1
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Fu X, Hoskins AA. Dynamics and Evolutionary Conservation of B Complex Protein Recruitment During Spliceosome Activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.606642. [PMID: 39149324 PMCID: PMC11326307 DOI: 10.1101/2024.08.08.606642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Spliceosome assembly and catalytic site formation (called activation) involve dozens of protein and snRNA binding and unbinding events. The B-complex specific proteins Prp38, Snu23, and Spp381 have critical roles in stabilizing the spliceosome during conformational changes essential for activation. While these proteins are conserved, different mechanisms have been proposed for their recruitment to spliceosomes. To visualize recruitment directly, we used Colocalization Single Molecule Spectroscopy (CoSMoS) to study the dynamics of Prp38, Snu23, and Spp381 during splicing in real time. These proteins bind to and release from spliceosomes simultaneously and are likely associated with one another. We designate the complex of Prp38, Snu23, and Spp381 as the B Complex Protein (BCP) subcomplex. Under splicing conditions, the BCP associates with pre-mRNA after tri-snRNP binding. BCP release predominantly occurs after U4 snRNP dissociation and after NineTeen Complex (NTC) association. Under low concentrations of ATP, the BCP pre-associates with the tri-snRNP resulting in their simultaneous binding to pre-mRNA. Together, our results reveal that the BCP recruitment pathway to the spliceosome is conserved between S. cerevisiae and humans. Binding of the BCP to the tri-snRNP when ATP is limiting may result in formation of unproductive complexes that could be used to regulate splicing.
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Affiliation(s)
- Xingyang Fu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Current Address: Department of Neuroscience, Yale University, New Haven, CT, 06520, USA
| | - Aaron A. Hoskins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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2
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White DS, Dunyak BM, Vaillancourt FH, Hoskins AA. A Sequential Binding Mechanism for 5' Splice Site Recognition and Modulation for the Human U1 snRNP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590139. [PMID: 38659798 PMCID: PMC11042371 DOI: 10.1101/2024.04.18.590139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Splice site recognition is essential for defining the transcriptome. Drugs like risdiplam and branaplam change how U1 snRNP recognizes particular 5' splice sites (5'SS) and promote U1 snRNP binding and splicing at these locations. Despite the therapeutic potential of 5'SS modulators, the complexity of their interactions and snRNP substrates have precluded defining a mechanism for 5'SS modulation. We have determined a sequential binding mechanism for modulation of -1A bulged 5'SS by branaplam using a combination of ensemble kinetic measurements and colocalization single molecule spectroscopy (CoSMoS). Our mechanism establishes that U1-C protein binds reversibly to U1 snRNP, and branaplam binds to the U1 snRNP/U1-C complex only after it has engaged a -1A bulged 5'SS. Obligate orders of binding and unbinding explain how reversible branaplam interactions cause formation of long-lived U1 snRNP/5'SS complexes. Branaplam is a ribonucleoprotein, not RNA duplex alone, targeting drug whose action depends on fundamental properties of 5'SS recognition.
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Affiliation(s)
- David S. White
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI
- Present Address: Element Biosciences, San Diego, CA
| | | | | | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI
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3
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Gada KD, Kamuene JM, Kawano T, Plant LD. Imaging Membrane Proteins Using Total Internal Reflection Fluorescence Microscopy (TIRFM) in Mammalian Cells. Bio Protoc 2023; 13:e4614. [PMID: 36845531 PMCID: PMC9947549 DOI: 10.21769/bioprotoc.4614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
The cell surfaceome is of vital importance across physiology, developmental biology, and disease states alike. The precise identification of proteins and their regulatory mechanisms at the cell membrane has been challenging and is typically determined using confocal microscopy, two-photon microscopy, or total internal reflection fluorescence microscopy (TIRFM). Of these, TIRFM is the most precise, as it harnesses the generation of a spatially delimited evanescent wave at the interface of two surfaces with distinct refractive indices. The limited penetration of the evanescent wave illuminates a narrow specimen field, which facilitates the localization of fluorescently tagged proteins at the cell membrane but not inside of the cell. In addition to constraining the depth of the image, TIRFM also significantly enhances the signal-to-noise ratio, which is particularly valuable in the study of live cells. Here, we detail a protocol for micromirror TIRFM analysis of optogenetically activated protein kinase C-ε in HEK293-T cells, as well as data analysis to demonstrate the translocation of this construct to the cell-surface following optogenetic activation. Graphic abstract.
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Affiliation(s)
- Kirin D. Gada
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, USA
| | - Jordie M. Kamuene
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, USA
| | - Takeharu Kawano
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, USA
| | - Leigh D. Plant
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, USA
- Center for Drug Discovery, Northeastern University, Boston, USA
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4
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Fu X, Kaur H, Rodgers ML, Montemayor EJ, Butcher SE, Hoskins AA. Identification of transient intermediates during spliceosome activation by single molecule fluorescence microscopy. Proc Natl Acad Sci U S A 2022; 119:e2206815119. [PMID: 36417433 PMCID: PMC9860250 DOI: 10.1073/pnas.2206815119] [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: 04/23/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022] Open
Abstract
Spliceosome activation is the process of creating the catalytic site for RNA splicing and occurs de novo on each intron following spliceosome assembly. Dozens of factors bind to or are released from the activating spliceosome including the Lsm2-8 heteroheptameric ring that binds the U6 small nuclear RNA 3'-end. Lsm2-8 must be released to permit active site stabilization by the Prp19-containing complex (NineTeen Complex, NTC); however, little is known about the temporal order of events and dynamic interactions that lead up to and follow Lsm2-8 release. We have used colocalization single molecule spectroscopy (CoSMoS) to visualize Lsm2-8 dynamics during activation of Saccharomyces cerevisiae spliceosomes in vitro. Lsm2-8 is recruited as a component of the tri-snRNP and is released after integration of the Prp19-containing complex (NTC). Despite Lsm2-8 and the NTC being mutually exclusive in existing cryo-EM structures of yeast B complex spliceosomes, we identify a transient intermediate containing both ([Formula: see text]) and provide a kinetic framework for its formation and transformation during activation. Prior to [Formula: see text] assembly, the NTC rapidly and reversibly samples the spliceosome suggesting a mechanism for preventing NTC sequestration by defective spliceosomes that fail to properly activate. In complementary ensemble assays, we show that a base-pairing-dependent ternary complex can form between Lsm2-8 and U2 and U6 helix II RNAs. We propose that this interaction may play a role in formation of transient spliceosome intermediates formed during activation.
