dynamics simulations show backbone amides determine ion energetics within the bCLC-k pore and how insertion of an α-hydroxy acid alters selectivity. We propose that backbone-ion interactions are determinants of Cl- specificity in CLC channels in a mechanism reminiscent of that described for K+ channels.
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Affiliation(s)
- Lilia Leisle
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Kin Lam
- Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sepehr Dehghani-Ghahnaviyeh
- Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Eva Fortea
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA.
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4
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Characterising ion channel structure and dynamics using fluorescence spectroscopy techniques. Biochem Soc Trans 2022; 50:1427-1445. [DOI: 10.1042/bst20220605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
Abstract
Ion channels undergo major conformational changes that lead to channel opening and ion conductance. Deciphering these structure-function relationships is paramount to understanding channel physiology and pathophysiology. Cryo-electron microscopy, crystallography and computer modelling provide atomic-scale snapshots of channel conformations in non-cellular environments but lack dynamic information that can be linked to functional results. Biophysical techniques such as electrophysiology, on the other hand, provide functional data with no structural information of the processes involved. Fluorescence spectroscopy techniques help bridge this gap in simultaneously obtaining structure-function correlates. These include voltage-clamp fluorometry, Förster resonance energy transfer, ligand binding assays, single molecule fluorescence and their variations. These techniques can be employed to unearth several features of ion channel behaviour. For instance, they provide real time information on local and global rearrangements that are inherent to channel properties. They also lend insights in trafficking, expression, and assembly of ion channels on the membrane surface. These methods have the advantage that they can be carried out in either native or heterologous systems. In this review, we briefly explain the principles of fluorescence and how these have been translated to study ion channel function. We also report several recent advances in fluorescence spectroscopy that has helped address and improve our understanding of the biophysical behaviours of different ion channel families.
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5
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Wilkinson EM, Spenkelink LM, van Oijen AM. Observing protein dynamics during DNA-lesion bypass by the replisome. Front Mol Biosci 2022; 9:968424. [PMID: 36213113 PMCID: PMC9534484 DOI: 10.3389/fmolb.2022.968424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Faithful DNA replication is essential for all life. A multi-protein complex called the replisome contains all the enzymatic activities required to facilitate DNA replication, including unwinding parental DNA and synthesizing two identical daughter molecules. Faithful DNA replication can be challenged by both intrinsic and extrinsic factors, which can result in roadblocks to replication, causing incomplete replication, genomic instability, and an increased mutational load. This increased mutational load can ultimately lead to a number of diseases, a notable example being cancer. A key example of a roadblock to replication is chemical modifications in the DNA caused by exposure to ultraviolet light. Protein dynamics are thought to play a crucial role to the molecular pathways that occur in the presence of such DNA lesions, including potential damage bypass. Therefore, many assays have been developed to study these dynamics. In this review, we discuss three methods that can be used to study protein dynamics during replisome–lesion encounters in replication reactions reconstituted from purified proteins. Specifically, we focus on ensemble biochemical assays, single-molecule fluorescence, and cryo-electron microscopy. We discuss two key model DNA replication systems, derived from Escherichia coli and Saccharomyces cerevisiae. The main methods of choice to study replication over the last decades have involved biochemical assays that rely on ensemble averaging. While these assays do not provide a direct readout of protein dynamics, they can often be inferred. More recently, single-molecule techniques including single-molecule fluorescence microscopy have been used to visualize replisomes encountering lesions in real time. In these experiments, individual proteins can be fluorescently labeled in order to observe the dynamics of specific proteins during DNA replication. Finally, cryo-electron microscopy can provide detailed structures of individual replisome components, which allows functional data to be interpreted in a structural context. While classic cryo-electron microscopy approaches provide static information, recent developments such as time-resolved cryo-electron microscopy help to bridge the gap between static structures and dynamic single-molecule techniques by visualizing sequential steps in biochemical pathways. In combination, these techniques will be capable of visualizing DNA replication and lesion encounter dynamics in real time, whilst observing the structural changes that facilitate these dynamics.
