201
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Perez-Gonzalez C, Grondin JP, Lafontaine DA, Carlos Penedo J. Biophysical Approaches to Bacterial Gene Regulation by Riboswitches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:157-91. [PMID: 27193543 DOI: 10.1007/978-3-319-32189-9_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The last decade has witnessed the discovery of a variety of non-coding RNA sequences that perform a broad range of crucial biological functions. Among these, the ability of certain RNA sequences, so-called riboswitches, has attracted considerable interest. Riboswitches control gene expression in response to the concentration of particular metabolites to which they bind without the need for any protein. These RNA switches not only need to adopt a very specific tridimensional structure to perform their function, but also their sequence has been evolutionary optimized to recognize a particular metabolite with high affinity and selectivity. Thus, riboswitches offer a unique opportunity to get fundamental insights into RNA plasticity and how folding dynamics and ligand recognition mechanisms have been efficiently merged to control gene regulation. Because riboswitch sequences have been mostly found in bacterial organisms controlling the expression of genes associated to the synthesis, degradation or transport of crucial metabolites for bacterial survival, they offer exciting new routes for antibiotic development in an era where bacterial resistance is more than ever challenging conventional drug discovery strategies. Here, we give an overview of the architecture, diversity and regulatory mechanisms employed by riboswitches with particular emphasis on the biophysical methods currently available to characterise their structure and functional dynamics.
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Affiliation(s)
- Cibran Perez-Gonzalez
- SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK
| | - Jonathan P Grondin
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
| | - J Carlos Penedo
- SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK. .,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK.
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202
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Orevi T, Rahamim G, Amir D, Kathuria S, Bilsel O, Matthews CR, Haas E. Sequential Closure of Loop Structures Forms the Folding Nucleus during the Refolding Transition of the Escherichia coli Adenylate Kinase Molecule. Biochemistry 2015; 55:79-91. [DOI: 10.1021/acs.biochem.5b00849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Tomer Orevi
- The
Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel 52900
| | - Gil Rahamim
- The
Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel 52900
| | - Dan Amir
- The
Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel 52900
| | - Sagar Kathuria
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Osman Bilsel
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - C. Robert Matthews
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Elisha Haas
- The
Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel 52900
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203
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Deniz AA. Deciphering Complexity in Molecular Biophysics with Single-Molecule Resolution. J Mol Biol 2015; 428:301-307. [PMID: 26707199 DOI: 10.1016/j.jmb.2015.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/16/2015] [Accepted: 12/16/2015] [Indexed: 01/12/2023]
Abstract
The structural features and dynamics of biological macromolecules underlie the molecular biology and correct functioning of cells. However, heterogeneity and other complexity of these molecules and their interactions often lead to loss of important information in traditional biophysical experiments. Single-molecule methods have dramatically altered the conceptual thinking and experimental tests available for such studies, leveraging their ability to avoid ensemble averaging. Here, I discuss briefly the rise of fluorescence single-molecule methods over the past two decades, a few key applications, and end with a view to challenges and future prospects.
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Affiliation(s)
- 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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204
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Banerjee PR, Mitrea DM, Kriwacki RW, Deniz AA. Asymmetric Modulation of Protein Order-Disorder Transitions by Phosphorylation and Partner Binding. Angew Chem Int Ed Engl 2015; 55:1675-9. [PMID: 26679013 DOI: 10.1002/anie.201507728] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/02/2015] [Indexed: 12/16/2022]
Abstract
As for many intrinsically disordered proteins, order-disorder transitions in the N-terminal oligomerization domain of the multifunctional nucleolar protein nucleophosmin (Npm-N) are central to its function, with phosphorylation and partner binding acting as regulatory switches. However, the mechanism of this transition and its regulation remain poorly understood. In this study, single-molecule and ensemble experiments revealed pathways with alternative sequences of folding and assembly steps for Npm-N. Pathways could be switched by altering the ionic strength. Phosphorylation resulted in pathway-specific effects, and decoupled folding and assembly steps to facilitate disorder. Conversely, binding to a physiological partner locked Npm-N in ordered pentamers and counteracted the effects of phosphorylation. The mechanistic plasticity found in the Npm-N order-disorder transition enabled a complex interplay of phosphorylation and partner-binding steps to modulate its folding landscape.
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Affiliation(s)
- Priya R Banerjee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92307, USA
| | - Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA. .,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA.
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92307, USA.
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205
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Banerjee PR, Mitrea DM, Kriwacki RW, Deniz AA. Asymmetric Modulation of Protein Order-Disorder Transitions by Phosphorylation and Partner Binding. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Priya R. Banerjee
- Department of Integrative Structural and Computational Biology; The Scripps Research Institute; La Jolla CA 92307 USA
| | - Diana M. Mitrea
- Department of Structural Biology; St. Jude Children's Research Hospital; Memphis TN 38105 USA
| | - Richard W. Kriwacki
- Department of Structural Biology; St. Jude Children's Research Hospital; Memphis TN 38105 USA
- Department of Microbiology; Immunology and Biochemistry; University of Tennessee Health Sciences Center; Memphis TN 38163 USA
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology; The Scripps Research Institute; La Jolla CA 92307 USA
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206
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Zheng W, Borgia A, Borgia MB, Schuler B, Best RB. Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations. J Chem Theory Comput 2015; 11:5543-53. [PMID: 26574341 PMCID: PMC6139257 DOI: 10.1021/acs.jctc.5b00778] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chemical denaturants are the most commonly used perturbation applied to study protein stability and folding kinetics as well as the properties of unfolded polypeptides. We build on recent work balancing the interactions of proteins and water, and accurate models for the solution properties of urea and guanidinium chloride, to develop a combined force field that is able to capture the strength of interactions between proteins and denaturants. We use solubility data for a model tetraglycine peptide in each denaturant to tune the protein-denaturant interaction by a novel simulation methodology. We validate the results against data for more complex sequences: single-molecule Förster resonance energy transfer data for a 34-residue fragment of the globular protein CspTm and photoinduced electron transfer quenching data for the disordered peptides C(AGQ)nW in denaturant solution as well as the chemical denaturation of the mini-protein Trp cage. The combined force field model should aid our understanding of denaturation mechanisms and the interpretation of experiment.
