1
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Maffeo C, Chou HY, Aksimentiev A. Single-molecule biophysics experiments in silico: Toward a physical model of a replisome. iScience 2022; 25:104264. [PMID: 35521518 PMCID: PMC9062759 DOI: 10.1016/j.isci.2022.104264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/23/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
The interpretation of single-molecule experiments is frequently aided by computational modeling of biomolecular dynamics. The growth of computing power and ongoing validation of computational models suggest that it soon may be possible to replace some experiments outright with computational mimics. Here, we offer a blueprint for performing single-molecule studies in silico using a DNA-binding protein as a test bed. We demonstrate how atomistic simulations, typically limited to sub-millisecond durations and zeptoliter volumes, can guide development of a coarse-grained model for use in simulations that mimic single-molecule experiments. We apply the model to recapitulate, in silico, force-extension characterization of protein binding to single-stranded DNA and protein and DNA replacement assays, providing a detailed portrait of the underlying mechanics. Finally, we use the model to simulate the trombone loop of a replication fork, a large complex of proteins and DNA. Coarse-grained model derived from all-atom simulation recapitulates experiments Model reproduces the elastic response to force and exchange dynamics Model reveals structure of intermediate states usually inaccessible to experiment Model applied to viral replisome with trombone loop containing tens of SSB proteins
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Matthews Avenue, Urbana, 61801 IL, USA
| | - Han-Yi Chou
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 61801 IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Matthews Avenue, Urbana, 61801 IL, USA
- Corresponding author
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2
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Luettmer-Strathmann J, Adeli Koudehi M, Paudyal N. Five-Site Model for Brownian Dynamics Simulations of a Molecular Walker in Three Dimensions. J Phys Chem B 2021; 125:4726-4733. [PMID: 33909422 DOI: 10.1021/acs.jpcb.1c02114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Motor proteins play an important role in many biological processes and have inspired the development of synthetic analogues. Molecular walkers, such as kinesin, dynein, and myosin V, fulfill a diverse set of functions including transporting cargo along tracks, pulling molecules through membranes, and deforming fibers. The complexity of molecular motors and their environment makes it difficult to model the detailed dynamics of molecular walkers over long time scales. In this work, we present a simple, three-dimensional model for a molecular walker on a bead-spring substrate. The walker is represented by five spherically symmetric particles that interact through common intermolecular potentials and can be simulated efficiently in Brownian dynamics simulations. The movement of motor protein walkers entails energy conversion through ATP hydrolysis while artificial motors typically rely on a local conversion of energy supplied through external fields. We model energy conversion through rate equations for mechanochemical states that couple positional and chemical degrees of freedom and determine the walker conformation through interaction potential parameters. We perform Brownian dynamics simulations for two scenarios: In the first, the model walker transports cargo by walking on a substrate whose ends are fixed. In the second, a tethered motor pulls a mobile substrate chain against a variable force. We measure relative displacements and determine the effects of cargo size and retarding force on the efficiency of the walker. We find that, while the efficiency of our model walker is less than for the biological system, our simulations reproduce trends observed in single-molecule experiments on kinesin. In addition, the model and simulation method presented here can be readily adapted to biological and synthetic systems with multiple walkers.
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Affiliation(s)
- Jutta Luettmer-Strathmann
- Department of Physics, The University of Akron, Akron, Ohio 44325-4001, United States.,Department of Chemistry, The University of Akron, Akron, Ohio 44325-4001, United States
| | - Maral Adeli Koudehi
- Department of Physics, The University of Akron, Akron, Ohio 44325-4001, United States
| | - Nabina Paudyal
- Department of Physics, The University of Akron, Akron, Ohio 44325-4001, United States
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3
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Paul T, Ha T, Myong S. Regeneration of PEG slide for multiple rounds of single-molecule measurements. Biophys J 2021; 120:1788-1799. [PMID: 33675764 DOI: 10.1016/j.bpj.2021.02.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022] Open
Abstract
Single-molecule fluorescence detection of protein and other biomolecules requires a polyethylene glycol (PEG)-passivated surface. Individual channels on a PEG-passivated slide are typically used only a few times, limiting the number of experiments per slide. Here, we report several strategies for regenerating PEG surfaces for multiple rounds of experiments. First, we show regeneration of DNA- or RNA-tethered surfaces by washing out the bound protein by 0.1% sodium dodecyl sulfate, which is significantly more effective than 6 M urea, 6 M GdmCl, or 100 μM proteinase K. Strikingly, 10 consecutive experiments in five different systems produced indistinguishable results both in molecule count and protein activity. Second, duplexed DNA unwound by helicase or denatured by 50 mM NaOH was reannealed with a complementary strand to regenerate the duplexed substrate with an exceptionally high recovery rate. Third, the biotin-PEG layer was regenerated by using 7 M NaOH to strip off NeutrAvidin, which can be reapplied for additional experiments. We demonstrate five cycles of regenerating antibody immobilized surface by which three different protein activity was measured. Altogether, our methods represent reliable and reproducible yet simple and rapid strategies that will enhance the efficiency of single-molecule experiments.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois; Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, Maryland
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois.