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Affiliation(s)
- Elise M. Wilkinson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Lisanne M. Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- *Correspondence: Lisanne M. Spenkelink, ; Antoine M. van Oijen,
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- *Correspondence: Lisanne M. Spenkelink, ; Antoine M. van Oijen,
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6
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Spontarelli K, Infield DT, Nielsen HN, Holm R, Young VC, Galpin JD, Ahern CA, Vilsen B, Artigas P. Role of a conserved ion-binding site tyrosine in ion selectivity of the Na+/K+ pump. J Gen Physiol 2022; 154:e202113039. [PMID: 35657726 PMCID: PMC9171065 DOI: 10.1085/jgp.202113039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 01/07/2023] Open
Abstract
The essential transmembrane Na+ and K+ gradients in animal cells are established by the Na+/K+ pump, a P-type ATPase that exports three Na+ and imports two K+ per ATP hydrolyzed. The mechanism by which the Na+/K+ pump distinguishes between Na+ and K+ at the two membrane sides is poorly understood. Crystal structures identify two sites (sites I and II) that bind Na+ or K+ and a third (site III) specific for Na+. The side chain of a conserved tyrosine at site III of the catalytic α-subunit (Xenopus-α1 Y780) has been proposed to contribute to Na+ binding by cation-π interaction. We substituted Y780 with natural and unnatural amino acids, expressed the mutants in Xenopus oocytes and COS-1 cells, and used electrophysiology and biochemistry to evaluate their function. Substitutions disrupting H-bonds impaired Na+ interaction, while Y780Q strengthened it, likely by H-bond formation. Utilizing the non-sense suppression method previously used to incorporate unnatural derivatives in ion channels, we were able to analyze Na+/K+ pumps with fluorinated tyrosine or phenylalanine derivatives inserted at position 780 to diminish cation-π interaction strength. In line with the results of the analysis of mutants with natural amino acid substitutions, the results with the fluorinated derivatives indicate that Na+-π interaction with the phenol ring at position 780 contributes minimally, if at all, to the binding of Na+. All Y780 substitutions decreased K+ apparent affinity, highlighting that a state-dependent H-bond network is essential for the selectivity switch at sites I and II when the pump changes conformational state.
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Affiliation(s)
- Kerri Spontarelli
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Daniel T. Infield
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA
| | - Hang N. Nielsen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Rikke Holm
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Victoria C. Young
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Jason D. Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA
| | - Christopher A. Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA
| | - Bente Vilsen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Pablo Artigas
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX
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7
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Gracheva IA, Tretiakova DS, Zamyshlyaeva OG, Kudriashova ES, Vodovozova EL, Fedorov AY, Boldyrev IA. Cy5-Labeled Phosphatidylcholine. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021050265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Blunck R. Determining stoichiometry of ion channel complexes using single subunit counting. Methods Enzymol 2021; 653:377-404. [PMID: 34099180 DOI: 10.1016/bs.mie.2021.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
Most membrane proteins, and ion channels in particular, assemble to multimeric biological complexes. This starts with the quarternary structure and continues with the recruitment of auxiliary subunits and oligomerization or clustering of the complexes. While the quarternary structure is best determined by atomic-scale structures, stoichiometry of heteromers and dynamic changes in the assembly cannot necessarily be investigated with structural methods. Here, single subunit counting has proven a powerful method to study the composition of these complexes. Single subunit counting uses the irreversible photodestruction of fluorescent tags as means to directly count a labeled subunit and thereby derive the composition of the assemblies. In this chapter, we discuss single subunit counting and its limitations. We present alternative methods and provide a detailed protocol for recording and analysis of single subunit counting data.
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Affiliation(s)
- Rikard Blunck
- Department of Physics, Université de Montréal, Montréal, QC, Canada.
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9
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Braun N, Sheikh ZP, Pless SA. The current chemical biology tool box for studying ion channels. J Physiol 2020; 598:4455-4471. [DOI: 10.1113/jp276695] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- N. Braun
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
| | - Z. P. Sheikh
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
| | - S. A. Pless
- Department of Drug Design and Pharmacology University of Copenhagen Jagtvej 160 Copenhagen 2100 Denmark
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10
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Wolf N, Kersting L, Herok C, Mihm C, Seibel J. High-Yielding Water-Soluble Asymmetric Cyanine Dyes for Labeling Applications. J Org Chem 2020; 85:9751-9760. [PMID: 32686416 DOI: 10.1021/acs.joc.0c01084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A simple and efficient microwave-assisted synthesis of asymmetric pentamethine cyanine dyes with various functional groups was developed, which allows high-yielding results. The synthesized dyes are modifiable and suitable for single-molecule imaging in biological and medical sciences by application of click chemistry or classic esterification and amidation.
