Koo, P. K., Mochrie, S. G. J. (2018) Applying Perturbation Expectation-Maximization to Protein Trajectories of Rho GTPases. Methods Mol Biol, 1821. pp. 57-70. ISSN 1064-3745
Abstract
Single-particle tracking (SPT) enables the ability to noninvasively probe the diffusive motions of individual proteins inside living cells at sub-diffraction-limit resolution. The stochastic motions of diffusing Rho GTPases encode information concerning its interactions with binding partners and with its local environment. By identifying Rho GTPases' diffusive states, insight can thus be gained into the spatiotemporal in vivo biochemistry inside live cells at a single-molecule resolution. Here we present perturbation expectation-maximization (pEM), a computational method which simultaneously analyzes a population of protein trajectories to uncover the system of diffusive behaviors: (1) the number of diffusive states, (2) the properties of each such diffusive state, and (3) the probabilities of each trajectory to a respective diffusive state. We provide a step-by-step guide to pEM and discuss considerations for its practical applications, including pEM's capabilities and limitations.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > GTPase bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > G protein > Rho Investigative techniques and equipment > cell culture organs, tissues, organelles, cell types and functions > tissues types and functions > transport > protein transport |
| CSHL Authors: | |
| Communities: | CSHL labs > Koo Lab |
| Depositing User: | Matthew Dunn |
| Date: | 2018 |
| Date Deposited: | 16 Sep 2019 16:35 |
| Last Modified: | 16 Sep 2019 16:35 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/38390 |
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