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Affiliation(s)
- Wenwei Zheng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892
| | - Alessandro Borgia
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | | | - Ben Schuler
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892
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207
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Hartmann A, Krainer G, Keller S, Schlierf M. Quantification of Millisecond Protein-Folding Dynamics in Membrane-Mimetic Environments by Single-Molecule Förster Resonance Energy Transfer Spectroscopy. Anal Chem 2015; 87:11224-32. [PMID: 26457727 DOI: 10.1021/acs.analchem.5b03207] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An increasing number of membrane proteins in different membrane-mimetic systems have become accessible to reversible unfolding experiments monitored by well-established ensemble techniques. However, only little information is available about kinetic processes during membrane-protein folding, mainly because of experimental challenges and a lack of methods suitable for observing highly dynamic membrane proteins. Here, we present single-molecule Förster resonance energy transfer (smFRET) confocal spectroscopy as a powerful tool in kinetic studies of membrane-protein folding in membrane-mimetic environments. We have developed a rigorous workflow demonstrating how to identify and quantify such dynamic processes using a set of qualitative, semiquantitative, and quantitative analytical tools. Using this workflow, we analyzed urea-induced folding and unfolding experiments on the α-helical membrane protein Mistic in the presence of the zwitterionic detergent n-dodecylphosphocholine (DPC). We identified two-state interconversion dynamics on the millisecond time scale of a protein folding into and out of detergent micelles. Our results demonstrate that smFRET is a promising tool for probing the chemical physics of membrane-protein structure and dynamics in the complex and anisotropic environment of a hydrophilic/hydrophobic interface, providing insights into protein interconversion dynamics without the need and challenges of synchronization.
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Affiliation(s)
- Andreas Hartmann
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstr. 18, 01307 Dresden, Germany
| | - Georg Krainer
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstr. 18, 01307 Dresden, Germany.,Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Michael Schlierf
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstr. 18, 01307 Dresden, Germany
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208
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Lee JW, Kim HI. Investigating acid-induced structural transitions of lysozyme in an electrospray ionization source. Analyst 2015; 140:661-9. [PMID: 25429398 DOI: 10.1039/c4an01794c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The effect of acids on the structure of lysozyme (Lyz) during electrospray ionization (ESI) was studied by comparing the solution and gas-phase structures of Lyz. Investigation using circular dichroism spectroscopy and small-angle X-ray scattering demonstrated that the folded conformation of Lyz was maintained in pH 2.2 solutions containing different acids. On the other hand, analysis of the charge state distributions and ion mobility (IM) distributions, combined with molecular dynamics simulations, demonstrated that the gas phase structures of Lyz depend on the pKa of the acid used to acidify the protein solution. Formic acid and acetic acid, which are weak acids (pKa > 3.5), induce unfolding of Lyz during ESI, presumably because the undissociated weak acids provide protons to maintain the acidic groups within Lyz protonated and prevent the formation of salt bridges. However, HCl suppressed the formation of the unfolded conformers because the acid is already dissociated in solution, and chloride anions within the ESI droplet can interact with Lyz to reduce the intramolecular electrostatic repulsion. These trends in the IM distributions are observed for all charge states, demonstrating the significance of the acid effect on the structure of Lyz during ESI.
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Affiliation(s)
- Jong Wha Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, South Korea.
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209
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Plasticity of an ultrafast interaction between nucleoporins and nuclear transport receptors. Cell 2015; 163:734-45. [PMID: 26456112 PMCID: PMC4622936 DOI: 10.1016/j.cell.2015.09.047] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/17/2015] [Accepted: 09/23/2015] [Indexed: 11/23/2022]
Abstract
The mechanisms by which intrinsically disordered proteins engage in rapid and highly selective binding is a subject of considerable interest and represents a central paradigm to nuclear pore complex (NPC) function, where nuclear transport receptors (NTRs) move through the NPC by binding disordered phenylalanine-glycine-rich nucleoporins (FG-Nups). Combining single-molecule fluorescence, molecular simulations, and nuclear magnetic resonance, we show that a rapidly fluctuating FG-Nup populates an ensemble of conformations that are prone to bind NTRs with near diffusion-limited on rates, as shown by stopped-flow kinetic measurements. This is achieved using multiple, minimalistic, low-affinity binding motifs that are in rapid exchange when engaging with the NTR, allowing the FG-Nup to maintain an unexpectedly high plasticity in its bound state. We propose that these exceptional physical characteristics enable a rapid and specific transport mechanism in the physiological context, a notion supported by single molecule in-cell assays on intact NPCs. Integrative structural biology reveals the basis of rapid nuclear transport Transient binding of disordered nucleoporins leaves their plasticity unaffected Multiple minimalistic low-affinity binding motifs create a polyvalent complex A highly reactive and dynamic surface permits an ultrafast binding mechanism
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210
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Platkov M, Gruebele M. Periodic and stochastic thermal modulation of protein folding kinetics. J Chem Phys 2015; 141:035103. [PMID: 25053342 DOI: 10.1063/1.4887360] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Chemical reactions are usually observed either by relaxation of a bulk sample after applying a sudden external perturbation, or by intrinsic fluctuations of a few molecules. Here we show that the two ideas can be combined to measure protein folding kinetics, either by periodic thermal modulation, or by creating artificial thermal noise that greatly exceeds natural thermal fluctuations. We study the folding reaction of the enzyme phosphoglycerate kinase driven by periodic temperature waveforms. As the temperature waveform unfolds and refolds the protein, its fluorescence color changes due to FRET (Förster resonant Energy Transfer) of two donor/acceptor fluorophores labeling the protein. We adapt a simple model of periodically driven kinetics that nicely fits the data at all temperatures and driving frequencies: The phase shifts of the periodic donor and acceptor fluorescence signals as a function of driving frequency reveal reaction rates. We also drive the reaction with stochastic temperature waveforms that produce thermal fluctuations much greater than natural fluctuations in the bulk. Such artificial thermal noise allows the recovery of weak underlying signals due to protein folding kinetics. This opens up the possibility for future detection of a stochastic resonance for protein folding subject to noise with controllable amplitude.
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Affiliation(s)
- Max Platkov
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA
| | - Martin Gruebele
- Departments of Chemistry and Physics and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, USA
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211
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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212
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Ghenuche P, Mivelle M, de Torres J, Moparthi SB, Rigneault H, Van Hulst NF, García-Parajó MF, Wenger J. Matching Nanoantenna Field Confinement to FRET Distances Enhances Förster Energy Transfer Rates. NANO LETTERS 2015; 15:6193-6201. [PMID: 26237534 DOI: 10.1021/acs.nanolett.5b02535] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Förster resonance energy transfer (FRET) is widely applied in chemistry, biology, and nanosciences to assess distances on sub-10 nm scale. Extending the range and applicability of FRET requires enhancement of the fluorescence energy transfer at a spatial scale comparable to the donor-acceptor distances. Plasmonic nanoantennas are ideal to concentrate optical fields at a nanoscale fully matching the FRET distance range. Here, we present a resonant aluminum nanogap antenna tailored to enhance single molecule FRET. A 20 nm gap confines light into a nanoscale volume, providing a field gradient on the scale of the donor-acceptor distance, a large 10-fold increase in the local density of optical states, and strong intensity enhancement. With our dedicated design, we obtain 20-fold enhancement on the fluorescence emission of donor and acceptor dyes, and most importantly up to 5-fold enhancement of the FRET rate for donor-acceptor separations of 10 nm. We also provide a thorough framework of the fluorescence photophysics occurring in the nanoscale gap volume. The presented enhancement of energy transfer flow at the nanoscale opens a yet unexplored facet of the various advantages of optical nanoantennas and provides a new strategy toward biological applications of single molecule FRET at micromolar concentrations.