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Affiliation(s)
- Natalia Wolf
- Institute of Organic Chemistry, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Louise Kersting
- Institute of Organic Chemistry, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Christoph Herok
- Institute of Organic Chemistry, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Cornelius Mihm
- Institute of Organic Chemistry, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Juergen Seibel
- Institute of Organic Chemistry, University of Wuerzburg, 97074 Wuerzburg, Germany
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11
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Lam K, Tajkhorshid E. Membrane Interactions of Cy3 and Cy5 Fluorophores and Their Effects on Membrane-Protein Dynamics. Biophys J 2020; 119:24-34. [PMID: 32533943 DOI: 10.1016/j.bpj.2020.05.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022] Open
Abstract
Organic fluorophores, such as Cy3 and Cy5, have been widely used as chemical labels to probe the structure and dynamics of membrane proteins. Although a number of previous studies have reported on the possibility of some of the water-soluble fluorophores to interact with lipid bilayers, detailed fluorophore-lipid interactions and, more importantly, the potential effect of such interactions on the natural dynamics of the labeled membrane proteins have not been well studied. We have performed a large set of all-atom molecular dynamics simulations employing the highly mobile membrane mimetic model to describe spontaneous partitioning of the fluorophores into lipid bilayers with different lipid compositions. Spontaneous membrane partitioning of Cy3 and Cy5 fluorophores captured in these simulations proceeds in two steps. Electrostatic interaction between the fluorophores and the lipid headgroups facilitates the initial, fast membrane association of the fluorophores, followed by slow insertion of hydrophobic moieties into the lipid bilayer core. After the conversion of the resulting membrane-bound systems to full-membrane representations, biased-exchange umbrella sampling simulations are performed for free energy calculations, revealing a higher energy barrier for partitioning into negatively charged (phosphatidylserine or phosphatidylcholine) membranes than purely zwitterionic (phosphatidylcholine or phosphatidylethanolamine) ones. Furthermore, the potential effect of fluorophore-lipid interactions on membrane proteins has been examined by covalently linking Cy5 to single- and multipass transmembrane helical proteins. Equilibrium simulations show strong position-dependent effects of Cy5-tagging on the structure and natural dynamics of membrane proteins. Interactions between the tagged protein and Cy5 were also observed. Our results suggest that fluorophore-lipid interactions can affect the structure and dynamics of membrane proteins to various extents, especially in systems with higher structural flexibility.
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Affiliation(s)
- Kin Lam
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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12
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Leisle L, Xu Y, Fortea E, Lee S, Galpin JD, Vien M, Ahern CA, Accardi A, Bernèche S. Divergent Cl - and H + pathways underlie transport coupling and gating in CLC exchangers and channels. eLife 2020; 9:e51224. [PMID: 32343228 PMCID: PMC7274781 DOI: 10.7554/elife.51224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
The CLC family comprises H+-coupled exchangers and Cl- channels, and mutations causing their dysfunction lead to genetic disorders. The CLC exchangers, unlike canonical 'ping-pong' antiporters, simultaneously bind and translocate substrates through partially congruent pathways. How ions of opposite charge bypass each other while moving through a shared pathway remains unknown. Here, we use MD simulations, biochemical and electrophysiological measurements to identify two conserved phenylalanine residues that form an aromatic pathway whose dynamic rearrangements enable H+ movement outside the Cl- pore. These residues are important for H+ transport and voltage-dependent gating in the CLC exchangers. The aromatic pathway residues are evolutionarily conserved in CLC channels where their electrostatic properties and conformational flexibility determine gating. We propose that Cl- and H+ move through physically distinct and evolutionarily conserved routes through the CLC channels and transporters and suggest a unifying mechanism that describes the gating mechanism of both CLC subtypes.