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4
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Single-Molecule FRET Detection of Sub-Nanometer Distance Changes in the Range below a 3-Nanometer Scale. BIOSENSORS-BASEL 2020; 10:bios10110168. [PMID: 33171642 PMCID: PMC7695202 DOI: 10.3390/bios10110168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/24/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
Single-molecule fluorescence energy transfer (FRET) detection has become a key technique to monitor intra- and intermolecular distance changes in biological processes. As the sensitive detection range of conventional FRET pairs is limited to 3-8 nm, complement probes are necessary for extending this typical working range. Here, we realized a single-molecule FRET assay for a short distance range of below 3 nm by using a Cy2-Cy7 pair having extremely small spectral overlap. Using two DNA duplexes with a small difference in the labeling position, we demonstrated that our assay can observe subtle changes at a short distance range. High sensitivity in the range of 1-3 nm and compatibility with the conventional FRET assay make this approach useful for understanding dynamics at a short distance.
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5
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Single-Molecule Mechanics in Ligand Concentration Gradient. MICROMACHINES 2020; 11:mi11020212. [PMID: 32093081 PMCID: PMC7074681 DOI: 10.3390/mi11020212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/09/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023]
Abstract
Single-molecule experiments provide unique insights into the mechanisms of biomolecular phenomena. However, because varying the concentration of a solute usually requires the exchange of the entire solution around the molecule, ligand-concentration-dependent measurements on the same molecule pose a challenge. In the present work we exploited the fact that a diffusion-dependent concentration gradient arises in a laminar-flow microfluidic device, which may be utilized for controlling the concentration of the ligand that the mechanically manipulated single molecule is exposed to. We tested this experimental approach by exposing a λ-phage dsDNA molecule, held with a double-trap optical tweezers instrument, to diffusionally-controlled concentrations of SYTOX Orange (SxO) and tetrakis(4-N-methyl)pyridyl-porphyrin (TMPYP). We demonstrate that the experimental design allows access to transient-kinetic, equilibrium and ligand-concentration-dependent mechanical experiments on the very same single molecule.
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6
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Sudhakar S, Jachowski TJ, Kittelberger M, Maqbool A, Hermsdorf GL, Abdosamadi MK, Schäffer E. Supported Solid Lipid Bilayers as a Platform for Single-Molecule Force Measurements. NANO LETTERS 2019; 19:8877-8886. [PMID: 31746618 DOI: 10.1021/acs.nanolett.9b03761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biocompatible surfaces are important for basic and applied research in life science with experiments ranging from the organismal to the single-molecule level. For the latter, examples include the translocation of kinesin motor proteins along microtubule cytoskeletal filaments or the study of DNA-protein interactions. Such experiments often employ single-molecule fluorescence or force microscopy. In particular for force measurements, a key requirement is to prevent nonspecific interactions of biomolecules and force probes with the surface, while providing specific attachments that can sustain loads. Common approaches to reduce nonspecific interactions include supported lipid bilayers or PEGylated surfaces. However, fluid lipid bilayers do not support loads and PEGylation may require harsh chemical surface treatments and have limited reproducibility. Here, we developed and applied a supported solid lipid bilayer (SSLB) as a platform for specific, load bearing attachments with minimal nonspecific interactions. Apart from single-molecule fluorescence measurements, anchoring molecules to lipids in the solid phase enabled us to perform force measurements of molecular motors and overstretch DNA. Furthermore, using a heating laser, we could switch the SSLB to its fluid state allowing for manipulation of anchoring points. The assay had little nonspecific interactions, was robust, reproducible, and time-efficient, and required less hazardous and toxic chemicals for preparation. In the long term, we expect that SSLBs can be widely employed for single-molecule fluorescence microscopy, force spectroscopy, and cellular assays in mechanobiology.
