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microKBA dataset

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posted on 10.03.2021, 09:57 authored by Marta UrbanskaMarta Urbanska, Annemarie Lüdecke, Wilhelm J. Walter, Antoine M. van Oijen, Karl E. Duderstadt, Stefan Diez

microKBA - microfluidic Kinesin Bead Assay

This dataset contains raw and post-processed bead tracking data used to derive results and figures presented in the following manuscript:

Marta Urbanska, Annemarie Lüdecke, Wim J. Walter, Antoine M. van Oijen, Karl E. Duderstadt, Stefan Diez

Highly-parallel microfluidics-based force spectroscopy on single cytoskeletal motors

Small 2021, 2007388, https://doi.org/10.1002/smll.202007388

BiorXiv, https://doi.org/10.1101/2020.08.11.245910


Abstract

Cytoskeletal motors transform chemical energy into mechanical work to drive essential cellular functions. Optical trapping experiments have provided crucial insights into the operation of these molecular machines under load. However, the throughput of such force spectroscopy experiments is typically limited to one measurement at a time. Here, we describe an alternative, highly-parallel, microfluidics-based method that allows for rapid collection of force-dependent motility parameters of cytoskeletal motors. We applied tunable hydrodynamic forces to stepping kinesin-1 motors via DNA-tethered beads and utilized a large field-of-view to simultaneously track the velocities, run lengths and interaction times of hundreds of individual kinesin-1 molecules under varying resisting and assisting loads. Importantly, the 16-μm long DNA tethers between the motors and the beads significantly reduced the vertical component of the applied force pulling the motors away from the microtubule. Our approach is readily applicable to other molecular systems and constitutes a new methodology for parallelized single-molecule force studies on cytoskeletal motors.


Content description

**Final Analysis Files**

* microKBA_Analysis.zip

contains a slim version of post-processed tracking data used for obtaining final results and figures presented in the manuscript, the data is accompanied by MatLab scripts necessary to generate the final results and figures, the content of this folder is also available on github https://github.com/MartaUrb/microKBA/, see microKBA_Analysis_DirStructure for more details on content

* microKBA_Analysis_DirStructure.txt

describes content of microKBA_Analysis


**Tracking Results**

*microKBA_TrackingResults_DirStructure.txt

describes directory structure of the zips below

Following zip files contain raw and post-processed tracking results from individual experiments, see microKBA_TrackingResults_DirStructure for more details:

* 141111_fc2_20ulpermin.zip

* 141112_fc2_20ulpermin.zip

* 150123_fc1_40ulpermin.zip

* 150123_fc2_10ulpermin.zip

* 150126_fc2_30ulpermin.zip

* 150128_fc1_10ulpermin.zip

* 150128_fc2_30ulpermin.zip

* 150130_fc3_50ulpermin.zip


**Software**

* MatLab Functions.zip

two MatLab functions necessary for running the post-tracking data filtering scripts


* s_m_b.jar

Single Molecule Biophysics plug-in for ImageJ used for generating and post-processing tracking results. This plug-in was developed by Karl E. Duderstadt, if you are interested in using a second generation of this tracking software called Molecular Archive Suite, mars, please visit the GitHub page of Duderstadt Lab https://github.com/duderstadt-lab/mars-core


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