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Affiliation(s)
- Lilia Leisle
- Department of Anesthesiology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Yanyan Xu
- SIB Swiss Institute of Bioinformatics, University of BaselBaselSwitzerland
- Biozentrum, University of BaselBaselSwitzerland
| | - Eva Fortea
- Department of Physiology and Biophysics, Weill Cornell Medical CollegeNew YorkUnited States
| | - Sangyun Lee
- Department of Anesthesiology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of MedicineIowa CityUnited States
| | - Malvin Vien
- Department of Anesthesiology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of MedicineIowa CityUnited States
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical CollegeNew YorkUnited States
- Department of Physiology and Biophysics, Weill Cornell Medical CollegeNew YorkUnited States
- Department of Biochemistry, Weill Cornell Medical CollegeNew YorkUnited States
| | - Simon Bernèche
- SIB Swiss Institute of Bioinformatics, University of BaselBaselSwitzerland
- Biozentrum, University of BaselBaselSwitzerland
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13
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Single-Molecule Imaging and Computational Microscopy Approaches Clarify the Mechanism of the Dimerization and Membrane Interactions of Green Fluorescent Protein. Int J Mol Sci 2019; 20:ijms20061410. [PMID: 30897814 PMCID: PMC6471090 DOI: 10.3390/ijms20061410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 02/01/2023] Open
Abstract
Green fluorescent protein (GFP) is widely used as a biomarker in living systems; however, GFP and its variants are prone to forming low-affinity dimers under physiological conditions. This undesirable tendency is exacerbated when fluorescent proteins (FP) are confined to membranes, fused to naturally-oligomeric proteins, or expressed at high levels in cells. Oligomerization of FPs introduces artifacts into the measurement of subunit stoichiometry, as well as interactions between proteins fused to FPs. Introduction of a single mutation, A206K, has been shown to disrupt hydrophobic interactions in the region responsible for GFP dimerization, thereby contributing to its monomerization. Nevertheless, a detailed understanding of how this single amino acid-dependent inhibition of dimerization in GFP occurs at the atomic level is still lacking. Single-molecule experiments combined with computational microscopy (atomistic molecular dynamics) revealed that the amino group of A206 contributes to GFP dimer formation via a multivalent electrostatic interaction. We further showed that myristoyl modification is an efficient mechanism to promote membrane attachment of GFP. Molecular dynamics-based site-directed mutagenesis has been used to identify the key functional residues in FPs. The data presented here have been utilized as a monomeric control in downstream single-molecule studies, facilitating more accurate stoichiometry quantification of functional protein complexes in living cells.
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Infield DT, Matulef K, Galpin JD, Lam K, Tajkhorshid E, Ahern CA, Valiyaveetil FI. Main-chain mutagenesis reveals intrahelical coupling in an ion channel voltage-sensor. Nat Commun 2018; 9:5055. [PMID: 30498243 PMCID: PMC6265297 DOI: 10.1038/s41467-018-07477-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 11/01/2018] [Indexed: 11/20/2022] Open
Abstract
Membrane proteins are universal signal decoders. The helical transmembrane segments of these proteins play central roles in sensory transduction, yet the mechanistic contributions of secondary structure remain unresolved. To investigate the role of main-chain hydrogen bonding on transmembrane function, we encoded amide-to-ester substitutions at sites throughout the S4 voltage-sensing segment of Shaker potassium channels, a region that undergoes rapid, voltage-driven movement during channel gating. Functional measurements of ester-harboring channels highlight a transitional region between α-helical and 310 segments where hydrogen bond removal is particularly disruptive to voltage-gating. Simulations of an active voltage sensor reveal that this region features a dynamic hydrogen bonding pattern and that its helical structure is reliant upon amide support. Overall, the data highlight the specialized role of main-chain chemistry in the mechanism of voltage-sensing; other catalytic transmembrane segments may enlist similar strategies in signal transduction mechanisms. The helical transmembrane segments of membrane proteins play central roles in sensory transduction but the mechanistic basis for their function remains unresolved. Here the authors identify regions in the S4 voltage-sensing segment of Shaker potassium channels where local helical structure is reliant upon backbone amide support.
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Affiliation(s)
- Daniel T Infield
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, 52242, USA
| | - Kimberly Matulef
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health Sciences University, Portland, 97239, OR, USA
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, 52242, USA
| | - Kin Lam
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Emad Tajkhorshid
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, 52242, USA.
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health Sciences University, Portland, 97239, OR, USA.