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Affiliation(s)
- Swathi Sudhakar
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | - Tobias Jörg Jachowski
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | - Michael Kittelberger
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | - Ammara Maqbool
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | - Gero Lutz Hermsdorf
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | | | - Erik Schäffer
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
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7
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Tutkus M, Rakickas T, Kopu Stas A, Ivanovaitė ŠN, Venckus O, Navikas V, Zaremba M, Manakova E, Valiokas RN. Fixed DNA Molecule Arrays for High-Throughput Single DNA-Protein Interaction Studies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5921-5930. [PMID: 30955328 DOI: 10.1021/acs.langmuir.8b03424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The DNA Curtains assay is a recently developed experimental platform for protein-DNA interaction studies at the single-molecule level that is based on anchoring and alignment of DNA fragments. The DNA Curtains so far have been made by using chromium barriers and fluid lipid bilayer membranes, which makes such a specialized assay technically challenging and relatively unstable. Herein, we report on an alternative strategy for DNA arraying for analysis of individual DNA-protein interactions. It relies on stable DNA tethering onto nanopatterned protein templates via high affinity molecular recognition. We describe fabrication of streptavidin templates (line features as narrow as 200 nm) onto modified glass coverslips by combining surface chemistry, atomic force microscopy (AFM), and soft lithography techniques with affinity-driven assembly. We have employed such chips for arraying single- and double-tethered DNA strands, and we characterized the obtained molecular architecture: we evaluated the structural characteristics and specific versus nonspecific binding of fluorescence-labeled DNA using AFM and total internal reflection fluorescence microscopy. We demonstrate the feasibility of our DNA molecule arrays for short single-tethered as well as for lambda single- and double-tethered DNA. The latter type of arrays proved very suitable for localization of single DNA-protein interactions employing restriction endonucleases. The presented molecular architecture and facile method of fabrication of our nanoscale platform does not require clean room equipment, and it offers advanced functional studies of DNA machineries and the development of future nanodevices.
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Affiliation(s)
| | | | - Aurimas Kopu Stas
- Vilnius University, Life Sciences Center, Institute of Biotechnology , Sauletekio av. 7 , Vilnius LT-10257 , Lithuania
| | | | | | | | - Mindaugas Zaremba
- Vilnius University, Life Sciences Center, Institute of Biotechnology , Sauletekio av. 7 , Vilnius LT-10257 , Lithuania
| | - Elena Manakova
- Vilnius University, Life Sciences Center, Institute of Biotechnology , Sauletekio av. 7 , Vilnius LT-10257 , Lithuania
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8
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Eilert T, Kallis E, Nagy J, Röcker C, Michaelis J. Complete Kinetic Theory of FRET. J Phys Chem B 2018; 122:11677-11694. [DOI: 10.1021/acs.jpcb.8b07719] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tobias Eilert
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - Eleni Kallis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - Julia Nagy
- Center for Translational Imaging (MoMAN), Ulm University, Albert-Einstein-Allee 11, Ulm 89091, Germany
| | - Carlheinz Röcker
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
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9
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Lee TC, Moran CR, Cistrone PA, Dawson PE, Deniz AA. Site-Specific Three-Color Labeling of α-Synuclein via Conjugation to Uniquely Reactive Cysteines during Assembly by Native Chemical Ligation. Cell Chem Biol 2018; 25:797-801.e4. [PMID: 29681525 DOI: 10.1016/j.chembiol.2018.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/09/2017] [Accepted: 03/22/2018] [Indexed: 12/15/2022]
Abstract
Single-molecule fluorescence is widely used to study conformational complexity in proteins, and has proven especially valuable with intrinsically disordered proteins (IDPs). Protein studies using dual-color single-molecule Förster resonance energy transfer (smFRET) are now quite common, but many could benefit from simultaneous measurement of multiple distances through multi-color labeling. Such studies, however, have suffered from limitations in site-specific incorporation of more than two dyes per polypeptide. Here we present a fully site-specific three-color labeling scheme for α-synuclein, an IDP with important putative functions and links to Parkinson disease. The convergent synthesis combines native chemical ligation with regiospecific cysteine protection of expressed protein fragments to permit highly controlled labeling via standard cysteine-maleimide chemistry, enabling more global smFRET studies. Furthermore, this modular approach is generally compatible with recombinant proteins and expandable to accommodate even more complex experiments, such as by labeling with additional colors.