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Affiliation(s)
- Petru Ghenuche
- CNRS, Aix-Marseille Université, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
| | - Mathieu Mivelle
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Spain
| | - Juan de Torres
- CNRS, Aix-Marseille Université, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
| | - Satish Babu Moparthi
- CNRS, Aix-Marseille Université, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
| | - Hervé Rigneault
- CNRS, Aix-Marseille Université, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
| | - Niek F Van Hulst
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats, Barcelona 08010, Spain
| | - María F García-Parajó
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats, Barcelona 08010, Spain
| | - Jérôme Wenger
- CNRS, Aix-Marseille Université, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
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213
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Krainer G, Hartmann A, Schlierf M. farFRET: Extending the Range in Single-Molecule FRET Experiments beyond 10 nm. NANO LETTERS 2015; 15:5826-5829. [PMID: 26104104 DOI: 10.1021/acs.nanolett.5b01878] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) has become a powerful nanoscopic tool in studies of biomolecular structures and nanoscale objects; however, conventional smFRET measurements are generally blind to distances above 10 nm thus impeding the study of long-distance phenomena. Here, we report the development of farFRET, a technique that extends the range in smFRET measurements beyond the 10 nm line by enhanced energy transfer using multiple acceptors. We demonstrate that farFRET can be readily employed to quantify FRET efficiencies and conformational dynamics using double-stranded DNA molecules, RecA-filament formation on single-stranded DNA and Holliday junction dynamics. farFRET allows quantitative measurements of large biomolecular complexes and nanostructures thus bridging the remaining gap to superresolution microscopy.
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Affiliation(s)
- Georg Krainer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstraße 18, 01307 Dresden, Germany
- Molecular Biophysics, University of Kaiserslautern , Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstraße 18, 01307 Dresden, Germany
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden , Arnoldstraße 18, 01307 Dresden, Germany
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214
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Ray PC, Fan Z, Crouch RA, Sinha SS, Pramanik A. Nanoscopic optical rulers beyond the FRET distance limit: fundamentals and applications. Chem Soc Rev 2015; 43:6370-404. [PMID: 24902784 DOI: 10.1039/c3cs60476d] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the last few decades, Förster resonance energy transfer (FRET) based spectroscopy rulers have served as a key tool for the understanding of chemical and biochemical processes, even at the single molecule level. Since the FRET process originates from dipole-dipole interactions, the length scale of a FRET ruler is limited to a maximum of 10 nm. Recently, scientists have reported a nanomaterial based long-range optical ruler, where one can overcome the FRET optical ruler distance dependence limit, and which can be very useful for monitoring biological processes that occur across a greater distance than the 10 nm scale. Advancement of nanoscopic long range optical rulers in the last ten years indicate that, in addition to their long-range capability, their brightness, long lifetime, lack of blinking, and chemical stability make nanoparticle based rulers a good choice for long range optical probes. The current review discusses the basic concepts and unique light-focusing properties of plasmonic nanoparticles which are useful in the development of long range one dimensional to three dimensional optical rulers. In addition, to provide the readers with an overview of the exciting opportunities within this field, this review discusses the applications of long range rulers for monitoring biological and chemical processes. At the end, we conclude by speculating on the role of long range optical rulers in future scientific research and discuss possible problems, outlooks and future needs in the use of optical rulers for technological applications.
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Affiliation(s)
- Paresh Chandra Ray
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, USA.
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215
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Dai X, Xun Q, Liu XQ, Meng Q. Cysteine-free non-canonical C-intein for versatile protein C-terminal labeling through trans-splicing. Appl Microbiol Biotechnol 2015; 99:8151-61. [DOI: 10.1007/s00253-015-6796-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/17/2015] [Accepted: 06/23/2015] [Indexed: 11/21/2022]
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216
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Nam GM, Makarov DE. Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force spectroscopy experiments. Protein Sci 2015; 25:123-34. [PMID: 26088347 DOI: 10.1002/pro.2727] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 11/12/2022]
Abstract
Single-molecule studies in which a mechanical force is transmitted to the molecule of interest and the molecular extension or position is monitored as a function of time are versatile tools for probing the dynamics of protein folding, stepping of molecular motors, and other biomolecular processes involving activated barrier crossing. One complication in interpreting such studies, however, is the fact that the typical size of a force probe (e.g., a dielectric bead in optical tweezers or the atomic force microscope tip/cantilever assembly) is much larger than the molecule itself, and so the observed molecular motion is affected by the hydrodynamic drag on the probe. This presents the experimenter with a nontrivial task of deconvolving the intrinsic molecular parameters, such as the intrinsic free energy barrier and the effective diffusion coefficient exhibited while crossing the barrier from the experimental signal. Here we focus on the dynamical aspect of this task and show how the intrinsic diffusion coefficient along the molecular reaction coordinate can be inferred from single-molecule measurements of the rates of biomolecular folding and unfolding. We show that the feasibility of accomplishing this task is strongly dependent on the relationship between the intrinsic molecular elasticity and that of the linker connecting the molecule to the force probe and identify the optimal range of instrumental parameters allowing determination of instrument-free molecular dynamics.
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Affiliation(s)
- Gi-Moon Nam
- Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712
| | - Dmitrii E Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712.,Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, 78712
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217
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Reddy G, Thirumalai D. Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model. J Phys Chem B 2015; 119:11358-70. [DOI: 10.1021/acs.jpcb.5b03471] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Govardhan Reddy
- Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka, India 560012
| | - D. Thirumalai
- Biophysics
Program, Institute for Physical Science and Technology, and Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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218
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Levi F, Mostarda S, Rao F, Mintert F. Quantum mechanics of excitation transport in photosynthetic complexes: a key issues review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:082001. [PMID: 26194028 DOI: 10.1088/0034-4885/78/8/082001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
For a long time microscopic physical descriptions of biological processes have been based on quantum mechanical concepts and tools, and routinely employed by chemical physicists and quantum chemists. However, the last ten years have witnessed new developments on these studies from a different perspective, rooted in the framework of quantum information theory. The process that more, than others, has been subject of intense research is the transfer of excitation energy in photosynthetic light-harvesting complexes, a consequence of the unexpected experimental discovery of oscillating signals in such highly noisy systems. The fundamental interdisciplinary nature of this research makes it extremely fascinating, but can also constitute an obstacle to its advance. Here in this review our objective is to provide an essential summary of the progress made in the theoretical description of excitation energy dynamics in photosynthetic systems from a quantum mechanical perspective, with the goal of unifying the language employed by the different communities. This is initially realized through a stepwise presentation of the fundamental building blocks used to model excitation transfer, including protein dynamics and the theory of open quantum system. Afterwards, we shall review how these models have evolved as a consequence of experimental discoveries; this will lead us to present the numerical techniques that have been introduced to quantitatively describe photo-absorbed energy dynamics. Finally, we shall discuss which mechanisms have been proposed to explain the unusual coherent nature of excitation transport and what insights have been gathered so far on the potential functional role of such quantum features.