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Affiliation(s)
- Xingyang Fu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Harpreet Kaur
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Margaret L. Rodgers
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Eric J. Montemayor
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Aaron A. Hoskins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
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5
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Huisjes NM, Retzer TM, Scherr MJ, Agarwal R, Rajappa L, Safaric B, Minnen A, Duderstadt KE. Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages. eLife 2022; 11:e75899. [PMID: 36098381 PMCID: PMC9470159 DOI: 10.7554/elife.75899] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid development of new imaging approaches is generating larger and more complex datasets, revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex, multistage molecular pathways. However, few standards exist for processing these information-rich datasets, posing challenges for wider dissemination. Here, we present Mars, an open-source platform for storing and processing image-derived properties of biomolecules. Mars provides Fiji/ImageJ2 commands written in Java for common single-molecule analysis tasks using a Molecule Archive architecture that is easily adapted to complex, multistep analysis workflows. Three diverse workflows involving molecule tracking, multichannel fluorescence imaging, and force spectroscopy, demonstrate the range of analysis applications. A comprehensive graphical user interface written in JavaFX enhances biomolecule feature exploration by providing charting, tagging, region highlighting, scriptable dashboards, and interactive image views. The interoperability of ImageJ2 ensures Molecule Archives can easily be opened in multiple environments, including those written in Python using PyImageJ, for interactive scripting and visualization. Mars provides a flexible solution for reproducible analysis of image-derived properties, facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible to everyone.
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Affiliation(s)
- Nadia M Huisjes
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Thomas M Retzer
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
- Physik Department, Technische Universität MünchenGarchingGermany
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Rohit Agarwal
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
- Physik Department, Technische Universität MünchenGarchingGermany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Anita Minnen
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of BiochemistryMartinsriedGermany
- Physik Department, Technische Universität MünchenGarchingGermany
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6
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Hansen SR, White DS, Scalf M, Corrêa IR, Smith LM, Hoskins AA. Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP. eLife 2022; 11:70534. [PMID: 35959885 PMCID: PMC9436412 DOI: 10.7554/elife.70534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5' splice site (5' SS) through a combination of base pairing, protein-RNA contacts, and interactions with other splicing factors. Previous studies investigating the mechanisms of 5' SS recognition have largely been done in vivo or in cellular extracts where the U1/5' SS interaction is difficult to deconvolute from the effects of trans-acting factors or RNA structure. In this work we used colocalization single-molecule spectroscopy (CoSMoS) to elucidate the pathway of 5' SS selection by purified yeast U1 snRNP. We determined that U1 reversibly selects 5' SS in a sequence-dependent, two-step mechanism. A kinetic selection scheme enforces pairing at particular positions rather than overall duplex stability to achieve long-lived U1 binding. Our results provide a kinetic basis for how U1 may rapidly surveil nascent transcripts for 5' SS and preferentially accumulate at these sequences rather than on close cognates.
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Affiliation(s)
- Sarah R Hansen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - David S White
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
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7
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Dequeker BJH, Scherr MJ, Brandão HB, Gassler J, Powell S, Gaspar I, Flyamer IM, Lalic A, Tang W, Stocsits R, Davidson IF, Peters JM, Duderstadt KE, Mirny LA, Tachibana K. MCM complexes are barriers that restrict cohesin-mediated loop extrusion. Nature 2022; 606:197-203. [PMID: 35585235 PMCID: PMC9159944 DOI: 10.1038/s41586-022-04730-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/06/2022] [Indexed: 12/23/2022]
Abstract
Eukaryotic genomes are compacted into loops and topologically associating domains (TADs)1-3, which contribute to transcription, recombination and genomic stability4,5. Cohesin extrudes DNA into loops that are thought to lengthen until CTCF boundaries are encountered6-12. Little is known about whether loop extrusion is impeded by DNA-bound machines. Here we show that the minichromosome maintenance (MCM) complex is a barrier that restricts loop extrusion in G1 phase. Single-nucleus Hi-C (high-resolution chromosome conformation capture) of mouse zygotes reveals that MCM loading reduces CTCF-anchored loops and decreases TAD boundary insulation, which suggests that loop extrusion is impeded before reaching CTCF. This effect extends to HCT116 cells, in which MCMs affect the number of CTCF-anchored loops and gene expression. Simulations suggest that MCMs are abundant, randomly positioned and partially permeable barriers. Single-molecule imaging shows that MCMs are physical barriers that frequently constrain cohesin translocation in vitro. Notably, chimeric yeast MCMs that contain a cohesin-interaction motif from human MCM3 induce cohesin pausing, indicating that MCMs are 'active' barriers with binding sites. These findings raise the possibility that cohesin can arrive by loop extrusion at MCMs, which determine the genomic sites at which sister chromatid cohesion is established. On the basis of in vivo, in silico and in vitro data, we conclude that distinct loop extrusion barriers shape the three-dimensional genome.
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Affiliation(s)
- Bart J H Dequeker
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Hugo B Brandão
- Harvard Program in Biophysics, Harvard University, Cambridge, MA, USA
- Illumina Inc., San Diego, CA, USA
| | - Johanna Gassler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Sean Powell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Imre Gaspar
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Ilya M Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, UK
| | - Aleksandar Lalic
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Roman Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany.
- Department of Physics, Technical University of Munich, Garching, Germany.
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
| | - Kikuë Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Martinsried, Germany.
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8
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Scherr MJ, Wahab SA, Remus D, Duderstadt KE. Mobile origin-licensing factors confer resistance to conflicts with RNA polymerase. Cell Rep 2022; 38:110531. [PMID: 35320708 PMCID: PMC8961423 DOI: 10.1016/j.celrep.2022.110531] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 12/10/2021] [Accepted: 02/23/2022] [Indexed: 12/30/2022] Open
Abstract
Fundamental to our understanding of chromosome duplication is the idea that replication origins function both as sites where MCM helicases are loaded during the G1 phase and where synthesis begins in S phase. However, the temporal delay between phases exposes the replisome assembly pathway to potential disruption prior to replication. Using multicolor, single-molecule imaging, we systematically study the consequences of encounters between actively transcribing RNA polymerases (RNAPs) and replication initiation intermediates in the context of chromatin. We demonstrate that RNAP can push multiple licensed MCM helicases over long distances with nucleosomes ejected or displaced. Unexpectedly, we observe that MCM helicase loading intermediates also can be repositioned by RNAP and continue origin licensing after encounters with RNAP, providing a web of alternative origin specification pathways. Taken together, our observations reveal a surprising mobility in origin-licensing factors that confers resistance to the complex challenges posed by diverse obstacles encountered on chromosomes.