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Affiliation(s)
- Taehyung C Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Crystal R Moran
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Philip A Cistrone
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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10
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Sun L, Gao Y, Xu Y, Chao J, Liu H, Wang L, Li D, Fan C. Real-Time Imaging of Single-Molecule Enzyme Cascade Using a DNA Origami Raft. J Am Chem Soc 2017; 139:17525-17532. [DOI: 10.1021/jacs.7b09323] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Lele Sun
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanjing Gao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Xu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Chao
- Key
Laboratory for Organic Electronics and Information Displays (KLOEID),
Institute of Advanced Materials (IAM), School of Materials Science
and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210046, China
| | - Huajie Liu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lianhui Wang
- Key
Laboratory for Organic Electronics and Information Displays (KLOEID),
Institute of Advanced Materials (IAM), School of Materials Science
and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210046, China
| | - Di Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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11
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Serwer P, Wright ET. ATP-Driven Contraction of Phage T3 Capsids with DNA Incompletely Packaged In Vivo. Viruses 2017; 9:v9050119. [PMID: 28534826 PMCID: PMC5454431 DOI: 10.3390/v9050119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/01/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023] Open
Abstract
Adenosine triphosphate (ATP) cleavage powers packaging of a double-stranded DNA (dsDNA) molecule in a pre-assembled capsid of phages that include T3. Several observations constitute a challenge to the conventional view that the shell of the capsid is energetically inert during packaging. Here, we test this challenge by analyzing the in vitro effects of ATP on the shells of capsids generated by DNA packaging in vivo. These capsids retain incompletely packaged DNA (ipDNA) and are called ipDNA-capsids; the ipDNA-capsids are assumed to be products of premature genome maturation-cleavage. They were isolated via preparative Nycodenz buoyant density centrifugation. For some ipDNA-capsids, Nycodenz impermeability increases hydration and generates density so low that shell hyper-expansion must exist to accommodate associated water. Electron microscopy (EM) confirmed hyper-expansion and low permeability and revealed that 3.0 mM magnesium ATP (physiological concentration) causes contraction of hyper-expanded, low-permeability ipDNA-capsids to less than mature size; 5.0 mM magnesium ATP (border of supra-physiological concentration) or more disrupts them. Additionally, excess sodium ADP reverses 3.0 mM magnesium ATP-induced contraction and re-generates hyper-expansion. The Nycodenz impermeability implies assembly perfection that suggests selection for function in DNA packaging. These findings support the above challenge and can be explained via the assumption that T3 DNA packaging includes a back-up cycle of ATP-driven capsid contraction and hyper-expansion.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.
| | - Elena T Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA.
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12
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Pierse CA, Dudko OK. Distinguishing Signatures of Multipathway Conformational Transitions. PHYSICAL REVIEW LETTERS 2017; 118:088101. [PMID: 28282172 PMCID: PMC6863504 DOI: 10.1103/physrevlett.118.088101] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Indexed: 05/16/2023]
Abstract
The folding and binding of biomolecules into functional conformations are thought to be commonly mediated by multiple pathways rather than a unique route. Yet even in experiments where one can "see" individual conformational transitions, their stochastic nature generally precludes one from determining whether the transitions occurred through one or multiple pathways. We establish model-free, observable signatures in the response of macromolecules to force that unambiguously identify multiple pathways-even when the pathways themselves cannot be resolved. The unified analytical description reveals that, through multiple pathways, the response of molecules to external forces can be shaped in diverse ways, resulting in a rich design space for a tailored biological function already at the single-molecule level.
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Affiliation(s)
- Christopher A Pierse
- Department of Physics, University of California at San Diego, La Jolla, California 92093, USA
| | - Olga K Dudko
- Department of Physics, University of California at San Diego, La Jolla, California 92093, USA
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13
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Chen W, Zhang K, Liu L, Chen J, Li Y, An L. Conformation and Dynamics of Individual Star in Shear Flow and Comparison with Linear and Ring Polymers. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02636] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Kexin Zhang
- School
of Environmental Science, Northeast Normal University, 5268 Renmin
Street, Changchun, P. R. China 130024
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14
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Serwer P, Wright ET. Testing a proposed paradigm shift in analysis of phage DNA packaging. BACTERIOPHAGE 2017; 6:e1268664. [PMID: 28090387 PMCID: PMC5221748 DOI: 10.1080/21597081.2016.1268664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 01/09/2023]
Abstract
We argue that a paradigm shift is needed in the analysis of phage DNA packaging. We then test a prediction of the following paradigm shift-engendering hypothesis. The motor of phage DNA packaging has two cycles: (1) the well-known packaging ATPase-driven (type 1) cycle and (2) a proposed back-up, shell expansion/contraction-driven (type 2) cycle that reverses type 1 cycle stalls by expelling accidentally packaged non-DNA molecules. We test the prediction that increasing the cellular concentration of all macromolecules will cause packaging-active capsids to divert to states of hyper-expansion and contraction. We use a directed evolution-derived, 3-site phage T3 mutant, adapted to propagation in concentrated bacterial cytoplasm. We find this prediction correct while discovering novel T3 capsids previously obscure.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center , San Antonio, TX, USA
| | - Elena T Wright
- Department of Biochemistry, The University of Texas Health Science Center , San Antonio, TX, USA
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15
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Whitley K, Comstock M, Chemla Y. High-Resolution Optical Tweezers Combined With Single-Molecule Confocal Microscopy. Methods Enzymol 2017; 582:137-169. [PMID: 28062033 PMCID: PMC5540136 DOI: 10.1016/bs.mie.2016.10.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We describe the design, construction, and application of an instrument combining dual-trap, high-resolution optical tweezers and a confocal microscope. This hybrid instrument allows nanomechanical manipulation and measurement simultaneously with single-molecule fluorescence detection. We present the general design principles that overcome the challenges of maximizing optical trap resolution while maintaining single-molecule fluorescence sensitivity, and provide details on the construction and alignment of the instrument. This powerful new tool is just beginning to be applied to biological problems. We present step-by-step instructions on an application of this technique that highlights the instrument's capabilities, detecting conformational dynamics in a nucleic acid-processing enzyme.
