Literature DB >> 29401427

Increasing the Time Resolution of Single-Molecule Experiments with Bayesian Inference.

Colin D Kinz-Thompson1, Ruben L Gonzalez2.   

Abstract

Many time-resolved single-molecule biophysics experiments seek to characterize the kinetics of biomolecular systems exhibiting dynamics that challenge the time resolution of the given technique. Here, we present a general, computational approach to this problem that employs Bayesian inference to learn the underlying dynamics of such systems, even when they are much faster than the time resolution of the experimental technique being used. By accurately and precisely inferring rate constants, our Bayesian inference for the analysis of subtemporal resolution dynamics approach effectively enables the experimenter to super-resolve the poorly resolved dynamics that are present in their data.
Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2018        PMID: 29401427      PMCID: PMC5984981          DOI: 10.1016/j.bpj.2017.11.3741

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  35 in total

1.  Slaving: solvent fluctuations dominate protein dynamics and functions.

Authors:  P W Fenimore; H Frauenfelder; B H McMahon; F G Parak
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-20       Impact factor: 11.205

2.  Nonblinking and long-lasting single-molecule fluorescence imaging.

Authors:  Ivan Rasnik; Sean A McKinney; Taekjip Ha
Journal:  Nat Methods       Date:  2006-10-01       Impact factor: 28.547

3.  Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments.

Authors:  Eyal Nir; Xavier Michalet; Kambiz M Hamadani; Ted A Laurence; Daniel Neuhauser; Yevgeniy Kovchegov; Shimon Weiss
Journal:  J Phys Chem B       Date:  2006-11-09       Impact factor: 2.991

4.  Triplet-relaxation microscopy with bunched pulsed excitation.

Authors:  Gerald Donnert; Christian Eggeling; Stefan W Hell
Journal:  Photochem Photobiol Sci       Date:  2009-03-09       Impact factor: 3.982

5.  Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data.

Authors:  Jonathan E Bronson; Jingyi Fei; Jake M Hofman; Ruben L Gonzalez; Chris H Wiggins
Journal:  Biophys J       Date:  2009-12-16       Impact factor: 4.033

6.  Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation.

Authors:  Jingyi Fei; Pallav Kosuri; Daniel D MacDougall; Ruben L Gonzalez
Journal:  Mol Cell       Date:  2008-05-09       Impact factor: 17.970

7.  Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments.

Authors:  Jan-Willem van de Meent; Jonathan E Bronson; Chris H Wiggins; Ruben L Gonzalez
Journal:  Biophys J       Date:  2014-03-18       Impact factor: 4.033

8.  Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories.

Authors:  Hoi Sung Chung; Troy Cellmer; John M Louis; William A Eaton
Journal:  Chem Phys       Date:  2013-08-30       Impact factor: 2.348

9.  Precisely and Accurately Inferring Single-Molecule Rate Constants.

Authors:  C D Kinz-Thompson; N A Bailey; R L Gonzalez
Journal:  Methods Enzymol       Date:  2016-10-07       Impact factor: 1.600

10.  RELION: implementation of a Bayesian approach to cryo-EM structure determination.

Authors:  Sjors H W Scheres
Journal:  J Struct Biol       Date:  2012-09-19       Impact factor: 2.867

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  6 in total

1.  Bayesian-Estimated Hierarchical HMMs Enable Robust Analysis of Single-Molecule Kinetic Heterogeneity.

Authors:  Jason Hon; Ruben L Gonzalez
Journal:  Biophys J       Date:  2019-04-02       Impact factor: 4.033

2.  Bayesian inference of kinetic schemes for ion channels by Kalman filtering.

Authors:  Jan L Münch; Fabian Paul; Ralf Schmauder; Klaus Benndorf
Journal:  Elife       Date:  2022-05-04       Impact factor: 8.713

Review 3.  FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.

Authors:  Eitan Lerner; Anders Barth; Jelle Hendrix; Benjamin Ambrose; Victoria Birkedal; Scott C Blanchard; Richard Börner; Hoi Sung Chung; Thorben Cordes; Timothy D Craggs; Ashok A Deniz; Jiajie Diao; Jingyi Fei; Ruben L Gonzalez; Irina V Gopich; Taekjip Ha; Christian A Hanke; Gilad Haran; Nikos S Hatzakis; Sungchul Hohng; Seok-Cheol Hong; Thorsten Hugel; Antonino Ingargiola; Chirlmin Joo; Achillefs N Kapanidis; Harold D Kim; Ted Laurence; Nam Ki Lee; Tae-Hee Lee; Edward A Lemke; Emmanuel Margeat; Jens Michaelis; Xavier Michalet; Sua Myong; Daniel Nettels; Thomas-Otavio Peulen; Evelyn Ploetz; Yair Razvag; Nicole C Robb; Benjamin Schuler; Hamid Soleimaninejad; Chun Tang; Reza Vafabakhsh; Don C Lamb; Claus Am Seidel; Shimon Weiss
Journal:  Elife       Date:  2021-03-29       Impact factor: 8.140

Review 4.  Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments.

Authors:  Colin D Kinz-Thompson; Korak Kumar Ray; Ruben L Gonzalez
Journal:  Annu Rev Biophys       Date:  2021-02-03       Impact factor: 12.981

5.  Generalizing HMMs to Continuous Time for Fast Kinetics: Hidden Markov Jump Processes.

Authors:  Zeliha Kilic; Ioannis Sgouralis; Steve Pressé
Journal:  Biophys J       Date:  2021-01-07       Impact factor: 3.699

6.  Extraction of rapid kinetics from smFRET measurements using integrative detectors.

Authors:  Zeliha Kilic; Ioannis Sgouralis; Wooseok Heo; Kunihiko Ishii; Tahei Tahara; Steve Pressé
Journal:  Cell Rep Phys Sci       Date:  2021-04-22
  6 in total

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