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Affiliation(s)
- Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Syafiq Abd Wahab
- Memorial Sloan Kettering Cancer Center, Molecular Biology Program, 1275 York Avenue, New York, NY 10065, USA
| | - Dirk Remus
- Memorial Sloan Kettering Cancer Center, Molecular Biology Program, 1275 York Avenue, New York, NY 10065, USA
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Physik Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany.
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9
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Ordabayev YA, Friedman LJ, Gelles J, Theobald DL. Bayesian machine learning analysis of single-molecule fluorescence colocalization images. eLife 2022; 11:73860. [PMID: 35319463 PMCID: PMC9183235 DOI: 10.7554/elife.73860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/19/2022] [Indexed: 01/07/2023] Open
Abstract
Multi-wavelength single-molecule fluorescence colocalization (CoSMoS) methods allow elucidation of complex biochemical reaction mechanisms. However, analysis of CoSMoS data is intrinsically challenging because of low image signal-to-noise ratios, non-specific surface binding of the fluorescent molecules, and analysis methods that require subjective inputs to achieve accurate results. Here, we use Bayesian probabilistic programming to implement Tapqir, an unsupervised machine learning method that incorporates a holistic, physics-based causal model of CoSMoS data. This method accounts for uncertainties in image analysis due to photon and camera noise, optical non-uniformities, non-specific binding, and spot detection. Rather than merely producing a binary 'spot/no spot' classification of unspecified reliability, Tapqir objectively assigns spot classification probabilities that allow accurate downstream analysis of molecular dynamics, thermodynamics, and kinetics. We both quantitatively validate Tapqir performance against simulated CoSMoS image data with known properties and also demonstrate that it implements fully objective, automated analysis of experiment-derived data sets with a wide range of signal, noise, and non-specific binding characteristics.
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Affiliation(s)
| | - Larry J Friedman
- Department of Biochemistry, Brandeis UniversityWalthamUnited States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis UniversityWalthamUnited States
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10
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Patel VR, Salinas AM, Qi D, Gupta S, Sidote DJ, Goldschen-Ohm MP. Single-molecule imaging with cell-derived nanovesicles reveals early binding dynamics at a cyclic nucleotide-gated ion channel. Nat Commun 2021; 12:6459. [PMID: 34753946 PMCID: PMC8578382 DOI: 10.1038/s41467-021-26816-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/21/2021] [Indexed: 12/05/2022] Open
Abstract
Ligand binding to membrane proteins is critical for many biological signaling processes. However, individual binding events are rarely directly observed, and their asynchronous dynamics are occluded in ensemble-averaged measures. For membrane proteins, single-molecule approaches that resolve these dynamics are challenged by dysfunction in non-native lipid environments, lack of access to intracellular sites, and costly sample preparation. Here, we introduce an approach combining cell-derived nanovesicles, microfluidics, and single-molecule fluorescence colocalization microscopy to track individual binding events at a cyclic nucleotide-gated TAX-4 ion channel critical for sensory transduction. Our observations reveal dynamics of both nucleotide binding and a subsequent conformational change likely preceding pore opening. Kinetic modeling suggests that binding of the second ligand is either independent of the first ligand or exhibits up to ~10-fold positive binding cooperativity. This approach is broadly applicable to studies of binding dynamics for proteins with extracellular or intracellular domains in native cell membrane.
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Affiliation(s)
- Vishal R Patel
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
- Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Arturo M Salinas
- Department of Physics, The University of Texas at Austin, Austin, TX, USA
| | - Darong Qi
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - Shipra Gupta
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - David J Sidote
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
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11
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Lei KH, Yang HL, Chang HY, Yeh HY, Nguyen DD, Lee TY, Lyu X, Chastain M, Chai W, Li HW, Chi P. Crosstalk between CST and RPA regulates RAD51 activity during replication stress. Nat Commun 2021; 12:6412. [PMID: 34741010 PMCID: PMC8571288 DOI: 10.1038/s41467-021-26624-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
Replication stress causes replication fork stalling, resulting in an accumulation of single-stranded DNA (ssDNA). Replication protein A (RPA) and CTC1-STN1-TEN1 (CST) complex bind ssDNA and are found at stalled forks, where they regulate RAD51 recruitment and foci formation in vivo. Here, we investigate crosstalk between RPA, CST, and RAD51. We show that CST and RPA localize in close proximity in cells. Although CST stably binds to ssDNA with a high affinity at low ionic strength, the interaction becomes more dynamic and enables facilitated dissociation at high ionic strength. CST can coexist with RPA on the same ssDNA and target RAD51 to RPA-coated ssDNA. Notably, whereas RPA-coated ssDNA inhibits RAD51 activity, RAD51 can assemble a functional filament and exhibit strand-exchange activity on CST-coated ssDNA at high ionic strength. Our findings provide mechanistic insights into how CST targets and tethers RAD51 to RPA-coated ssDNA in response to replication stress.
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Affiliation(s)
- Kai-Hang Lei
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Han-Lin Yang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Dinh Duc Nguyen
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Tzu-Yu Lee
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Xinxing Lyu
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Megan Chastain
- Office of Research, Washington State University, Spokane, WA, USA
| | - Weihang Chai
- Department of Cancer Biology, Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan. .,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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12
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Meng X, Kukura P, Faez S. Sensing force and charge at the nanoscale with a single-molecule tether. NANOSCALE 2021; 13:12687-12696. [PMID: 34477619 PMCID: PMC8319944 DOI: 10.1039/d1nr01970h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Measuring the electrophoretic mobility of molecules is a powerful experimental approach for investigating biomolecular processes. A frequent challenge in the context of single-particle measurements is throughput, limiting the obtainable statistics. Here, we present a molecular force sensor and charge detector based on parallelised imaging and tracking of tethered double-stranded DNA functionalised with charged nanoparticles interacting with an externally applied electric field. Tracking the position of the tethered particle with simultaneous nanometre precision and microsecond temporal resolution allows us to detect and quantify the electrophoretic force down to the sub-piconewton scale. Furthermore, we demonstrate that this approach is suitable for detecting changes to the particle charge state, as induced by the addition of charged biomolecules or changes to pH. Our approach provides an alternative route to studying structural and charge dynamics at the single molecule level.