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Affiliation(s)
- K.D. Whitley
- University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - M.J. Comstock
- Michigan State University, East Lansing, MI, United States
| | - Y.R. Chemla
- University of Illinois at Urbana–Champaign, Urbana, IL, United States,Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Urbana, IL, United States,Corresponding author:
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16
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Hohlbein J, Kapanidis AN. Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET. Methods Enzymol 2016; 581:353-378. [PMID: 27793286 DOI: 10.1016/bs.mie.2016.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Monitoring conformational changes in DNA polymerases using single-molecule Förster resonance energy transfer (smFRET) has provided new tools for studying fidelity-related mechanisms that promote the rejection of incorrect nucleotides before DNA synthesis. In addition to the previously known open and closed conformations of DNA polymerases, our smFRET assays utilizing doubly labeled variants of Escherichia coli DNA polymerase I were pivotal in identifying and characterizing a partially closed conformation as a primary checkpoint for nucleotide selection. Here, we provide a comprehensive overview of the methods we used for the conformational analysis of wild-type DNA polymerase and some of its low-fidelity derivatives; these methods include strategies for protein labeling and our procedures for solution-based single-molecule fluorescence data acquisition and data analysis. We also discuss alternative single-molecule fluorescence strategies for analyzing the conformations of DNA polymerases in vitro and in vivo.
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Affiliation(s)
- J Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Wageningen, The Netherlands; Microspectroscopy Centre, Wageningen University and Research, Wageningen, The Netherlands.
| | - A N Kapanidis
- Clarendon Laboratory, University of Oxford, Oxford, United Kingdom.
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17
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Cai H, Wind SJ. Improved Glass Surface Passivation for Single-Molecule Nanoarrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10034-10041. [PMID: 27622455 PMCID: PMC5050166 DOI: 10.1021/acs.langmuir.6b02444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Single-molecule fluorescence techniques provide a critical tool for probing biomolecular and cellular interactions with unprecedented resolution and precision. Unfortunately, many of these techniques are hindered by a common problem, namely, the nonspecific adsorption of target biomolecules. This issue is mostly addressed by passivating the glass surfaces with a poly(ethylene glycol) (PEG) brush. This is effective only at low concentrations of the probe molecule because there are defects inherent to polymer brushes formed on glass coverslips due to the presence of surface impurities. Tween-20, a detergent, is a promising alternative that can improve surface passivation, but it is incompatible with living cells, and it also possesses limited selectivity for glass background over metallic nanoparticles, which are frequently used as anchors for the probe molecules. To address these issues, we have developed a more versatile method to improve the PEG passivation. A thin film of hydrogen silsesquioxane (HSQ) is spin-coated and thermally cured on glass coverslips in order to cover the surface impurities. This minimizes the formation of PEG defects and reduces nonspecific adsorption, resulting in an improvement comparable to Tween-20 treatment. This approach was applied to single-molecule nanoarrays of streptavidin bound to AuPd nanodots patterned by e-beam lithography (EBL). The fluorescence signal to background ratio (SBR) on HSQ-coated glass was improved by ∼4-fold as compared to PEG directly on glass. This improvement enables direct imaging of ordered arrays of single molecules anchored to lithographically patterned arrays of metallic nanodots.