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Affiliation(s)
- Federico Levi
- FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludgwigs Universität Freiburg, 79104 Freiburg im Breisgau, Germany
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219
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Zerze GH, Best RB, Mittal J. Modest influence of FRET chromophores on the properties of unfolded proteins. Biophys J 2015; 107:1654-60. [PMID: 25296318 DOI: 10.1016/j.bpj.2014.07.071] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 05/10/2014] [Accepted: 07/11/2014] [Indexed: 11/27/2022] Open
Abstract
Single-molecule Förster resonance energy transfer (FRET) experiments are often used to study the properties of unfolded and intrinsically disordered proteins. Because of their large extinction coefficients and quantum yields, synthetic heteroaromatic chromophores covalently linked to the protein are often used as donor and acceptor fluorophores. A key issue in the interpretation of such experiments is the extent to which the properties of the unfolded chain may be affected by the presence of these chromophores. In this article, we investigate this question using all-atom explicit solvent replica exchange molecular dynamics simulations of three different unfolded or intrinsically disordered proteins. We find that the secondary structure and long-range contacts are largely the same in the presence or absence of the fluorophores, and that the dimensions of the chain with and without chromophores are similar. This suggests that, at least in the cases studied, extrinsic fluorophores have little effect on the structural properties of unfolded or disordered proteins. We also find that the critical FRET orientational factor κ(2), has an average value and equilibrium distribution very close to that expected for isotropic orientations, which supports one of the assumptions frequently made when interpreting FRET efficiency in terms of distances.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania.
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220
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Rinaldi AJ, Suddala KC, Walter NG. Native purification and labeling of RNA for single molecule fluorescence studies. Methods Mol Biol 2015; 1240:63-95. [PMID: 25352138 DOI: 10.1007/978-1-4939-1896-6_6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recent discovery that non-coding RNAs are considerably more abundant and serve a much wider range of critical cellular functions than recognized over previous decades of research into molecular biology has sparked a renewed interest in the study of structure-function relationships of RNA. To perform their functions in the cell, RNAs must dominantly adopt their native conformations, avoiding deep, non-productive kinetic traps that may exist along a frustrated (rugged) folding free energy landscape. Intracellularly, RNAs are synthesized by RNA polymerase and fold co-transcriptionally starting from the 5' end, sometimes with the aid of protein chaperones. By contrast, in the laboratory RNAs are commonly generated by in vitro transcription or chemical synthesis, followed by purification in a manner that includes the use of high concentrations of urea, heat and UV light (for detection), resulting in the denaturation and subsequent refolding of the entire RNA. Recent studies into the nature of heterogeneous RNA populations resulting from this process have underscored the need for non-denaturing (native) purification methods that maintain the co-transcriptional fold of an RNA. Here, we present protocols for the native purification of an RNA after its in vitro transcription and for fluorophore and biotin labeling methods designed to preserve its native conformation for use in single molecule fluorescence resonance energy transfer (smFRET) inquiries into its structure and function. Finally, we present methods for taking smFRET data and for analyzing them, as well as a description of plausible overall preparation schemes for the plethora of non-coding RNAs.
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Affiliation(s)
- Arlie J Rinaldi
- W. M. Keck Science Center, The Claremont Colleges, Claremont, CA, 91711, USA
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221
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Matsunaga Y, Kidera A, Sugita Y. Sequential data assimilation for single-molecule FRET photon-counting data. J Chem Phys 2015; 142:214115. [DOI: 10.1063/1.4921983] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Yasuhiro Matsunaga
- Advanced Institute for Computational Science, RIKEN, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Akinori Kidera
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yuji Sugita
- Advanced Institute for Computational Science, RIKEN, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- iTHES, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- Quantitative Biology Center, RIKEN, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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222
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Kim SE, Lee IB, Hyeon C, Hong SC. Deciphering Kinetic Information from Single-Molecule FRET Data That Show Slow Transitions. J Phys Chem B 2015; 119:6974-8. [DOI: 10.1021/acs.jpcb.5b03991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sung Eun Kim
- Department
of Physics, Korea University, Seoul 136-713, Republic of Korea
| | - Il-Buem Lee
- Department
of Physics, Korea University, Seoul 136-713, Republic of Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 130-722, Republic of Korea
| | - Seok-Cheol Hong
- Department
of Physics, Korea University, Seoul 136-713, Republic of Korea
- Korea Institute for Advanced Study, Seoul 130-722, Republic of Korea
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223
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Jiang L, Zeng Y, Sun Q, Sun Y, Guo Z, Qu JY, Yao S. Microsecond protein folding events revealed by time-resolved fluorescence resonance energy transfer in a microfluidic mixer. Anal Chem 2015; 87:5589-95. [PMID: 25938953 DOI: 10.1021/acs.analchem.5b00366] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the combination of the time-resolved fluorescence resonance energy transfer (tr-FRET) measurement and the ultrarapid hydrodynamic focusing microfluidic mixer. The combined technique is capable of probing the intermolecular distance change with temporal resolution at microsecond level and structural resolution at Angstrom level, and the use of two-photon excitation enables a broader exploration of FRET with spectrum from near-ultraviolet to visible wavelength. As a proof of principle, we used the coupled microfluidic laminar flow and time-resolved two-photon excitation microscopy to investigate the early folding states of Cytochrome c (cyt c) by monitoring the distance between the tryptophan (Trp-59)-heme donor-acceptor (D-A) pair. The transformation of folding states of cyt c in the early 500 μs of refolding was revealed on the microsecond time scale. For the first time, we clearly resolved the early transient state of cyt c, which is populated within the dead time of the mixer (<10 μs) and has a characteristic Trp-59-heme distance of ∼31 Å. We believe this tool can find more applications in studying the early stages of biological processes with FRET as the probe.