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Affiliation(s)
- Xuanhui Meng
- Physical and Theoretical Chemistry Laboratory, University of OxfordSouth Parks RoadOX1 3QZ OxfordUK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, University of OxfordSouth Parks RoadOX1 3QZ OxfordUK
| | - Sanli Faez
- Nanophotonics, Debye Institute for Nanomaterials Research, Utrecht UniversityNLThe Netherlands
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13
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Lee TY, Li YC, Lin MG, Hsiao CD, Li HW. Single-molecule binding characterization of primosomal protein PriA involved in replication restart. Phys Chem Chem Phys 2021; 23:13745-13751. [PMID: 34159970 DOI: 10.1039/d1cp00638j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA damage leads to stalled or collapsed replication forks. Replication restart primosomes re-initiate DNA synthesis at these stalled or collapsed DNA replication forks, which is important for bacterial survival. Primosomal protein PriA specifically recognizes the DNA fork structure and recruits other primosomal proteins to load the replicative helicase, in order to re-establish the replication fork. PriA binding on DNA is the first step to restart replication forks for proper DNA repair. Using a single-molecule fluorescence colocalization experiment, we measured the thermodynamic and real-time kinetic properties of fluorescence-labeled Gram-positive bacteria Geobacillus stearothermophilus PriA binding on DNA forks. We showed that PriA preferentially binds to a DNA fork structure with a fully duplexed leading strand at sub-nanomolar affinity (Kd = 268 ± 99 pM). PriA binds dynamically, and its association and dissociation rate constants can be determined using the appearance and disappearance of the fluorescence signal. In addition, we showed that PriA binds to DNA forks as a monomer using photobleaching step counting. This information offers a molecular basis essential for understanding the mechanism of replication restart.
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Affiliation(s)
- Tzu-Yu Lee
- Department of Chemistry, National Taiwan University, Taiwan.
| | - Yi-Ching Li
- Institute of Molecular Biology, Academia Sinica, Taiwan.
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taiwan.
| | | | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taiwan.
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14
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Ningoo M, Plant LD, Greka A, Logothetis DE. PIP 2 regulation of TRPC5 channel activation and desensitization. J Biol Chem 2021; 296:100726. [PMID: 33933453 PMCID: PMC8191310 DOI: 10.1016/j.jbc.2021.100726] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 10/27/2022] Open
Abstract
Transient receptor potential canonical type 5 (TRPC5) ion channels are expressed in the brain and kidney and have been identified as promising therapeutic targets whose selective inhibition can protect against diseases driven by a leaky kidney filter, such as focal segmental glomerular sclerosis. TRPC5 channels are activated not only by elevated levels of extracellular Ca2+or lanthanide ions but also by G protein (Gq/11) stimulation. Phosphatidylinositol 4,5-bisphosphate (PIP2) hydrolysis by phospholipase C enzymes leads to PKC-mediated phosphorylation of TRPC5 channels and their subsequent desensitization. However, the roles of PIP2 in activation and maintenance of TRPC5 channel activity via its hydrolysis product diacyl glycerol (DAG), as well as the mechanism of desensitization of TRPC5 activity by DAG-stimulated PKC activity, remain unclear. Here, we designed experiments to distinguish between the processes underlying channel activation and inhibition. Employing whole-cell patch-clamp, we used an optogenetic tool to dephosphorylate PIP2 and assess channel-PIP2 interactions influenced by activators, such as DAG, or inhibitors, such as PKC phosphorylation. Using total internal reflection microscopy, we assessed channel cell surface density. We show that PIP2 controls both the PKC-mediated inhibition and the DAG- and lanthanide-mediated activation of TRPC5 currents via control of gating rather than channel cell surface density. These mechanistic insights promise to aid in the development of more selective and precise inhibitors to block TRPC5 channel activity and illuminate new opportunities for targeted therapies for a group of chronic kidney diseases for which there is currently a great unmet need.
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Affiliation(s)
- Mehek Ningoo
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Leigh D Plant
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, USA; Center for Drug Discovery, Northeastern University, Boston, Massachusetts, USA
| | - Anna Greka
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Diomedes E Logothetis
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, Massachusetts, USA; Center for Drug Discovery, Northeastern University, Boston, Massachusetts, USA; Department of Chemistry and Chemical Biology, College of Science, Northeastern University, Boston, Massachusetts, USA.
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15
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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16
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Li T, Li Z, Deans EE, Mittler E, Liu M, Chandran K, Ivanovic T. The shape of pleomorphic virions determines resistance to cell-entry pressure. Nat Microbiol 2021; 6:617-629. [PMID: 33737748 DOI: 10.1038/s41564-021-00877-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/10/2021] [Indexed: 11/09/2022]
Abstract
Many enveloped animal viruses produce a variety of particle shapes, ranging from small spherical to long filamentous types. Characterization of how the shape of the virion affects infectivity has been difficult because the shape is only partially genetically encoded, and most pleomorphic virus structures have no selective advantage in vitro. Here, we apply virus fractionation using low-force sedimentation, as well as antibody neutralization coupled with RNAScope, single-particle membrane fusion experiments and stochastic simulations to evaluate the effects of differently shaped influenza A viruses and influenza viruses pseudotyped with Ebola glycoprotein on the infection of cells. Our results reveal that the shape of the virus particles determines the probability of both virus attachment and membrane fusion when viral glycoprotein activity is compromised. The larger contact interface between a cell and a larger particle offers a greater probability that several active glycoproteins are adjacent to each other and can cooperate to induce membrane merger. Particles with a length of tens of micrometres can fuse even when 95% of the glycoproteins are inactivated. We hypothesize that non-genetically encoded variable particle shapes enable pleomorphic viruses to overcome selective pressure and may enable adaptation to infection of cells by emerging viruses such as Ebola. Our results suggest that therapeutics targeting filamentous virus particles could overcome antiviral drug resistance and immune evasion in pleomorphic viruses.
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Affiliation(s)
- Tian Li
- Biochemistry Department, Brandeis University, Waltham, MA, USA
| | - Zhenyu Li
- Biochemistry Department, Brandeis University, Waltham, MA, USA
| | - Erin E Deans
- Biochemistry Department, Brandeis University, Waltham, MA, USA
| | - Eva Mittler
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Meisui Liu
- Biochemistry Department, Brandeis University, Waltham, MA, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Tijana Ivanovic
- Biochemistry Department, Brandeis University, Waltham, MA, USA.