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15
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Pantazis A, Westerberg K, Althoff T, Abramson J, Olcese R. Harnessing photoinduced electron transfer to optically determine protein sub-nanoscale atomic distances. Nat Commun 2018; 9:4738. [PMID: 30413716 PMCID: PMC6226468 DOI: 10.1038/s41467-018-07218-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 10/16/2018] [Indexed: 11/29/2022] Open
Abstract
Proteins possess a complex and dynamic structure, which is influenced by external signals and may change as they perform their biological functions. We present an optical approach, distance-encoding photoinduced electron transfer (DEPET), capable of the simultaneous study of protein structure and function. An alternative to FRET-based methods, DEPET is based on the quenching of small conjugated fluorophores by photoinduced electron transfer: a reaction that requires contact of the excited fluorophore with a suitable electron donor. This property allows DEPET to exhibit exceptional spatial and temporal resolution capabilities in the range pertinent to protein conformational change. We report the first implementation of DEPET on human large-conductance K+ (BK) channels under voltage clamp. We describe conformational rearrangements underpinning BK channel sensitivity to electrical excitation, in conducting channels expressed in living cells. Finally, we validate DEPET in synthetic peptide length standards, to evaluate its accuracy in measuring sub- and near-nanometer intramolecular distances.
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Affiliation(s)
- Antonios Pantazis
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, UCLA, Los Angeles, CA, 90095, USA. .,Division of Neurobiology, Department of Clinical and Experimental Medicine (IKE), Linköping University, Linköping, 581 83, Sweden. .,Wallenberg Center for Molecular Medicine, Linköping University, Linköping, 581 83, Sweden.
| | - Karin Westerberg
- 0000 0001 0657 5612grid.417886.4Amgen, Thousand Oaks, CA 91320 USA
| | - Thorsten Althoff
- 0000 0000 9632 6718grid.19006.3eDepartment of Physiology, UCLA, Los Angeles, CA 90095 USA
| | - Jeff Abramson
- 0000 0000 9632 6718grid.19006.3eDepartment of Physiology, UCLA, Los Angeles, CA 90095 USA
| | - Riccardo Olcese
- Division of Molecular Medicine, Department of Anesthesiology & Perioperative Medicine, UCLA, Los Angeles, CA, 90095, USA. .,Department of Physiology, UCLA, Los Angeles, CA, 90095, USA.
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16
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Morisaki T, Stasevich TJ. Quantifying Single mRNA Translation Kinetics in Living Cells. Cold Spring Harb Perspect Biol 2018; 10:a032078. [PMID: 30385605 PMCID: PMC6211384 DOI: 10.1101/cshperspect.a032078] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
One of the last hurdles to quantifying the full central dogma of molecular biology in living cells with single-molecule resolution has been the imaging of single messenger RNA (mRNA) translation. Here we describe how recent advances in protein tagging and imaging technologies are being used to precisely visualize and quantify the synthesis of nascent polypeptide chains from single mRNA in living cells. We focus on recent applications of repeat-epitope tags and describe how they enable quantification of single mRNA ribosomal densities, translation initiation and elongation rates, and translation site mobility and higher-order structure. Together with complementary live-cell assays to monitor translation using fast-maturing fluorophores and mRNA-binding protein knockoff, single-molecule studies are beginning to uncover striking and unexpected heterogeneity in gene expression at the level of translation.
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Affiliation(s)
- Tatsuya Morisaki
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Timothy J Stasevich
- Institute of Genome Architecture and Function and Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
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17
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Infield DT, Lee EEL, Galpin JD, Galles GD, Bezanilla F, Ahern CA. Replacing voltage sensor arginines with citrulline provides mechanistic insight into charge versus shape. J Gen Physiol 2018; 150:1017-1024. [PMID: 29866793 PMCID: PMC6028492 DOI: 10.1085/jgp.201812075] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/08/2018] [Indexed: 01/06/2023] Open
Abstract
Activation of voltage-gated channels results from the outward movement of arginine residues on the S4 segments. Infield et al. use in vivo nonsense suppression to replace Shaker's S4 arginine residues with citrulline and reveal that a positive charge is required on R4 for voltage-dependent deactivation. Voltage-dependent activation of voltage-gated cation channels results from the outward movement of arginine-bearing helices within proteinaceous voltage sensors. The voltage-sensing residues in potassium channels have been extensively characterized, but current functional approaches do not allow a distinction between the electrostatic and steric contributions of the arginine side chain. Here we use chemical misacylation and in vivo nonsense suppression to encode citrulline, a neutral and nearly isosteric analogue of arginine, into the voltage sensor of the Shaker potassium channel. We functionally characterize the engineered channels and compare them with those bearing conventional mutations at the same positions. We observe effects on both voltage sensitivity and gating kinetics, enabling dissection of the roles of residue structure versus positive charge in channel function. In some positions, substitution with citrulline causes mild effects on channel activation compared with natural mutations. In contrast, substitution of the fourth S4 arginine with citrulline causes substantial changes in the conductance–voltage relationship and the kinetics of the channel, which suggests that a positive charge is required at this position for efficient voltage sensor deactivation and channel closure. The encoding of citrulline is expected to enable enhanced precision for the study of arginine residues located in crowded transmembrane environments in other membrane proteins. In addition, the method may facilitate the study of citrullination in vivo.