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Affiliation(s)
- Liguo Jiang
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Yan Zeng
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Qiqi Sun
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Yueru Sun
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Zhihong Guo
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Jianan Y Qu
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Shuhuai Yao
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
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224
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Systematically constructing kinetic transition network in polypeptide from top to down: trajectory mapping. PLoS One 2015; 10:e0125932. [PMID: 25962177 PMCID: PMC4427365 DOI: 10.1371/journal.pone.0125932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/24/2015] [Indexed: 11/23/2022] Open
Abstract
Molecular dynamics (MD) simulation is an important tool for understanding bio-molecules in microscopic temporal/spatial scales. Besides the demand in improving simulation techniques to approach experimental scales, it becomes more and more crucial to develop robust methodology for precisely and objectively interpreting massive MD simulation data. In our previous work [J Phys Chem B 114, 10266 (2010)], the trajectory mapping (TM) method was presented to analyze simulation trajectories then to construct a kinetic transition network of metastable states. In this work, we further present a top-down implementation of TM to systematically detect complicate features of conformational space. We first look at longer MD trajectory pieces to get a coarse picture of transition network at larger time scale, and then we gradually cut the trajectory pieces in shorter for more details. A robust clustering algorithm is designed to more effectively identify the metastable states and transition events. We applied this TM method to detect the hierarchical structure in the conformational space of alanine-dodeca-peptide from microsecond to nanosecond time scales. The results show a downhill folding process of the peptide through multiple pathways. Even in this simple system, we found that single common-used order parameter is not sufficient either in distinguishing the metastable states or predicting the transition kinetics among these states.
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225
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Kang HJ, Kim JH, Chung SJ. Homogeneous detection of caspase-3 using intrinsic fluorescence resonance energy transfer (iFRET). Biosens Bioelectron 2015; 67:413-8. [DOI: 10.1016/j.bios.2014.08.074] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/11/2014] [Accepted: 08/27/2014] [Indexed: 11/16/2022]
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226
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Roethlein C, Miettinen MS, Ignatova Z. A flexible approach to assess fluorescence decay functions in complex energy transfer systems. BMC BIOPHYSICS 2015; 8:5. [PMID: 25897394 PMCID: PMC4403788 DOI: 10.1186/s13628-015-0020-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/23/2015] [Indexed: 12/14/2022]
Abstract
Background Time-correlated Förster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions. Results Here we develop a new approach based on Monte Carlo simulations of time-correlated FRET events to estimate the time-correlated single photon counts (TCSPC) histograms in complex systems. This simulation solution assesses the full statistics of time-correlated photon counts and distance distributions of fluorescently labeled biomolecules. The simulations are consistent with the theoretical predictions of the dye behavior in FRET systems with defined dye distances and measurements of randomly distributed dye solutions. We validate the simulation results using a highly heterogeneous aggregation system and explore the conditions to use this tool in complex systems. Conclusion This approach is powerful in distinguishing distance distributions in a wide variety of experimental setups, thus providing a versatile tool to accurately distinguish between different structural assemblies in highly complex systems. Electronic supplementary material The online version of this article (doi:10.1186/s13628-015-0020-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Zoya Ignatova
- Biochemistry and Biology, University of Potsdam, Potsdam, Germany ; Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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227
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Ganguly D, Chen J. Modulation of the disordered conformational ensembles of the p53 transactivation domain by cancer-associated mutations. PLoS Comput Biol 2015; 11:e1004247. [PMID: 25897952 PMCID: PMC4405366 DOI: 10.1371/journal.pcbi.1004247] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/17/2015] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are frequently associated with human diseases such as cancers, and about one-fourth of disease-associated missense mutations have been mapped into predicted disordered regions. Understanding how these mutations affect the structure-function relationship of IDPs is a formidable task that requires detailed characterization of the disordered conformational ensembles. Implicit solvent coupled with enhanced sampling has been proposed to provide a balance between accuracy and efficiency necessary for systematic and comparative assessments of the effects of mutations as well as post-translational modifications on IDP structure and interaction. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in implicit solvent. The simulations are critically assessed by quantitative comparisons with several types of experimental data that provide structural information on both secondary and tertiary levels. The results show that the calculated ensembles reproduce local structural features of wild-type p53-TAD and the effects of K24N mutation quantitatively. On the tertiary level, the simulated ensembles are overly compact, even though they appear to recapitulate the overall features of transient long-range contacts qualitatively. A key finding is that, while p53-TAD and its cancer mutants sample a similar set of conformational states, cancer mutants could introduce both local and long-range structural modulations to potentially perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The current study clearly demonstrates the promise of atomistic simulations for detailed characterization of IDP conformations, and at the same time reveals important limitations in the current implicit solvent protein force field that must be sufficiently addressed for reliable description of long-range structural features of the disordered ensembles. Tumor suppressor p53 is the most frequently mutated protein in human cancers. Clinical studies have suggested that the type of p53 mutation can be linked to cancer prognosis, response to drug treatment, and patient survival. It is thus crucial to understand the molecular basis of p53 inactivation by various types of mutations, so as to understand the biological outcomes and assess potential cancer intervention strategies. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in an implicit solvent protein force field. The calculated ensembles are in quantitative agreement with several types of existing NMR data on the wild-type protein and the K24N mutant. The results suggest that, while all sequences sample a similar set of conformational substates, cancer mutants could introduce both local and long-range structural modulations and in turn perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The study also reveals important limitations in implicit solvent for simulations of disordered proteins like p53-TAD.
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Affiliation(s)
- Debabani Ganguly
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
- Indian Institute of Engineering Science and Technology, Shibpur Howrah, India
- * E-mail: (DG); (JC)
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail: (DG); (JC)
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228
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Wang Z, Lu HP. Probing Single-Molecule Protein Spontaneous Folding–Unfolding Conformational Fluctuation Dynamics: The Multiple-State and Multiple-Pathway Energy Landscape. J Phys Chem B 2015; 119:6366-78. [DOI: 10.1021/acs.jpcb.5b00735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Zijian Wang
- Center for Photochemical
Sciences, Department of Chemistry, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - H. Peter Lu
- Center for Photochemical
Sciences, Department of Chemistry, Bowling Green State University, Bowling
Green, Ohio 43403, United States
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229
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230
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Moparthi SB, Thieulin-Pardo G, de Torres J, Ghenuche P, Gontero B, Wenger J. FRET analysis of CP12 structural interplay by GAPDH and PRK. Biochem Biophys Res Commun 2015; 458:488-493. [PMID: 25666947 DOI: 10.1016/j.bbrc.2015.01.135] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 01/27/2015] [Indexed: 10/24/2022]
Abstract
CP12 is an intrinsically disordered protein playing a key role in the regulation of the Benson-Calvin cycle. Due to the high intrinsic flexibility of CP12, it is essential to consider its structural modulation induced upon binding to the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) enzymes. Here, we report for the first time detailed structural modulation about the wild-type CP12 and its site-specific N-terminal and C-terminal disulfide bridge mutants upon interaction with GAPDH and PRK by Förster resonance energy transfer (FRET). Our results indicate an increase in CP12 compactness when the complex is formed with GAPDH or PRK. In addition, the distributions in FRET histograms show the elasticity and conformational flexibility of CP12 in all supra molecular complexes. Contrarily to previous beliefs, our FRET results importantly reveal that both N-terminal and C-terminal site-specific CP12 mutants are able to form the monomeric (GAPDH-CP12-PRK) complex.