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17
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Wang W, Liu D, Gu M, Han P, Xiao M. Generation of a sub-diffracted Bessel beam via diffraction interference in a combined amplitude structure. OPTICS EXPRESS 2021; 29:597-603. [PMID: 33726292 DOI: 10.1364/oe.410360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
We have theoretically investigated the use of a simple combined amplitude structure to produce a sub-diffracted Bessel beam via diffraction interference. This powerful structure is composed of a spiral slit and radial grating. When a vortex beam illuminates this combined amplitude structure, a subwavelength Bessel beam with a size of 0.39λ and a long working distance of approximately 100 µm is numerically realized. By tailoring the parameters of the spiral slit, we can obtain a longer sub-diffracted Bessel beam. Moreover, the observed Bessel beam has low-energy side-lobes. The peculiar features of our theoretically generated Bessel beam have numerous potential applications, such as in nanoparticles manipulation, super-resolution imaging, and lithography.
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18
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Haraszti RA, Braun JE. Comparative Colocalization Single-Molecule Spectroscopy (CoSMoS) with Multiple RNA Species. Methods Mol Biol 2020; 2113:23-29. [PMID: 32006305 DOI: 10.1007/978-1-0716-0278-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Colocalization single-molecule spectroscopy (CoSMoS) allows studying RNA-protein complexes in the full complexity of their cellular environment at single-molecule resolution. Conventionally, the interaction between a single RNA species and multiple proteins is monitored in real time. However, comparing interactions of the same proteins with different RNA species in the same cell extract promises unique insights into RNA biology. Here, we describe an approach to monitor multiple RNA species simultaneously to enable direct comparison. This approach represents a technological development to avoid conventional inter-experiment comparisons.
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Affiliation(s)
- Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Joerg E Braun
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
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19
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Fujita K, Ohmachi M, Ikezaki K, Yanagida T, Iwaki M. Direct visualization of human myosin II force generation using DNA origami-based thick filaments. Commun Biol 2019; 2:437. [PMID: 31799438 PMCID: PMC6881340 DOI: 10.1038/s42003-019-0683-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/07/2019] [Indexed: 11/08/2022] Open
Abstract
The sarcomere, the minimal mechanical unit of muscle, is composed of myosins, which self-assemble into thick filaments that interact with actin-based thin filaments in a highly-structured lattice. This complex imposes a geometric restriction on myosin in force generation. However, how single myosins generate force within the restriction remains elusive and conventional synthetic filaments do not recapitulate the symmetric bipolar filaments in sarcomeres. Here we engineered thick filaments using DNA origami that incorporate human muscle myosin to directly visualize the motion of the heads during force generation in a restricted space. We found that when the head diffuses, it weakly interacts with actin filaments and then strongly binds preferentially to the forward region as a Brownian ratchet. Upon strong binding, the two-step lever-arm swing dominantly halts at the first step and occasionally reverses direction. Our results illustrate the usefulness of our DNA origami-based assay system to dissect the mechanistic details of motor proteins.
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Affiliation(s)
- Keisuke Fujita
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Masashi Ohmachi
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
| | | | - Toshio Yanagida
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Center for Information and Neural Networks, NICT, Osaka, Japan
| | - Mitsuhiro Iwaki
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- AMED-PRIME, Japan Agency for Medical Research and Development, Tokyo, Japan
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20
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Abstract
This chapter describes methods for high-speed, unloaded, in vitro single-molecule kinesin tracking experiments. Instructions are presented for constructing a total internal reflection dark-field microscope (TIRDFM) and labeling motors with gold nanoparticles. An AMP-PNP unlocking assay is introduced as a specialized means of capturing processive events in a reduced field of view. Finally, step-finding tools for analyzing high frame-rate tracking data are described.
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21
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Combined smFRET and NMR analysis of riboswitch structural dynamics. Methods 2019; 153:22-34. [DOI: 10.1016/j.ymeth.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022] Open
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22
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Kaur H, Jamalidinan F, Condon SGF, Senes A, Hoskins AA. Analysis of spliceosome dynamics by maximum likelihood fitting of dwell time distributions. Methods 2018; 153:13-21. [PMID: 30472247 DOI: 10.1016/j.ymeth.2018.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 11/17/2022] Open
Abstract
Colocalization single-molecule methods can provide a wealth of information concerning the ordering and dynamics of biomolecule assembly. These have been used extensively to study the pathways of spliceosome assembly in vitro. Key to these experiments is the measurement of binding times-either the dwell times of a multi-molecular interaction or times in between binding events. By analyzing hundreds of these times, many new insights into the kinetic pathways governing spliceosome assembly have been obtained. Collections of binding times are often plotted as histograms and can be fit to kinetic models using a variety of methods. Here, we describe the use of maximum likelihood methods to fit dwell time distributions without binning. In addition, we discuss several aspects of analyzing these distributions with histograms and pitfalls that can be encountered if improperly binned histograms are used. We have automated several aspects of maximum likelihood fitting of dwell time distributions in the AGATHA software package.
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Affiliation(s)
- Harpreet Kaur
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fatemehsadat Jamalidinan
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samson G F Condon
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alessandro Senes
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA.
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23
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Portman JR, Strick TR. Transcription-Coupled Repair and Complex Biology. J Mol Biol 2018; 430:4496-4512. [DOI: 10.1016/j.jmb.2018.04.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 10/24/2022]
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24
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Kilic S, Felekyan S, Doroshenko O, Boichenko I, Dimura M, Vardanyan H, Bryan LC, Arya G, Seidel CAM, Fierz B. Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α. Nat Commun 2018; 9:235. [PMID: 29339721 PMCID: PMC5770380 DOI: 10.1038/s41467-017-02619-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/11/2017] [Indexed: 01/17/2023] Open
Abstract
The dynamic architecture of chromatin fibers, a key determinant of genome regulation, is poorly understood. Here, we employ multimodal single-molecule Förster resonance energy transfer studies to reveal structural states and their interconversion kinetics in chromatin fibers. We show that nucleosomes engage in short-lived (micro- to milliseconds) stacking interactions with one of their neighbors. This results in discrete tetranucleosome units with distinct interaction registers that interconvert within hundreds of milliseconds. Additionally, we find that dynamic chromatin architecture is modulated by the multivalent architectural protein heterochromatin protein 1α (HP1α), which engages methylated histone tails and thereby transiently stabilizes stacked nucleosomes. This compacted state nevertheless remains dynamic, exhibiting fluctuations on the timescale of HP1α residence times. Overall, this study reveals that exposure of internal DNA sites and nucleosome surfaces in chromatin fibers is governed by an intrinsic dynamic hierarchy from micro- to milliseconds, allowing the gene regulation machinery to access compact chromatin. Chromatin fibers undergo continuous structural rearrangements but their dynamic architecture is poorly understood. Here, the authors use single-molecule FRET to determine the structural states and interconversion kinetics of chromatin fibers, monitoring their effector protein-dependent dynamic motions.