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Affiliation(s)
- Daniel T Infield
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
| | - Elizabeth E L Lee
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
| | - Grace D Galles
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA .,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
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18
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Klippenstein V, Mony L, Paoletti P. Probing Ion Channel Structure and Function Using Light-Sensitive Amino Acids. Trends Biochem Sci 2018; 43:436-451. [PMID: 29650383 DOI: 10.1016/j.tibs.2018.02.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/25/2018] [Accepted: 02/27/2018] [Indexed: 12/13/2022]
Abstract
Approaches to remotely control and monitor ion channel operation with light are expanding rapidly in the biophysics and neuroscience fields. A recent development directly introduces light sensitivity into proteins by utilizing photosensitive unnatural amino acids (UAAs) incorporated using the genetic code expansion technique. The introduction of UAAs results in unique molecular level control and, when combined with the maximal spatiotemporal resolution and poor invasiveness of light, enables direct manipulation and interrogation of ion channel functionality. Here, we review the diverse applications of light-sensitive UAAs in two superfamilies of ion channels (voltage- and ligand-gated ion channels; VGICs and LGICs) and summarize existing UAA tools, their mode of action, potential, caveats, and technical considerations to their use in illuminating ion channel structure and function.
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Affiliation(s)
- Viktoria Klippenstein
- Institut de Biologie de I'ENS (IBENS), CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Université PSL, 46 rue d'Ulm, 75005 Paris, France; These authors contributed equally to this work
| | - Laetitia Mony
- Institut de Biologie de I'ENS (IBENS), CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Université PSL, 46 rue d'Ulm, 75005 Paris, France; These authors contributed equally to this work
| | - Pierre Paoletti
- Institut de Biologie de I'ENS (IBENS), CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Université PSL, 46 rue d'Ulm, 75005 Paris, France.
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19
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Abstract
Chemical aminoacylation of orthogonal tRNA allows for the genetic encoding of a wide range of synthetic amino acids without the need to evolve specific aminoacyl-tRNA synthetases. This method, when paired with protein expression in the Xenopus laevis oocyte expression system, can extract atomic scale functional data from a protein structure to advance the study of membrane proteins. The utility of the method depends on the orthogonality of the tRNA species used to deliver the amino acid. Here, we report that the pyrrolysyl tRNA (pylT) from Methanosarcina barkeri fusaro is orthogonal and highly competent for genetic code expansion experiments in the Xenopus oocyte. The data show that pylT is amendable to chemical acylation in vitro; it is then used to rescue a cytoplasmic site within a voltage-gated sodium channel. Further, the high fidelity of the pylT is demonstrated via encoding of lysine within the selectivity filter of the sodium channel, where sodium ion recognition by the distal amine of this side-chain is essential. Thus, pylT is an appropriate tRNA species for delivery of amino acids via nonsense suppression in the Xenopus oocyte. It may prove useful in experimental contexts wherein reacylation of suppressor tRNAs have been observed.
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20
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Stracy M, Kapanidis AN. Single-molecule and super-resolution imaging of transcription in living bacteria. Methods 2017; 120:103-114. [PMID: 28414097 PMCID: PMC5670121 DOI: 10.1016/j.ymeth.2017.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/21/2017] [Accepted: 04/05/2017] [Indexed: 12/20/2022] Open
Abstract
In vivo single-molecule and super-resolution techniques are transforming our ability to study transcription as it takes place in its native environment in living cells. This review will detail the methods for imaging single molecules in cells, and the data-analysis tools which can be used to extract quantitative information on the spatial organization, mobility, and kinetics of the transcription machinery from these experiments. Furthermore, we will highlight studies which have applied these techniques to shed new light on bacterial transcription.
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Affiliation(s)
- Mathew Stracy
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
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