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Affiliation(s)
- Satish Babu Moparthi
- Aix Marseille Université, CNRS, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France.
| | - Gabriel Thieulin-Pardo
- Aix Marseille Université, CNRS, UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, 13402 Marseille Cedex 20, France
| | - Juan de Torres
- Aix Marseille Université, CNRS, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
| | - Petru Ghenuche
- Aix Marseille Université, CNRS, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
| | - Brigitte Gontero
- Aix Marseille Université, CNRS, UMR 7281 Laboratoire de Bioénergétique et Ingénierie des Protéines, 13402 Marseille Cedex 20, France
| | - Jérôme Wenger
- Aix Marseille Université, CNRS, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille, France
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231
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Yano Y, Kondo K, Kitani R, Yamamoto A, Matsuzaki K. Cholesterol-Induced Lipophobic Interaction between Transmembrane Helices Using Ensemble and Single-Molecule Fluorescence Resonance Energy Transfer. Biochemistry 2015; 54:1371-9. [DOI: 10.1021/bi501528e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kotaro Kondo
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryota Kitani
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Arisa Yamamoto
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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232
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Colomb W, Sarkar SK. Extracting physics of life at the molecular level: A review of single-molecule data analyses. Phys Life Rev 2015; 13:107-37. [PMID: 25660417 DOI: 10.1016/j.plrev.2015.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 12/31/2022]
Abstract
Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.
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Affiliation(s)
- Warren Colomb
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States.
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233
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de Torres J, Ghenuche P, Moparthi SB, Grigoriev V, Wenger J. FRET enhancement in aluminum zero-mode waveguides. Chemphyschem 2015; 16:782-8. [PMID: 25640052 DOI: 10.1002/cphc.201402651] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/14/2014] [Indexed: 11/08/2022]
Abstract
Zero-mode waveguides (ZMWs) can confine light into attoliter volumes, which enables single molecule fluorescence experiments at physiological micromolar concentrations. Of the fluorescence spectroscopy techniques that can be enhanced by ZMWs, Förster resonance energy transfer (FRET) is one of the most widely used in life sciences. Combining zero-mode waveguides with FRET provides new opportunities to investigate biochemical structures or follow interaction dynamics at micromolar concentrations with single-molecule resolution. However, prior to any quantitative FRET analysis on biological samples, it is crucial to establish first the influence of the ZMW on the FRET process. Here, we quantify the FRET rates and efficiencies between individual donor-acceptor fluorophore pairs that diffuse into aluminum zero-mode waveguides. Aluminum ZMWs are important structures thanks to their commercial availability and the large amount of literature that describe their use for single-molecule fluorescence spectroscopy. We also compared the results between ZMWs milled in gold and aluminum, and found that although gold has a stronger influence on the decay rates, the lower losses of aluminum in the green spectral region provide larger fluorescence brightness enhancement factors. For both aluminum and gold ZMWs, we observed that the FRET rate scales linearly with the isolated donor decay rate and the local density of optical states. Detailed information about FRET in ZMWs unlocks their application as new devices for enhanced single-molecule FRET at physiological concentrations.
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Affiliation(s)
- Juan de Torres
- CNRS, Aix-Marseille Université, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille (France)
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234
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Mugnai ML, Elber R. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning. J Chem Phys 2015; 142:014105. [PMID: 25573551 PMCID: PMC4288545 DOI: 10.1063/1.4904882] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 12/09/2014] [Indexed: 01/15/2023] Open
Abstract
We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system-the diffusion along the backbone torsions of a solvated alanine dipeptide.
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Affiliation(s)
- Mauro L Mugnai
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
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235
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Lopes PEM, Guvench O, MacKerell AD. Current status of protein force fields for molecular dynamics simulations. Methods Mol Biol 2015; 1215:47-71. [PMID: 25330958 PMCID: PMC4554537 DOI: 10.1007/978-1-4939-1465-4_3] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.
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Affiliation(s)
- Pedro E M Lopes
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street HSFII, Baltimore, MD, 21201, USA
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236
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Xiao C, Pérez LM, Russell DH. Effects of charge states, charge sites and side chain interactions on conformational preferences of a series of model peptide ions. Analyst 2015; 140:6933-44. [DOI: 10.1039/c5an00826c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The factors affecting conformational preference of gas phase peptide ions are investigated by IM-MS and molecular dynamics simulation.
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Affiliation(s)
- Chunying Xiao
- Texas A&M University
- Department of Chemistry
- College Station
- USA
| | - Lisa M. Pérez
- Texas A&M University
- Department of Chemistry
- College Station
- USA
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237
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Mondal P, Chattoraj S, Chowdhury R, Bhunia D, Ghosh S, Bhattacharyya K. Direct observation of the growth and shrinkage of microtubules by single molecule Förster resonance energy transfer. Phys Chem Chem Phys 2015; 17:6687-90. [DOI: 10.1039/c4cp06031h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Single molecule Förster resonance energy transfer (FRET) has been applied to monitor the growth and the shrinkage of the dynamic microtubules.
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Affiliation(s)
- Prasenjit Mondal
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Jadavpur
- India
| | - Shyamtanu Chattoraj
- Department of Physical Chemistry
- Indian Association for the Cultivation of Science
- Jadavpur
- India
| | - Rajdeep Chowdhury
- Department of Physical Chemistry
- Indian Association for the Cultivation of Science
- Jadavpur
- India
| | - Debmalya Bhunia
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Jadavpur
- India
| | - Surajit Ghosh
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Jadavpur
- India
| | - Kankan Bhattacharyya
- Department of Physical Chemistry
- Indian Association for the Cultivation of Science
- Jadavpur
- India
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238
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McMorran LM, Brockwell DJ, Radford SE. Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date? Arch Biochem Biophys 2014; 564:265-80. [PMID: 24613287 PMCID: PMC4262575 DOI: 10.1016/j.abb.2014.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/16/2014] [Accepted: 02/20/2014] [Indexed: 11/17/2022]
Abstract
Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation now allows studies of folding into lipid bilayers in vitro to be performed. Consequently, mechanistic details and structural information about membrane protein folding are now emerging at an ever increasing pace. Using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.