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Affiliation(s)
- Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zurich, 8057, Zurich, Switzerland
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Olga Doroshenko
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Iuliia Boichenko
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Mykola Dimura
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hayk Vardanyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Louise C Bryan
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Gaurav Arya
- Pratt School of Engineering, Duke University, 144 Hudson Hall, Box 90300, Durham, NC, 27708, USA
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
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25
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Seol Y, Neuman KC. Combined Magnetic Tweezers and Micro-mirror Total Internal Reflection Fluorescence Microscope for Single-Molecule Manipulation and Visualization. Methods Mol Biol 2018; 1665:297-316. [PMID: 28940076 PMCID: PMC5672814 DOI: 10.1007/978-1-4939-7271-5_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Magnetic tweezers is a versatile yet simple single-molecule manipulation technique that has been used to study a broad range of nucleic acids and nucleic acid-based molecular motors. In this chapter, we combine micro-mirror-based total internal reflection microscopy with a magnetic tweezers instrument, permitting simultaneous single-molecule visualization and mechanical manipulation. We provide a simple method to calibrate the evanescent wave penetration depth via supercoiling of DNA with a fluorescent nanodiamond-labeled magnetic bead and a complementary method employing a surface-immobilized fluorescent nanodiamond.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Room 3517, 50 South Drive, Bethesda, 20892, MD, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Room 3517, 50 South Drive, Bethesda, 20892, MD, USA.
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26
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Abstract
Human RAD51 promotes accurate DNA repair by homologous recombination and is involved in protection and repair of damaged DNA replication forks. The active species of RAD51 and related recombinases in all organisms is a nucleoprotein filament assembled on single-stranded DNA (ssDNA). The formation of a nucleoprotein filament competent for the recombination reaction, or for DNA replication support, is a delicate and strictly regulated process, which occurs through filament nucleation followed by filament extension. The rates of these two phases of filament formation define the capacity of RAD51 to compete with the ssDNA-binding protein RPA, as well as the lengths of the resulting filament segments. Single-molecule approaches can provide a wealth of quantitative information on the kinetics of RAD51 nucleoprotein filament assembly, internal dynamics, and disassembly. In this chapter, we describe how to set up a single-molecule total internal reflection fluorescence microscopy experiment to monitor the initial steps of RAD51 nucleoprotein filament formation in real-time and at single-monomer resolution. This approach is based on the unique, stretched-ssDNA conformation within the recombinase nucleoprotein filament and follows the efficiency of Förster resonance energy transfer (EFRET) between two DNA-conjugated fluorophores. We will discuss the practical aspects of the experimental setup, extraction of the FRET trajectories, and how to analyze and interpret the data to obtain information on RAD51 nucleation kinetics, the mechanism of nucleation, and the oligomeric species involved in filament formation.
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27
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Larson JD, Hoskins AA. Dynamics and consequences of spliceosome E complex formation. eLife 2017; 6:27592. [PMID: 28829039 PMCID: PMC5779234 DOI: 10.7554/elife.27592] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/21/2017] [Indexed: 12/26/2022] Open
Abstract
The spliceosome must identify the correct splice sites (SS) and branchsite (BS) used during splicing. E complex is the earliest spliceosome precursor in which the 5' SS and BS are defined. Definition occurs by U1 small nuclear ribonucleoprotein (snRNP) binding the 5' SS and recognition of the BS by the E complex protein (ECP) branchpoint bridging protein (BBP). We have used single molecule fluorescence to study Saccharomyces cerevisiae U1 and BBP interactions with RNAs. E complex is dynamic and permits frequent redefinition of the 5' SS and BS. BBP influences U1 binding at the 5' SS by promoting long-lived complex formation. ECPs facilitate U1 association with RNAs with weak 5' SS and prevent U1 accumulation on RNAs containing hyperstabilized 5' SS. The data reveal a mechanism for how U1 binds the 5' SS and suggest that E complex harnesses this mechanism to stimulate recruitment and retention of U1 on introns. Our genes contain coded instructions for making the molecules in our bodies, but this information must be extensively processed before it can be used. The instructions from each gene are first copied into a molecule called a pre-mRNA, before a process known as splicing removes certain sections to form a mature mRNA molecule. Splicing can remove different sections of the pre-mRNA to make different mRNA molecules from the same gene depending on the current needs of the cell. Splicing is controlled by a combination of proteins and other molecules, collectively called the spliceosome. A part of the spliceosome called U1 recognizes the start of pre-mRNA sections that need to be removed, which is referred to as the five-prime splice site (or “5’ SS” for short). The attachment of U1 to such a site allows other molecules to also attach to the pre-mRNA, which eventually assemble a spliceosome. The very first steps in this process involve U1 and a set of other proteins that create what is called the “Early” or “E” complex. Although there are many molecules involved in the E complex, it was not known how they interact with each other and how this affects which splice sites are used for splicing in different cells. Using advanced microscopy, Larson and Hoskins examined individual U1 molecules from yeast cells while the molecules formed E complexes and identified two different ways U1 can bind to five-prime splice sites. One process involved U1 attaching to pre-mRNA for a short time, whilst the other involved a longer association between U1 and pre-mRNA. Sometimes U1 could also transition between the first process and the second. The results showed that other parts of the E complex affected which process was used at different sites by affecting the type or duration of U1’s attachment. All U1 particles use the same components to attach to splice sites in all pre-mRNAs, but the most used splice sites are not always those that are predicted to have the strongest attachments to U1. This work helps to reveal how other proteins involved in splicing influence this effect, altering U1’s ability to attach to pre-mRNAs to suit each new situation. This also allows cells to change gene splicing to fit different situations. Many genes in our bodies rely on splicing and understanding this process in detail could be the key to diagnosing and treating a range of different illnesses.
