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Preparation of ribosomes for smFRET studies: A simplified approach [PDF]
Archives of Biochemistry and Biophysics, 2016 During the past decade, single-molecule studies of the ribosome have significantly advanced our understanding of protein synthesis. The broadest application of these methods has been towards the investigation of ribosome conformational dynamics using single-molecule Förster resonance energy transfer (smFRET).
Donald Burke +2 more
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Extraction of rapid kinetics from smFRET measurements using integrative detectors
Cell Reports Physical Science, 2021 Hidden Markov models (HMMs) are used to learn single-molecule kinetics across a range of experimental techniques. By their construction, HMMs assume that single-molecule events occur on slower timescales than those of data acquisition. To move beyond that HMM limitation and allow for single-molecule events to occur on any timescale, we must treat ...
Kunihiko Ishii +2 more
exaly +3 more sources
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smFRET study of rRNA dimerization at the peptidyl transfer center
Biophysical Chemistry, 2021The ribosome is a ribozyme. At the peptidyl transfer center (PTC) of 180 nt, two loops (the A- and P- loops) bind to tRNAs and position them in close proximity for efficient peptidyl ligation. There is also a 2-fold rotational symmetry in the PTC, which suggests that the precursor of the modern ribosome possibly emerged through dimerization and gene ...
Doris, Xu, Yuhong, Wang
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Ribosome Structure and Dynamics by smFRET Microscopy
Methods in Enzymology, 2014Composed of both RNA and protein components, the ribosome is one of the largest macromolecular machines in life responsible for the production of all protein. Interestingly, the major catalytic center of the ribosome (the peptidyl transferase center) and much of the binding regions for both mRNA and tRNA are composed of RNA making the ribosome one of ...
Peter V Cornish, Bassem Shebl
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8-spot smFRET analysis using two 8-pixel SPAD arrays
Proceedings of SPIE, 2013 Single-molecule Förster resonance energy transfer (smFRET) techniques are now widely used to address outstanding problems in biology and biophysics. In order to study freely diffusing molecules, current approaches consist in exciting a low concentration
Xavier Michalet +2 more
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Protein Science, 2023 Ligand binding to proteins often is accompanied by conformational transitions. Here, we describe a competition assay based on single molecule Förster resonance energy transfer (smFRET) to investigate the ligand-induced conformational changes of the ...
Stefan J Hammerschmidt +2 more
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smFRET experiments of the RNA polymerase II transcription initiation complex
Methods, 2017Single-molecule fluorescence and in particular single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful tool to provide real-time information on the dynamic architecture of large macromolecular structures such as eukaryotic transcription initiation complexes.
Jens Michaelis
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Combined smFRET and NMR analysis of riboswitch structural dynamics
Methods, 2019Harald Schwalbe +2 more
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smFRET-assisted RNA structure prediction
Communications in Information and SystemsSingle-molecule Förster Resonance Energy Transfer (smFRET) is a powerful biophysical technique that utilizes the distance-dependent energy transfer between donor and acceptor dyes linked to individual molecules, providing insights into molecular conformational changes and interactions at the single-molecule level.
Jun Li, Nils G. Walter, Shi-Jie Chen
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Multi-channel smFRET study reveals a compact conformation of EF-G on the ribosome
International Journal of Biochemistry and Cell BiologyABSTRACT While elongation factor G (EF-G) is crucial for ribosome translocation, the role of its GTP hydrolysis remains ambiguous. EF-G’s indispensability is further exemplified by the phosphorylation of human eukaryotic elongation factor 2 (eEF2) at Thr56, which inhibits protein synthesis globally, but its exact ...
Yuhong Wang
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