scholarly journals Molecular Dynamics Revealed by Single-Molecule FRET Measurement

2019 ◽  
pp. 105-113
Author(s):  
Tomohiro Shima ◽  
Sotaro Uemura
Keyword(s):  
Molecular Dynamics ◽  
Single Molecule ◽  
Single Molecule Fret

scholarly journals Hierarchical dynamics in allostery following ATP hydrolysis monitored by single molecule FRET measurements and MD simulations

2021 ◽  
Author(s):  
Steffen Wolf ◽  
Benedikt Sohmen ◽  
Björn Hellenkamp ◽  
Johann Thurn ◽  
Gerhard Stock ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Atp Hydrolysis ◽  
Md Simulations ◽  
Large Protein ◽  
Single Molecule Fret ◽  
Fluorescence Methods ◽  
Dynamics Simulations

We report on a study that combines advanced fluorescence methods with molecular dynamics simulations to cover timescales from nanoseconds to milliseconds for a large protein, the chaperone Hsp90.

scholarly journals Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts

2020 ◽  
Vol 48 (5) ◽  
pp. 2232-2245 ◽  
Author(s):  
Pengning Xu ◽  
Feng Pan ◽  
Christopher Roland ◽  
Celeste Sagui ◽  
Keith Weninger
Keyword(s):  
Molecular Dynamics ◽  
Single Molecule ◽  
Neurodegenerative Disorders ◽  
Atomic Level ◽  
Trinucleotide Repeats ◽  
Cag Repeats ◽  
Dna Hairpins ◽  
Disease Phenotypes ◽  
Single Molecule Fret ◽  
Insight Into

Abstract DNA trinucleotide repeats (TRs) can exhibit dynamic expansions by integer numbers of trinucleotides that lead to neurodegenerative disorders. Strand slipped hairpins during DNA replication, repair and/or recombination may contribute to TR expansion. Here, we combine single-molecule FRET experiments and molecular dynamics studies to elucidate slipping dynamics and conformations of (CAG)n TR hairpins. We directly resolve slipping by predominantly two CAG units. The slipping kinetics depends on the even/odd repeat parity. The populated states suggest greater stability for 5′-AGCA-3′ tetraloops, compared with alternative 5′-CAG-3′ triloops. To accommodate the tetraloop, even(odd)-numbered repeats have an even(odd) number of hanging bases in the hairpin stem. In particular, a paired-end tetraloop (no hanging TR) is stable in (CAG)n = even, but such situation cannot occur in (CAG)n = odd, where the hairpin is “frustrated’’ and slips back and forth between states with one TR hanging at the 5′ or 3′ end. Trinucleotide interrupts in the repeating CAG pattern associated with altered disease phenotypes select for specific conformers with favorable loop sequences. Molecular dynamics provide atomic-level insight into the loop configurations. Reducing strand slipping in TR hairpins by sequence interruptions at the loop suggests disease-associated variations impact expansion mechanisms at the level of slipped hairpins.

scholarly journals 2P-167 Site-directed single molecule FRET measurement to clarify the intra molecular dynamics of actin(The 46th Annual Meeting of the Biophysical Society of Japan)

2008 ◽  
Vol 48 (supplement) ◽  
pp. S101
Author(s):  
Masatoshi Morimatsu ◽  
So Nishikawa ◽  
Mitsuhiro Sugawa ◽  
Atsuko H Iwane ◽  
Toshio Yanagida
Keyword(s):  
Molecular Dynamics ◽  
Annual Meeting ◽  
Single Molecule ◽  
Single Molecule Fret ◽  
Biophysical Society

scholarly journals Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis

2011 ◽  
Vol 100 (6) ◽  
pp. 1568-1577 ◽  
Author(s):  
Joseph P. Torella ◽  
Seamus J. Holden ◽  
Yusdi Santoso ◽  
Johannes Hohlbein ◽  
Achillefs N. Kapanidis
Keyword(s):  
Molecular Dynamics ◽  
Single Molecule ◽  
Variance Analysis ◽  
Single Molecule Fret

scholarly journals FRETraj: Integrating single-molecule spectroscopy with molecular dynamics

2021 ◽  
Author(s):  
Fabio D Steffen ◽  
Roland K O Sigel ◽  
Richard Börner
Keyword(s):  
Molecular Dynamics ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Supplementary Information ◽  
Fully Integrated ◽  
Single Molecule Fret ◽  
Donor Acceptor ◽  
Molecular Dynamics Trajectory ◽  
Cross Platform ◽  
Protein Nucleic Acid

Abstract Summary Quantitative interpretation of single-molecule FRET experiments requires a model of the dye dynamics to link experimental energy transfer efficiencies to distances between atom positions. We have developed FRETraj, a Python module to predict FRET distributions based on accessible-contact volumes (ACV) and simulated photon statistics. FRETraj helps to identify optimal fluorophore positions on a biomolecule of interest by rapidly evaluating donor-acceptor distances. FRETraj is scalable and fully integrated into PyMOL and the Jupyter ecosystem. Here we describe the conformational dynamics of a DNA hairpin by computing multiple ACVs along a molecular dynamics trajectory and compare the predicted FRET distribution with single-molecule experiments. FRET-assisted modeling will accelerate the analysis of structural ensembles in particular dynamic, non-coding RNAs and transient protein-nucleic acid complexes. Availability FRETraj is implemented as a cross-platform Python package available under the GPL-3.0 on Github (https://github.com/RNA-FRETools/fretraj) and is documented at https://RNA-FRETools.github.io/fretraj Supplementary information Supplementary data are available at Bioinformatics online.

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