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Affiliation(s)
- Joshua Donald Larson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.,Biophysics Graduate Program, University of Wisconsin-Madison, Madison, United States
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.,Biophysics Graduate Program, University of Wisconsin-Madison, Madison, United States
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28
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Leisle L, Chadda R, Lueck JD, Infield DT, Galpin JD, Krishnamani V, Robertson JL, Ahern CA. Cellular encoding of Cy dyes for single-molecule imaging. eLife 2016; 5:e19088. [PMID: 27938668 PMCID: PMC5207767 DOI: 10.7554/elife.19088] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/09/2016] [Indexed: 12/20/2022] Open
Abstract
A general method is described for the site-specific genetic encoding of cyanine dyes as non-canonical amino acids (Cy-ncAAs) into proteins. The approach relies on an improved technique for nonsense suppression with in vitro misacylated orthogonal tRNA. The data show that Cy-ncAAs (based on Cy3 and Cy5) are tolerated by the eukaryotic ribosome in cell-free and whole-cell environments and can be incorporated into soluble and membrane proteins. In the context of the Xenopus laevis oocyte expression system, this technique yields ion channels with encoded Cy-ncAAs that are trafficked to the plasma membrane where they display robust function and distinct fluorescent signals as detected by TIRF microscopy. This is the first demonstration of an encoded cyanine dye as a ncAA in a eukaryotic expression system and opens the door for the analysis of proteins with single-molecule resolution in a cellular environment.
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Affiliation(s)
- Lilia Leisle
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Rahul Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - John D Lueck
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Venkatramanan Krishnamani
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Janice L Robertson
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
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29
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Chadda R, Robertson JL. Measuring Membrane Protein Dimerization Equilibrium in Lipid Bilayers by Single-Molecule Fluorescence Microscopy. Methods Enzymol 2016; 581:53-82. [PMID: 27793292 PMCID: PMC5568537 DOI: 10.1016/bs.mie.2016.08.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dimerization of membrane protein interfaces occurs during membrane protein folding and cell receptor signaling. Here, we summarize a method that allows for measurement of equilibrium dimerization reactions of membrane proteins in lipid bilayers, by measuring the Poisson distribution of subunit capture into liposomes by single-molecule photobleaching analysis. This strategy is grounded in the fact that given a comparable labeling efficiency, monomeric or dimeric forms of a membrane protein will give rise to distinctly different photobleaching probability distributions. These methods have been used to verify the dimer stoichiometry of the Fluc F- ion channel and the dimerization equilibrium constant of the ClC-ec1 Cl-/H+ antiporter in lipid bilayers. This approach can be applied to any membrane protein system provided it can be purified, fluorescently labeled in a quantitative manner, and verified to be correctly folded by functional assays, even if the structure is not yet known.
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Affiliation(s)
- R Chadda
- The University of Iowa, Iowa City, IA, United States
| | - J L Robertson
- The University of Iowa, Iowa City, IA, United States.
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30
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Hansen SR, Rodgers ML, Hoskins AA. Fluorescent Labeling of Proteins in Whole Cell Extracts for Single-Molecule Imaging. Methods Enzymol 2016; 581:83-104. [PMID: 27793294 DOI: 10.1016/bs.mie.2016.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cellular machines such as the spliceosome and ribosome can be composed of dozens of individual proteins and nucleic acids. Given this complexity, it is not surprising that many cellular activities have not yet been biochemically reconstituted. Such processes are often studied in vitro in whole cell or fractionated lysates. This presents a challenge for obtaining detailed biochemical information when the components being investigated may be only a minor component of the extract and unrelated processes may interfere with the assay. Single-molecule fluorescence microscopy methods allow particular biomolecules to be analyzed even in the complex milieu of a cell extract. This is due to the use of bright fluorophores that emit light at wavelengths at which few cellular components fluoresce, and the development of chemical biology tools for attaching these fluorophores to specific cellular proteins. Here, we describe a protocol for fluorescent labeling of endogenous, SNAP-tagged yeast proteins in whole cell extract. This method allows biochemical reactions to be followed in cell lysates in real time using colocalization single-molecule fluorescence microscopy. Labeled complexes can also be isolated from extract and characterized by SNAP tag single-molecule pull-down (SNAP-SiMPull). These approaches have proven useful for studying complex biological machines such as the spliceosome that cannot yet be reconstituted from purified components.
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Affiliation(s)
- S R Hansen
- University of Wisconsin-Madison, Madison, WI, United States
| | - M L Rodgers
- University of Wisconsin-Madison, Madison, WI, United States
| | - A A Hoskins
- University of Wisconsin-Madison, Madison, WI, United States.
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31
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Li X, Xing J, Qiu Z, He Q, Lin J. Quantification of Membrane Protein Dynamics and Interactions in Plant Cells by Fluorescence Correlation Spectroscopy. MOLECULAR PLANT 2016; 9:1229-1239. [PMID: 27381442 DOI: 10.1016/j.molp.2016.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/25/2016] [Accepted: 06/27/2016] [Indexed: 05/25/2023]
Abstract
Deciphering the dynamics of protein and lipid molecules on appropriate spatial and temporal scales may shed light on protein function and membrane organization. However, traditional bulk approaches cannot unambiguously quantify the extremely diverse mobility and interactions of proteins in living cells. Fluorescence correlation spectroscopy (FCS) is a powerful technique to describe events that occur at the single-molecule level and on the nanosecond to second timescales; therefore, FCS can provide data on the heterogeneous organization of membrane systems. FCS can also be combined with other microscopy techniques, such as super-resolution techniques. More importantly, FCS is minimally invasive, which makes it an ideal approach to detect the heterogeneous distribution and dynamics of key proteins during development. In this review, we give a brief introduction about the development of FCS and summarize the significant contributions of FCS in understanding the organization of plant cell membranes and the dynamics and interactions of membrane proteins. We also discuss the potential applications of this technique in plant biology.
