ArticleMethods in enzymology2016
Precisely and Accurately Inferring Single-Molecule Rate Constants.
Article in Methods in enzymology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Membrane extraction in native lipid nanodiscs reveals dynamic regulation of Cdc42 complexes during cell polarization.Biophysical journal · 2025Article
- Thermodynamic compensation to temperature extremes in B. subtilis vs T. maritima lysine riboswitches.Biophysical journal · 2024Article
- Increasing the accuracy of single-molecule data analysis using tMAVEN.Biophysical journal · 2024Article
- Atypical Protein Kinase C Promotes its own Asymmetric Localisation by Phosphorylating Cdc42 in thebioRxiv : the preprint server for biology · 2024Article
- Increasing the accuracy of single-molecule data analysis using tMAVEN.bioRxiv : the preprint server for biology · 2024Article
- Entropic control of the free-energy landscape of an archetypal biomolecular machine.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Advances in single-molecule junctions as tools for chemical and biochemical analysis.Nature chemistry · 2023Review
- A particle size threshold governs diffusion and segregation of PAR-3 during cell polarization.Cell reports · 2022Article
- High-speed atomic force microscopy reveals a three-state elevator mechanism in the citrate transporter CitS.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Rapid extraction and kinetic analysis of protein complexes from single cells.Biophysical journal · 2021Article
- Lateral gate dynamics of the bacterial translocon during cotranslational membrane protein insertion.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Generalizing HMMs to Continuous Time for Fast Kinetics: Hidden Markov Jump Processes.Biophysical journal · 2021Article
- Bayesian-Estimated Hierarchical HMMs Enable Robust Analysis of Single-Molecule Kinetic Heterogeneity.Biophysical journal · 2019Article
- Dynamics and selective remodeling of the DNA-binding domains of RPA.Nature structural & molecular biology · 2019Article
- Exploring the effects of cosolutes and crowding on the volumetric and kinetic profile of the conformational dynamics of a poly dA loop DNA hairpin: a single-molecule FRET study.Nucleic acids research · 2019Article
- mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.Nature communications · 2018Article
- Increasing the Time Resolution of Single-Molecule Experiments with Bayesian Inference.Biophysical journal · 2018Article
- Observation and Analysis of RAD51 Nucleation Dynamics at Single-Monomer Resolution.Methods in enzymology · 2018Article
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3 authors.
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Abstract
The kinetics of biomolecular systems can be quantified by calculating the stochastic rate constants that govern the biomolecular state vs time trajectories (i.e., state trajectories) of individual biomolecules. To do so, the experimental signal vs time trajectories (i.e., signal trajectories) obtained from observing individual biomolecules are often idealized to generate state trajectories by methods such as thresholding or hidden Markov modeling. Here, we discuss approaches for idealizing signal trajectories and calculating stochastic rate constants from the resulting state trajectories. Importantly, we provide an analysis of how the finite length of signal trajectories restricts the precision of these approaches and demonstrate how Bayesian inference-based versions of these approaches allow rigorous determination of this precision. Similarly, we provide an analysis of how the finite lengths and limited time resolutions of signal trajectories restrict the accuracy of these approaches, and describe methods that, by accounting for the effects of the finite length and limited time resolution of signal trajectories, substantially improve this accuracy. Collectively, therefore, the methods we consider here enable a rigorous assessment of the precision, and a significant enhancement of the accuracy, with which stochastic rate constants can be calculated from single-molecule signal trajectories.
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