Journal article
KERA: analysis tool for multi-process, multi-state single-molecule data
Nucleic acids research, Vol.49(9), pp.e53-e53
05/21/2021
DOI: 10.1093/nar/gkab087
PMCID: PMC8136784
PMID: 33660771
Abstract
Molecular machines within cells dynamically assemble, disassemble and reorganize. Molecular interactions between their components can be observed at the single-molecule level and quantified using colocalization single-molecule spectroscopy, in which individual labeled molecules are seen transiently associating with a surface-tethered partner, or other total internal reflection fluorescence microscopy approaches in which the interactions elicit changes in fluorescence in the labeled surface-tethered partner. When multiple interacting partners can form ternary, quaternary and higher order complexes, the types of spatial and temporal organization of these complexes can be deduced from the order of appearance and reorganization of the components. Time evolution of complex architectures can be followed by changes in the fluorescence behavior in multiple channels. Here, we describe the kinetic event resolving algorithm (KERA), a software tool for organizing and sorting the discretized fluorescent trajectories from a range of single-molecule experiments. KERA organizes the data in groups by transition patterns, and displays exhaustive dwell time data for each interaction sequence. Enumerating and quantifying sequences of molecular interactions provides important information regarding the underlying mechanism of the assembly, dynamics and architecture of the macromolecular complexes. We demonstrate KERA's utility by analyzing conformational dynamics of two DNA binding proteins: replication protein A and xeroderma pigmentosum complementation group D helicase.
Details
- Title: Subtitle
- KERA: analysis tool for multi-process, multi-state single-molecule data
- Creators
- Joseph Tibbs - University of Northern IowaMohamed Ghoneim - University of Colorado Anschutz Medical CampusColleen C. Caldwell - University of IowaTroy Buzynski - University of Northern IowaWayne Bowie - University of Northern IowaElizabeth M. Boehm - University of IowaM. Todd Washington - University of IowaS. M. Ali Tabei - University of Northern IowaMaria Spies - University of Iowa
- Resource Type
- Journal article
- Publication Details
- Nucleic acids research, Vol.49(9), pp.e53-e53
- DOI
- 10.1093/nar/gkab087
- PMID
- 33660771
- PMCID
- PMC8136784
- NLM abbreviation
- Nucleic Acids Res
- ISSN
- 0305-1048
- eISSN
- 1362-4962
- Publisher
- Oxford Univ Press
- Number of pages
- 13
- Grant note
- T32 GM067795 / NIH, T32 Pharmacological Sciences Training Grant; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA ISF 20-17 / Iowa Science Foundation Iowa Space Grant Consortium, Collaborative Grant University of Northern Iowa, Office of Research and Sponsored Programs' Capacity Building Grant R35GM131704; GM081433 / NIH/NIGMS; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) UNI, Physics Undergraduate Summer Research Fellowship University of Iowa, FUTURE in Biomedicine Program
- Language
- English
- Date published
- 05/21/2021
- Academic Unit
- Radiation Oncology; Biochemistry and Molecular Biology
- Record Identifier
- 9984288732602771
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