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Affiliation(s)
- Xiaojuan Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jingjing Xing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 10049, China
| | - Zongbo Qiu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qihua He
- The Health Science Center, Peking University, Beijing 100191, China
| | - Jinxing Lin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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32
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DeHaven AC, Norden IS, Hoskins AA. Lights, camera, action! Capturing the spliceosome and pre-mRNA splicing with single-molecule fluorescence microscopy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:683-701. [PMID: 27198613 PMCID: PMC4990488 DOI: 10.1002/wrna.1358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/20/2016] [Accepted: 04/04/2016] [Indexed: 11/06/2022]
Abstract
The process of removing intronic sequences from a precursor to messenger RNA (pre-mRNA) to yield a mature mRNA transcript via splicing is an integral step in eukaryotic gene expression. Splicing is carried out by a cellular nanomachine called the spliceosome that is composed of RNA components and dozens of proteins. Despite decades of study, many fundamentals of spliceosome function have remained elusive. Recent developments in single-molecule fluorescence microscopy have afforded new tools to better probe the spliceosome and the complex, dynamic process of splicing by direct observation of single molecules. These cutting-edge technologies enable investigators to monitor the dynamics of specific splicing components, whole spliceosomes, and even cotranscriptional splicing within living cells. WIREs RNA 2016, 7:683-701. doi: 10.1002/wrna.1358 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alexander C. DeHaven
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Ian S. Norden
- Integrated Program in Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
| | - Aaron A. Hoskins
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706
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33
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Chadda R, Krishnamani V, Mersch K, Wong J, Brimberry M, Chadda A, Kolmakova-Partensky L, Friedman LJ, Gelles J, Robertson JL. The dimerization equilibrium of a ClC Cl(-)/H(+) antiporter in lipid bilayers. eLife 2016; 5. [PMID: 27484630 PMCID: PMC5010387 DOI: 10.7554/elife.17438] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 07/29/2016] [Indexed: 12/20/2022] Open
Abstract
Interactions between membrane protein interfaces in lipid bilayers play an important role in membrane protein folding but quantification of the strength of these interactions has been challenging. Studying dimerization of ClC-type transporters offers a new approach to the problem, as individual subunits adopt a stable and functionally verifiable fold that constrains the system to two states - monomer or dimer. Here, we use single-molecule photobleaching analysis to measure the probability of ClC-ec1 subunit capture into liposomes during extrusion of large, multilamellar membranes. The capture statistics describe a monomer to dimer transition that is dependent on the subunit/lipid mole fraction density and follows an equilibrium dimerization isotherm. This allows for the measurement of the free energy of ClC-ec1 dimerization in lipid bilayers, revealing that it is one of the strongest membrane protein complexes measured so far, and introduces it as new type of dimerization model to investigate the physical forces that drive membrane protein association in membranes.
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Affiliation(s)
- Rahul Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | | | - Kacey Mersch
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Jason Wong
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States.,Department of Natural Sciences, University of Bath, Bath, United Kingdom
| | - Marley Brimberry
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Ankita Chadda
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | | | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Janice L Robertson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
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34
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Chen GY, Mickolajczyk KJ, Hancock WO. The Kinesin-5 Chemomechanical Cycle Is Dominated by a Two-heads-bound State. J Biol Chem 2016; 291:20283-20294. [PMID: 27402829 DOI: 10.1074/jbc.m116.730697] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 12/29/2022] Open
Abstract
Single-molecule microscopy and stopped-flow kinetics assays were carried out to understand the microtubule polymerase activity of kinesin-5 (Eg5). Four lines of evidence argue that the motor primarily resides in a two-heads-bound (2HB) state. First, upon microtubule binding, dimeric Eg5 releases both bound ADPs. Second, microtubule dissociation in saturating ADP is 20-fold slower for the dimer than for the monomer. Third, ATP-triggered mant-ADP release is 5-fold faster than the stepping rate. Fourth, ATP binding is relatively fast when the motor is locked in a 2HB state. Shortening the neck-linker does not facilitate rear-head detachment, suggesting a minimal role for rear-head-gating. This 2HB state may enable Eg5 to stabilize incoming tubulin at the growing microtubule plus-end. The finding that slowly hydrolyzable ATP analogs trigger slower nucleotide release than ATP suggests that ATP hydrolysis in the bound head precedes stepping by the tethered head, leading to a mechanochemical cycle in which processivity is determined by the race between unbinding of the bound head and attachment of the tethered head.
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Affiliation(s)
- Geng-Yuan Chen
- From the Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Keith J Mickolajczyk
- From the Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
| | - William O Hancock
- From the Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
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35
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Duboc C, Graves ET, Strick TR. Simple calibration of TIR field depth using the supercoiling response of DNA. Methods 2016; 105:56-61. [PMID: 27038746 DOI: 10.1016/j.ymeth.2016.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/29/2016] [Indexed: 11/29/2022] Open
Abstract
The combination of single-molecule fluorescence and nanomanipulation techniques into a single experimental platform enables one to carry out correlative analysis of the composition and the activity of complex, multicomponent molecular systems. Here we describe implementation and calibration of such a combined system allowing simultaneous single-molecule force spectroscopy and fluorescence imaging of proteins acting on the DNA using magnetic trapping coupled with fluorescence excitation based on a Total Internal Reflection (TIR), or evanescent, field. We propose a simple and robust in situ method for calibration of the TIR field depth against the mechanical properties of nanomanipulated DNA, and which is made possible by the fact that the magnetic bead used to trap and nanomanipulate DNA and measure its conformation also exhibits autofluorescence in the TIR field. Indeed, the fact that the bead size is on the 1-micron scale does not preclude sensitive probing of an intensity field which decays exponentially on the 0.1micron-scale. We demonstrate the usefulness of this approach by mapping out TIR field depth as a function of the angle of incidence of the illuminating laser at the glass-water interface and showing that one recovers the expected theoretical relationship between field depth and angle of incidence.
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Affiliation(s)
- Camille Duboc
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - Evan T Graves
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - Terence R Strick
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France; Ecole Normale Supérieure, Institut de Biologie de l'ENS (iBENS), INSERM, CNRS, PSL Research University, Paris, France.
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36
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Ortega Arroyo J, Cole D, Kukura P. Interferometric scattering microscopy and its combination with single-molecule fluorescence imaging. Nat Protoc 2016; 11:617-33. [DOI: 10.1038/nprot.2016.022] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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37
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Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy. Methods Enzymol 2016; 581:105-145. [PMID: 27793278 PMCID: PMC5403009 DOI: 10.1016/bs.mie.2016.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Large, dynamic macromolecular complexes play essential roles in many cellular processes. Knowing how the components of these complexes associate with one another and undergo structural rearrangements is critical to understanding how they function. Single-molecule total internal reflection fluorescence (TIRF) microscopy is a powerful approach for addressing these fundamental issues. In this article, we first discuss single-molecule TIRF microscopes and strategies to immobilize and fluorescently label macromolecules. We then review the use of single-molecule TIRF microscopy to study the formation of binary macromolecular complexes using one-color imaging and inhibitors. We conclude with a discussion of the use of TIRF microscopy to examine the formation of higher-order (i.e., ternary) complexes using multicolor setups. The focus throughout this article is on experimental design, controls, data acquisition, and data analysis. We hope that single-molecule TIRF microscopy, which has largely been the province of specialists, will soon become as common in the tool box of biophysicists and biochemists as structural approaches have become today.
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