Results 21 to 30 of about 4,596 (191)

The smfBox is an open-source platform for single-molecule FRET [PDF]

Nature Communications, 2020
Broad uptake of smFRET has been hindered by high instrument costs and a lack of open-source hardware and acquisition software. Here, the authors present the smfBox, a cost-effective open-source platform capable of measuring precise FRET efficiencies ...
Benjamin Ambrose, James M. Baxter, John Cully, Matthew Willmott, Elliot M. Steele, Benji C. Bateman, Marisa L. Martin-Fernandez, Ashley Cadby, Jonathan Shewring, Marleen Aaldering, Timothy D. Craggs   +10 more
doaj   +2 more sources

Conformational ensembles of the disordered 4E-BP2:eIF4E complex restrained by smFRET experiments. [PDF]

Protein Sci
Abstract Eukaryotic cap‐dependent translation initiation is regulated by binding of the predominantly folded eukaryotic initiation factor 4E (eIF4E) to the intrinsically disordered eIF4E binding proteins (4E‐BPs). Here, we report full‐length atomistic conformational ensembles generated by IDPConformerGenerator and optimized by X‐EISDv2 workflow for ...
Smyth S, Liu ZH, Tsangaris TE, Head-Gordon T, Forman-Kay JD, Gradinaru CC.   +5 more
europepmc   +2 more sources

Structural Dynamics of Glutamate Signaling Systems by smFRET [PDF]

Biophysical Journal, 2020
Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for investigating the structural dynamics of biological macromolecules. smFRET reveals the conformational landscape and dynamic changes of proteins by building on the static structures found using cryo-electron microscopy, x-ray crystallography, and other methods ...
Ryan J. Durham, Danielle R. Latham, Hugo Sanabria, Vasanthi Jayaraman   +3 more
openaire   +2 more sources

A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories

Nature Communications, 2022
Single-molecule FRET (smFRET) is a versatile technique to study the dynamics and function of biomolecules since it makes nanoscale movements detectable as fluorescence signals.
Markus Götz, Anders Barth, Søren S.-R. Bohr, Richard Börner, Jixin Chen, Thorben Cordes, Dorothy A. Erie, Christian Gebhardt, Mélodie C. A. S. Hadzic, George L. Hamilton, Nikos S. Hatzakis, Thorsten Hugel, Lydia Kisley, Don C. Lamb, Carlos de Lannoy, Chelsea Mahn, Dushani Dunukara, Dick de Ridder, Hugo Sanabria, Julia Schimpf, Claus A. M. Seidel, Roland K. O. Sigel, Magnus Berg Sletfjerding, Johannes Thomsen, Leonie Vollmar, Simon Wanninger, Keith R. Weninger, Pengning Xu, Sonja Schmid   +28 more
doaj   +1 more source

Heterogeneous migration routes of DNA triplet repeat slip-outs

Biophysical Reports, 2022
It is unclear how the length of a repetitive DNA tract determines the onset and progression of repeat expansion diseases, but the dynamics of secondary DNA structures formed by repeat sequences are believed to play an important role.
Simona Bianco, Tianyu Hu, Oliver Henrich, Steven W. Magennis   +3 more
doaj   +1 more source

Exploring Intra- and Inter-Regional Interactions in the IDP α‑Synuclein Using smFRET and MD Simulations [PDF]

, 2023
Theoretical concepts from polymer physics are often used to describe intrinsically disordered proteins (IDPs). However, amino acid interactions within and between regions of the protein can lead to deviations from typical polymer scaling behavior and ...
Christian Blum (1335768), Patrick R. Onck (2006029), Mohammad A. A. Fakhree (11789952), Gobert Heesink (16498028), Mirjam J. Marseille (16498031), Mireille M.A.E. Claessens (3073035), Mark D. Driver (11624363), Kirsten A. van Leijenhorst-Groener (6384284)   +7 more
core   +3 more sources

Simulations of camera-based single-molecule fluorescence experiments. [PDF]

PLoS ONE, 2018
Single-molecule microscopy has become a widely used technique in (bio)physics and (bio)chemistry. A popular implementation is single-molecule Förster Resonance Energy Transfer (smFRET), for which total internal reflection fluorescence microscopy is ...
Richard Börner, Danny Kowerko, Mélodie C A S Hadzic, Sebastian L B König, Marc Ritter, Roland K O Sigel   +5 more
doaj   +1 more source

Single-photon smFRET. III. Application to pulsed illumination

Biophysical Reports, 2022
Abstract Förster resonance energy transfer (FRET) using pulsed illumination has been pivotal in leveraging lifetime information in FRET analysis. However, there remain major challenges in quantitative single photon, single molecule FRET (smFRET) data analysis under pulsed illumination including: 1) simultaneously deducing kinetics and ...
Matthew Safar, Ayush Saurabh, Bidyut Sarkar, Mohamadreza Fazel, Kunihiko Ishii, Tahei Tahara, Ioannis Sgouralis, Steve Pressé   +7 more
openaire   +2 more sources

Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level

Frontiers in Molecular Biosciences, 2022
DNA polymerases are intrinsically dynamic macromolecular machines. The purpose of this review is to describe the single-molecule Förster resonance energy transfer (smFRET) methods that are used to probe the conformational dynamics of DNA polymerases ...
David P. Millar
doaj   +1 more source

An ATP-Driven N Protein-DDX21 Molecular Switch Dynamically Controls SARS-CoV-2 RNA G-Quadruplex Heterogeneity. [PDF]

Adv Sci (Weinh)
An ATP‐driven molecular switch, comprising viral nucleocapsid (N) protein and host helicase DDX21, dynamically modulates SARS‐CoV‐2 RNA G‐quadruplex (G4) heterogeneity. These viral G4s feature non‐canonical ion‐dependence and act as energy‐sensitive structural checkpoints.
Zheng YT, Zhai LY, Jin J, Chen QY, Fu H, Sun XQ, Lu Y, Li H, Hou XM.   +8 more
europepmc   +2 more sources