Extracting intracellular diffusive states and transition rates from single-molecule tracking data

Fredrik Persson; Martin Lindén; Cecilia Unoson; Johan Elf

doi:10.1038/nmeth.2367

Extracting intracellular diffusive states and transition rates from single-molecule tracking data

Nat Methods. 2013 Mar;10(3):265-9. doi: 10.1038/nmeth.2367. Epub 2013 Feb 10.

Authors

Fredrik Persson¹, Martin Lindén, Cecilia Unoson, Johan Elf

Affiliation

¹ Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

PMID: 23396281
DOI: 10.1038/nmeth.2367

Abstract

We provide an analytical tool based on a variational Bayesian treatment of hidden Markov models to combine the information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. The method identifies the number of diffusive states and the state transition rates. Using this method we have created an objective interaction map for Hfq, a protein that mediates interactions between small regulatory RNAs and their mRNA targets.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Binding Sites
Computer Simulation
Escherichia coli / genetics
Escherichia coli / metabolism*
Escherichia coli Proteins / genetics
Escherichia coli Proteins / metabolism*
Host Factor 1 Protein / genetics
Host Factor 1 Protein / metabolism*
Kinetics
Markov Chains*
Models, Biological*
Protein Binding
RNA, Messenger / genetics
RNA, Messenger / metabolism
RNA, Small Untranslated / genetics
RNA, Small Untranslated / metabolism

Substances

Escherichia coli Proteins
Hfq protein, E coli
Host Factor 1 Protein
RNA, Messenger
RNA, Small Untranslated