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Affiliation(s)
- Lindsay M McMorran
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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239
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Shi H, Atlasevich N, Merenbloom SI, Clemmer DE. Solution dependence of the collisional activation of ubiquitin [M + 7H](7+) ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2000-8. [PMID: 24658799 PMCID: PMC4171273 DOI: 10.1007/s13361-014-0834-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/31/2013] [Accepted: 01/10/2014] [Indexed: 05/12/2023]
Abstract
The solution dependence of gas-phase unfolding for ubiquitin [M + 7H](7+) ions has been studied by ion mobility spectrometry-mass spectrometry (IMS-MS). Different acidic water:methanol solutions are used to favor the native (N), more helical (A), or unfolded (U) solution states of ubiquitin. Unfolding of gas-phase ubiquitin ions is achieved by collisional heating and newly formed structures are examined by IMS. With an activation voltage of 100 V, a selected distribution of compact structures unfolds, forming three resolvable elongated states (E1-E3). The relative populations of these elongated structures depend strongly on the solution composition. Activation of compact ions from aqueous solutions known to favor N-state ubiquitin produces mostly the E1 type elongated state, whereas activation of compact ions from methanol containing solutions that populate A-state ubiquitin favors the E3 elongated state. Presumably, this difference arises because of differences in precursor ion structures emerging from solution. Thus, it appears that information about solution populations can be retained after ionization, selection, and activation to produce the elongated states. These data as well as others are discussed.
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240
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Ma L, Yang F, Zheng J. Application of fluorescence resonance energy transfer in protein studies. J Mol Struct 2014; 1077:87-100. [PMID: 25368432 DOI: 10.1016/j.molstruc.2013.12.071] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Since the physical process of fluorescence resonance energy transfer (FRET) was elucidated more than six decades ago, this peculiar fluorescence phenomenon has turned into a powerful tool for biomedical research due to its compatibility in scale with biological molecules as well as rapid developments in novel fluorophores and optical detection techniques. A wide variety of FRET approaches have been devised, each with its own advantages and drawbacks. Especially in the last decade or so, we are witnessing a flourish of FRET applications in biological investigations, many of which exemplify clever experimental design and rigorous analysis. Here we review the current stage of FRET methods development with the main focus on its applications in protein studies in biological systems, by summarizing the basic components of FRET techniques, most established quantification methods, as well as potential pitfalls, illustrated by example applications.
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Affiliation(s)
- Linlin Ma
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA ; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Fan Yang
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA
| | - Jie Zheng
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA
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241
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Graen T, Hoefling M, Grubmüller H. AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:5505-12. [PMID: 26583233 DOI: 10.1021/ct500869p] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Recent advances in single molecule fluorescence experiments and theory allow a direct comparison and improved interpretation of experiment and simulation. To this end, force fields for a larger number of dyes are required which are compatible with and can be integrated into existing biomolecular force fields. Here, we developed, characterized, and implemented AMBER-DYES, a modular fluorescent label force field, for a set of 22 fluorescent dyes and their linkers from the Alexa, Atto, and Cy families, which are in common use for single molecule spectroscopy experiments. The force field is compatible with the AMBER protein force fields and the GROMACS molecular dynamics simulation program. The high electronic polarizability of the delocalized π-electron orbitals, as found in many fluorescent dyes, poses a particular challenge to point charge based force fields such as AMBER. To quantify the charge fluctuations due to the electronic polarizability, we simulated the 22 dyes in explicit solvent and sampled the charge fluctuations using QM/MM simulations at the B3LYP/6-31G*//TIP3P level of theory. The analysis of the simulations enabled us to derive ensemble fitted RESP charges from the solvated charge distributions of multiple trajectories. We observed broad, single peaked charge distributions for the conjugated ring atoms with well-defined mean values. The charge fitting procedure was validated against published charges of the dyelike amino acid tryptophan, which showed good agreement with existing tryptophan parameters from the AMBER, CHARMM, and OPLS force field families. A principal component analysis of the charge fluctuations revealed that a small number of collective coordinates suffices to describe most of the in-plane dye polarizability. The AMBER-DYES force field allows the rapid preparation of all atom molecular dynamics simulations of fluorescent systems for state of the art multi microsecond trajectories.
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Affiliation(s)
- Timo Graen
- Max Planck Institute for Biophysical Chemistry , Am Faβberg 11, 37077 Göttingen, Germany
| | - Martin Hoefling
- Max Planck Institute for Biophysical Chemistry , Am Faβberg 11, 37077 Göttingen, Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry , Am Faβberg 11, 37077 Göttingen, Germany
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242
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Ries J, Schwarze S, Johnson CM, Neuweiler H. Microsecond Folding and Domain Motions of a Spider Silk Protein Structural Switch. J Am Chem Soc 2014; 136:17136-44. [DOI: 10.1021/ja508760a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Julia Ries
- Department of Biotechnology & Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Simone Schwarze
- Department of Biotechnology & Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christopher M. Johnson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Hannes Neuweiler
- Department of Biotechnology & Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
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243
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Bavishi K, Hatzakis NS. Shedding light on protein folding, structural and functional dynamics by single molecule studies. Molecules 2014; 19:19407-34. [PMID: 25429564 PMCID: PMC6272019 DOI: 10.3390/molecules191219407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 11/16/2022] Open
Abstract
The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.
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Affiliation(s)
- Krutika Bavishi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, Center for Synthetic Biology "bioSYNergy", Villum Research Center "Plant Plasticity", University of Copenhagen, Thorvaldsenvej 40, DK-1871 Frederiksberg C, Denmark.
| | - Nikos S Hatzakis
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center Biomembranes in Nanomedicine, University of Copenhagen, 2100 Copenhagen, Denmark.
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244
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Baiz CR, Lin YS, Peng CS, Beauchamp KA, Voelz VA, Pande VS, Tokmakoff A. A molecular interpretation of 2D IR protein folding experiments with Markov state models. Biophys J 2014; 106:1359-70. [PMID: 24655511 DOI: 10.1016/j.bpj.2014.02.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 01/28/2014] [Accepted: 02/03/2014] [Indexed: 11/24/2022] Open
Abstract
The folding mechanism of the N-terminal domain of ribosomal protein L9 (NTL91-39) is studied using temperature-jump (T-jump) amide I' two-dimensional infrared (2D IR) spectroscopy in combination with spectral simulations based on a Markov state model (MSM) built from millisecond-long molecular dynamics trajectories. The results provide evidence for a compact well-structured folded state and a heterogeneous fast-exchanging denatured state ensemble exhibiting residual secondary structure. The folding rate of 26.4 μs(-1) (at 80°C), extracted from the T-jump response of NTL91-39, compares favorably with the 18 μs(-1) obtained from the MSM. Structural decomposition of the MSM and analysis along the folding coordinate indicates that helix-formation nucleates the global folding. Simulated difference spectra, corresponding to the global folding transition of the MSM, are in qualitative agreement with measured T-jump 2D IR spectra. The experiments demonstrate the use of T-jump 2D IR spectroscopy as a valuable tool for studying protein folding, with direct connections to simulations. The results suggest that in addition to predicting the correct native structure and folding time constant, molecular dynamics simulations carried out with modern force fields provide an accurate description of folding mechanisms in small proteins.