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Affiliation(s)
- Haogang Cai
- Dept. of Mechanical Engineering, Columbia University, New York 10027, USA
| | - Shalom J. Wind
- Dept. of Applied Physics and Applied Mathematics, Columbia University, New York 10027, USA
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18
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Lee TC, Kang M, Kim CH, Schultz PG, Chapman E, Deniz AA. Dual Unnatural Amino Acid Incorporation and Click-Chemistry Labeling to Enable Single-Molecule FRET Studies of p97 Folding. Chembiochem 2016; 17:981-4. [PMID: 27115850 DOI: 10.1002/cbic.201500695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Indexed: 01/01/2023]
Abstract
Many cellular functions are critically dependent on the folding of complex multimeric proteins, such as p97, a hexameric multidomain AAA+ chaperone. Given the complex architecture of p97, single-molecule (sm) FRET would be a powerful tool for studying folding while avoiding ensemble averaging. However, dual site-specific labeling of such a large protein for smFRET is a significant challenge. Here, we address this issue by using bioorthogonal azide-alkyne chemistry to attach an smFRET dye pair to site-specifically incorporated unnatural amino acids, allowing us to generate p97 variants reporting on inter- or intradomain structural features. An initial proof-of-principle set of smFRET results demonstrated the strengths of this labeling method. Our results highlight this as a powerful tool for structural studies of p97 and other large protein machines.
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Affiliation(s)
- Taehyung C Lee
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Minjin Kang
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ, 85721, USA
| | - Chan Hyuk Kim
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter G Schultz
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ, 85721, USA.
| | - Ashok A Deniz
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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19
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Derrington IM, Craig JM, Stava E, Laszlo AH, Ross BC, Brinkerhoff H, Nova IC, Doering K, Tickman BI, Ronaghi M, Mandell JG, Gunderson KL, Gundlach JH. Subangstrom single-molecule measurements of motor proteins using a nanopore. Nat Biotechnol 2015; 33:1073-5. [PMID: 26414351 PMCID: PMC4915380 DOI: 10.1038/nbt.3357] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/24/2015] [Indexed: 12/18/2022]
Abstract
Present techniques for measuring the motion of single motor proteins, such as FRET and optical tweezers, are limited to a resolution of ~300 pm. We use ion current modulation through the protein nanopore MspA to observe translocation of helicase Hel308 on DNA with up to ~40 picometer sensitivity. This approach should be applicable to any protein that translocates on DNA or RNA, including helicases, polymerases, recombinases and DNA repair enzymes.
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Affiliation(s)
- Ian M Derrington
- Department of Physics, University of Washington, Seattle, Washington, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, Washington, USA
| | - Eric Stava
- Illumina Inc., San Diego, California, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, Washington, USA
| | - Brian C Ross
- Department of Physics, University of Washington, Seattle, Washington, USA
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, Washington, USA
| | - Ian C Nova
- Department of Physics, University of Washington, Seattle, Washington, USA
| | - Kenji Doering
- Department of Physics, University of Washington, Seattle, Washington, USA
| | - Benjamin I Tickman
- Department of Physics, University of Washington, Seattle, Washington, USA
| | | | | | | | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, Washington, USA
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20
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An improved surface passivation method for single-molecule studies. Nat Methods 2014; 11:1233-6. [PMID: 25306544 PMCID: PMC4245390 DOI: 10.1038/nmeth.3143] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 08/24/2014] [Indexed: 11/08/2022]
Abstract
We report a surface passivation method based on dichlorodimethylsilane (DDS)-Tween-20 for in vitro single-molecule studies, which, under the conditions tested here, more efficiently prevented nonspecific binding of biomolecules than the standard poly(ethylene glycol) surface. The DDS-Tween-20 surface was simple and inexpensive to prepare and did not perturb the behavior and activities of tethered biomolecules. It can also be used for single-molecule imaging in the presence of high concentrations of labeled species in solution.
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21
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Hohlbein J, Craggs TD, Cordes T. Alternating-laser excitation: single-molecule FRET and beyond. Chem Soc Rev 2014; 43:1156-71. [PMID: 24037326 DOI: 10.1039/c3cs60233h] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Förster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables the sorting of fluorescently labelled species based on the number and type of fluorophores present. ALEX also provides a convenient way of accessing the correction factors necessary for determining accurate molecular distances. Here, we provide a comprehensive overview of the concept and current applications of ALEX and we explicitly discuss how to obtain fully corrected distance information across the entire FRET range. We also present new ideas for applications of ALEX which will push the limits of smFRET-based experiments in terms of temporal and spatial resolution for the study of complex biological systems.
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Affiliation(s)
- Johannes Hohlbein
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands.
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22
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Juette MF, Terry DS, Wasserman MR, Zhou Z, Altman RB, Zheng Q, Blanchard SC. The bright future of single-molecule fluorescence imaging. Curr Opin Chem Biol 2014; 20:103-11. [PMID: 24956235 DOI: 10.1016/j.cbpa.2014.05.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 05/09/2014] [Indexed: 11/13/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is an essential and maturing tool to probe biomolecular interactions and conformational dynamics in vitro and, increasingly, in living cells. Multi-color smFRET enables the correlation of multiple such events and the precise dissection of their order and timing. However, the requirements for good spectral separation, high time resolution, and extended observation times place extraordinary demands on the fluorescent labels used in such experiments. Together with advanced experimental designs and data analysis, the development of long-lasting, non-fluctuating fluorophores is therefore proving key to progress in the field. Recently developed strategies for obtaining ultra-stable organic fluorophores spanning the visible spectrum are underway that will enable multi-color smFRET studies to deliver on their promise of previously unachievable biological insights.
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Affiliation(s)
- Manuel F Juette
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Michael R Wasserman
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Roger B Altman
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Qinsi Zheng
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States; Tri-Institutional Training Program in Chemical Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States; Tri-Institutional Training Program in Chemical Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, United States.
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23
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Fakhri N, Wessel AD, Willms C, Pasquali M, Klopfenstein DR, MacKintosh FC, Schmidt CF. High-resolution mapping of intracellular fluctuations using carbon nanotubes. Science 2014; 344:1031-5. [PMID: 24876498 DOI: 10.1126/science.1250170] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cells are active systems with molecular force generation that drives complex dynamics at the supramolecular scale. We present a quantitative study of molecular motions in cells over times from milliseconds to hours. Noninvasive tracking was accomplished by imaging highly stable near-infrared luminescence of single-walled carbon nanotubes targeted to kinesin-1 motor proteins in COS-7 cells. We observed a regime of active random "stirring" that constitutes an intermediate mode of transport, different from both thermal diffusion and directed motor activity. High-frequency motion was found to be thermally driven. At times greater than 100 milliseconds, nonequilibrium dynamics dominated. In addition to directed transport along microtubules, we observed strong random dynamics driven by myosins that result in enhanced nonspecific transport. We present a quantitative model connecting molecular mechanisms to mesoscopic fluctuations.
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Affiliation(s)
- Nikta Fakhri
- Drittes Physikalisches Institut-Biophysik, Georg-August-Universität, 37077 Göttingen, Germany
| | - Alok D Wessel
- Drittes Physikalisches Institut-Biophysik, Georg-August-Universität, 37077 Göttingen, Germany
| | - Charlotte Willms
- Drittes Physikalisches Institut-Biophysik, Georg-August-Universität, 37077 Göttingen, Germany
| | - Matteo Pasquali
- Department of Chemical and Biomolecular Engineering, Department of Chemistry, Smalley Institute for Nanoscale Science and Technology, Rice University, Houston, TX 77005, USA
| | - Dieter R Klopfenstein
- Drittes Physikalisches Institut-Biophysik, Georg-August-Universität, 37077 Göttingen, Germany
| | - Frederick C MacKintosh
- Department of Physics and Astronomy, Vrije Universiteit, 1081 HV Amsterdam, Netherlands.
| | - Christoph F Schmidt
- Drittes Physikalisches Institut-Biophysik, Georg-August-Universität, 37077 Göttingen, Germany.
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24
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Robison AD, Finkelstein IJ. High-throughput single-molecule studies of protein-DNA interactions. FEBS Lett 2014; 588:3539-46. [PMID: 24859086 DOI: 10.1016/j.febslet.2014.05.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 05/11/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Fluorescence and force-based single-molecule studies of protein-nucleic acid interactions continue to shed critical insights into many aspects of DNA and RNA processing. As single-molecule assays are inherently low-throughput, obtaining statistically relevant datasets remains a major challenge. Additionally, most fluorescence-based single-molecule particle-tracking assays are limited to observing fluorescent proteins that are in the low-nanomolar range, as spurious background signals predominate at higher fluorophore concentrations. These technical limitations have traditionally limited the types of questions that could be addressed via single-molecule methods. In this review, we describe new approaches for high-throughput and high-concentration single-molecule biochemical studies. We conclude with a discussion of outstanding challenges for the single-molecule biologist and how these challenges can be tackled to further approach the biochemical complexity of the cell.
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Affiliation(s)
- Aaron D Robison
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States.