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Affiliation(s)
- Carlos R Baiz
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Yu-Shan Lin
- Department of Chemistry, Stanford University, Stanford, California
| | - Chunte Sam Peng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania
| | - Vijay S Pande
- Department of Chemistry, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Department of Structural Biology, Stanford University, Stanford, California
| | - Andrei Tokmakoff
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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245
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Best RB, Zheng W, Mittal J. Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association. J Chem Theory Comput 2014; 10:5113-5124. [PMID: 25400522 PMCID: PMC4230380 DOI: 10.1021/ct500569b] [Citation(s) in RCA: 476] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Indexed: 12/22/2022]
Abstract
Some frequently encountered deficiencies in all-atom molecular simulations, such as nonspecific protein-protein interactions being too strong, and unfolded or disordered states being too collapsed, suggest that proteins are insufficiently well solvated in simulations using current state-of-the-art force fields. To address these issues, we make the simplest possible change, by modifying the short-range protein-water pair interactions, and leaving all the water-water and protein-protein parameters unchanged. We find that a modest strengthening of protein-water interactions is sufficient to recover the correct dimensions of intrinsically disordered or unfolded proteins, as determined by direct comparison with small-angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET) data. The modification also results in more realistic protein-protein affinities, and average solvation free energies of model compounds which are more consistent with experiment. Most importantly, we show that this scaling is small enough not to affect adversely the stability of the folded state, with only a modest effect on the stability of model peptides forming α-helix and β-sheet structures. The proposed adjustment opens the way to more accurate atomistic simulations of proteins, particularly for intrinsically disordered proteins, protein-protein association, and crowded cellular environments.
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Affiliation(s)
- Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Wenwei Zheng
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Jeetain Mittal
- Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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246
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Lee T, Moran-Gutierrez CR, Deniz AA. Probing protein disorder and complexity at single-molecule resolution. Semin Cell Dev Biol 2014; 37:26-34. [PMID: 25305580 DOI: 10.1016/j.semcdb.2014.09.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 09/15/2014] [Accepted: 09/30/2014] [Indexed: 12/16/2022]
Abstract
A substantial fraction of the human proteome encodes disordered proteins. Protein disorder is associated with a variety of cellular functions and misfunction, and is therefore of clear import to biological systems. However, disorder lends itself to conformational flexibility and heterogeneity, rendering proteins which feature prominent disorder difficult to study using conventional structural biology methods. Here we discuss a few examples of how single-molecule methods are providing new insight into the biophysics and complexity of these proteins by avoiding ensemble averaging, thereby providing direct information about the complex distributions and dynamics of this important class of proteins. Examples of note include characterization of isolated IDPs in solution as collapsed and dynamic species, detailed insight into complex IDP folding landscapes, and new information about how tunable regulation of structure-mediated binding cooperativity and consequent function can be achieved through protein disorder. With these exciting advances in view, we conclude with a discussion of a few complementary and emerging single-molecule efforts of particular promise, including complementary and enhanced methodologies for studying disorder in proteins, and experiments to investigate the potential role for IDP-induced phase separation as a critical functional element in biological systems.
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Affiliation(s)
- Taehyung Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Crystal R Moran-Gutierrez
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
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247
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Tapia-Rojo R, Arregui S, Mazo JJ, Falo F. Mechanical unfolding of a simple model protein goes beyond the reach of one-dimensional descriptions. J Chem Phys 2014; 141:135102. [PMID: 25296840 DOI: 10.1063/1.4896620] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition-path theory we also provide a quantitative description of the unfolding pathways followed by the system. Our study shows a complex dynamical scenario. In particular, we see that the usual one-dimensional picture: free-energy vs end-to-end distance representation, gives a misleading description of the process. Unfolding can occur following different pathways and configurations which seem to play a central role in one-dimensional pictures are not the intermediate states of the unfolding dynamics.
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Affiliation(s)
- R Tapia-Rojo
- Instituto de Biocomputación y Física de Sistemas Complejos and Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - S Arregui
- Instituto de Biocomputación y Física de Sistemas Complejos and Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - J J Mazo
- Instituto de Ciencia de Materiales de Aragón and Departamento de Física de la Materia Condensada, CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - F Falo
- Instituto de Biocomputación y Física de Sistemas Complejos and Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
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248
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Smith WW, Ho PY, O'Hern CS. Calibrated Langevin-dynamics simulations of intrinsically disordered proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:042709. [PMID: 25375525 DOI: 10.1103/physreve.90.042709] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 06/04/2023]
Abstract
We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the interresidue separations for 36 pairs of residues in five IDPs: α-, β-, and γ-synuclein, the microtubule-associated protein τ, and prothymosin α. We find that our CG model is able to recapitulate the average interresidue separations regardless of the choice of the hydrophobicity scale, which shows that our calibrated model can robustly capture the conformational dynamics of IDPs. We then employ our model to study the scaling of the radius of gyration with chemical distance in 11 known IDPs. We identify a strong correlation between the distance to the dividing line between folded proteins and IDPs in the mean charge and hydrophobicity space and the scaling exponent of the radius of gyration with chemical distance along the protein.
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Affiliation(s)
- W Wendell Smith
- Department of Physics, Yale University, New Haven, Connecticut 06520-8120, USA and Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520-8114, USA
| | - Po-Yi Ho
- Department of Physics, Yale University, New Haven, Connecticut 06520-8120, USA
| | - Corey S O'Hern
- Department of Physics, Yale University, New Haven, Connecticut 06520-8120, USA and Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520-8114, USA and Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520-8286, USA and Department of Applied Physics, Yale University, New Haven, Connecticut 06520-8267, USA and Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
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249
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Abstract
Single-molecule spectroscopy is widely used to study macromolecular dynamics. Although this technique provides unique information that cannot be obtained at the ensemble level, the possibility of studying fast molecular dynamics is limited by the number of photons detected per unit time (photon count rate), which is proportional to the illumination intensity. However, simply increasing the illumination intensity often does not help because of various photophysical and photochemical problems. In this Perspective, we show how to improve the dynamic range of single-molecule fluorescence spectroscopy at a given photon count rate by considering each and every photon and using a maximum likelihood method. For a photon trajectory with recorded photon colors and inter-photon times, the parameters of a model describing molecular dynamics are obtained by maximizing the appropriate likelihood function. We discuss various likelihood functions, their applicability, and the accuracy of the extracted parameters. The maximum likelihood method has been applied to analyze the experiments on fast two-state protein folding and to measure transition path times. Utilizing other information such as fluorescence lifetimes is discussed in the framework of two-dimensional FRET efficiency-lifetime histograms.
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Affiliation(s)
- Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD, 20892-0520
| | - Irina V. Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD, 20892-0520
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250
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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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