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25
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Amado-Azevedo J, Valent ET, Van Nieuw Amerongen GP. Regulation of the endothelial barrier function: a filum granum of cellular forces, Rho-GTPase signaling and microenvironment. Cell Tissue Res 2014; 355:557-76. [PMID: 24633925 DOI: 10.1007/s00441-014-1828-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/24/2014] [Indexed: 12/20/2022]
Abstract
Although the endothelium is an extremely thin single-cell layer, it performs exceedingly well in preventing blood fluids from leaking into the surrounding tissues. However, specific pathological conditions can affect this cell layer, compromising the integrity of the barrier. Vascular leakage is a hallmark of many cardiovascular diseases and despite its medical importance, no specialized therapies are available to prevent it or reduce it. Small guanosine triphosphatases (GTPases) of the Rho family are known to be key regulators of various aspects of cell behavior and studies have shown that they can exert both positive and negative effects on endothelial barrier integrity. Moreover, extracellular matrix stiffness has now been implicated in the regulation of Rho-GTPase signaling, which has a direct impact on the integrity of endothelial junctions. However, knowledge about both the precise mechanism of this regulation and the individual contribution of the specific regulatory proteins remains fragmentary. In this review, we discuss recent findings concerning the balanced activities of Rho-GTPases and, in particular, aspects of the regulation of the endothelial barrier. We highlight the role of Rho-GTPases in the intimate relationships between biomechanical forces, microenvironmental influences and endothelial intercellular junctions, which are all interwoven in a beautiful filigree-like fashion.
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Affiliation(s)
- Joana Amado-Azevedo
- Laboratory for Physiology, Institute for Cardiovascular Research, VU University Medical Center, Van den Boechorststraat 7, 1081BT, Amsterdam, The Netherlands
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26
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Farooq S, Fijen C, Hohlbein J. Studying DNA-protein interactions with single-molecule Förster resonance energy transfer. PROTOPLASMA 2014; 251:317-32. [PMID: 24374460 DOI: 10.1007/s00709-013-0596-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/09/2013] [Indexed: 05/21/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) has emerged as a powerful tool for elucidating biological structure and mechanisms on the molecular level. Here, we focus on applications of smFRET to study interactions between DNA and enzymes such as DNA and RNA polymerases. SmFRET, used as a nanoscopic ruler, allows for the detection and precise characterisation of dynamic and rarely occurring events, which are otherwise averaged out in ensemble-based experiments. In this review, we will highlight some recent developments that provide new means of studying complex biological systems either by combining smFRET with force-based techniques or by using data obtained from smFRET experiments as constrains for computer-aided modelling.
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Affiliation(s)
- Shazia Farooq
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands
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27
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Kozankiewicz B, Orrit M. Single-molecule photophysics, from cryogenic to ambient conditions. Chem Soc Rev 2014; 43:1029-43. [DOI: 10.1039/c3cs60165j] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Single-molecule and single-particle imaging of molecular motors in vitro and in vivo. EXPERIENTIA SUPPLEMENTUM (2012) 2014; 105:131-59. [PMID: 25095994 DOI: 10.1007/978-3-0348-0856-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Motor proteins are multi-potent molecular machines, whose localisation, function and regulation are achieved through tightly controlled processes involving conformational changes and interactions with their tracks, cargos and binding partners. Understanding how these complex machines work requires dissection of these processes both in space and time. Complementing the traditional ensemble measurements, single-molecule assays enable the detection of rare or short-lived intermediates and molecular heterogeneities, and the measurements of subpopulation dynamics. This chapter is focusing on the fluorescence imaging of single motors and their cargo. It discusses what is required in order to achieve single-molecule imaging with high temporal and spatial resolution and how these requirements are met both in vitro and in vivo. It also presents a general overview and applied examples of the major single-molecule imaging techniques and experimental assays which have been used to study motor proteins.
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29
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Moffitt JR, Bustamante C. Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations. FEBS J 2013; 281:498-517. [PMID: 24428386 DOI: 10.1111/febs.12545] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/17/2013] [Accepted: 09/23/2013] [Indexed: 12/25/2022]
Abstract
Enzyme-catalyzed reactions are naturally stochastic, and precision measurements of these fluctuations, made possible by single-molecule methods, promise to provide fundamentally new constraints on the possible mechanisms underlying these reactions. We review some aspects of statistical kinetics: a new field with the goal of extracting mechanistic information from statistical measures of fluctuations in chemical reactions. We focus on a widespread and important statistical measure known as the randomness parameter. This parameter is remarkably simple in that it is the squared coefficient of variation of the cycle completion times, although it places significant limits on the minimal complexity of possible enzymatic mechanisms. Recently, a general expression has been introduced for the substrate dependence of the randomness parameter that is for rate fluctuations what the Michaelis-Menten expression is for the mean rate of product generation. We discuss the information provided by the new kinetic parameters introduced by this expression and demonstrate that this expression can simplify the vast majority of published models.
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Affiliation(s)
- Jeffrey R Moffitt
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
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