Oligomeric state and ATP binding to E. coli Rho measured by native MS
Data files
Oct 13, 2025 version files 4.86 MB
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Billings_20251010.zip
4.84 MB
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README.md
12.23 KB
Abstract
Mass photometry and mass spectrometry data of E. coli Rho helicase over a range of concentrations, and in the presence of varying ATP concentrations. Python script for fitting population data. Data show that Rho adopts multiple oligomeric states over the range of sampled conditions and that ATP binds variably to these oligomeric states.
Dataset DOI: 10.5061/dryad.t76hdr8df
Description of the data and file structure
We have submitted all native mass spectra appearing in the paper, ratiometric contrast counts from mass photometry experiments, and A280 traces from analytical size-exclusion chromatography experiments. Scripts used to analyze data are included in their respective directories. The zip file Billings_20251010.zip contains the following.
Figure1B
20241209_10uMRho_IST100.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
Figure1C
2xTBS_SEC.csv
- mL-100nM: Running volume of column injected with 100 nanomolar Rho (mL)
- nI-100nM: Normalized intensity of A280 trace (unitless)
- mL-1uM: Running volume of column injected with 1 micromolar Rho (mL)
- nI-1uM: Normalized intensity of A280 trace (unitless)
- mL-10uM: Running volume of column injected with 10 micromolar Rho (mL)
- nI-10uM: Normalized intensity of A280 trace (unitless)
Figure1D
Fig1D_raw.csv
- frame_indices: Indices of images containing binding events (unitless)
- x_coords: x-coordinate of contrast signal
- y_coords: y-coordinate of contrast signal
- contrasts: Ratiometric contrast (intensity)
- calibrated_values: Computed mass of each binding event (kDa)
- nearest_neighbour_distances: Distance to nearest binding event (px), note: events under minimum allowable distance are removed from the histogram
- selections: Number of events observed at this index and coordinate set
Figure2A
20241209_10uMRho_IST100.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241209_10uMRho-10uMATP_IST100.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
Figure2B
20241222_10uMRho-0uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-1uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-3uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-5uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-7uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-20uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-40uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-100uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
FigureS1
20240716_2uMRho_IST200_HCD200.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
FigureS2A
20241209_10uMRho-emitter1_IST30.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241209_10uMRho-emitter1_IST100.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241209_10uMRho-emitter1_IST200.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241212_10uMRho-emitter2_IST200.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
FigureS2B
20250102_2uMRho-emitter1_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_2uMRho-emitter2_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20250102_2uMRho-emitter1_IST200.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_2uMRho-emitter2_IST200.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
FigureS3
20240908_S200Increase_Calibration.csv
- running_volume: Volume of running buffer passed through the column (mL)
- mAU: Absorbance at A280 (mAU)
- mass_standards: Names of species used to calibrate the column (categorical)
- Daltons: Molecular weights of species used to calibrate the column (Da)
- elution_volume: Volume at apex of peak assigned to each calibrant (mL)
- log(Daltons): Exponent of molecular weight in base 10 (unitless)
- Kav: Partition coefficient to represent the separation range of the column (unitless)
- column_volume: Volume of column bed, used to calculate the partition coefficient (mL)
- void_volume: The volume where the largest, unseparated components of the injection begin to elute from the column, used to calculate the partition coefficient (mL)
FigureS4
FigS4_raw.csv
- frame_indices: Indices of images containing binding events (unitless)
- x_coords: x-coordinate of contrast signal
- y_coords: y-coordinate of contrast signal
- contrasts: Ratiometric contrast (intensity)
- calibrated_values: Computed mass of each binding event (kDa)
- nearest_neighbour_distances: Distance to nearest binding event (px), note: events under minimum allowable distance are removed from the histogram
- selections: Number of events observed at this index and coordinate set
FigureS5
MP_oligomer_populations.csv
- micromolar ATP: Concentration of ATP in micromolar (uM)
- monomer: Percentage of particles falling under the monomer distribution (%)
- stdev-m: Standard deviation of monomer replicates (%)
- dimer: Percentage of particles falling under the dimer distribution (%)
- stdev-d: Standard deviation of dimer replicates (%)
- trimer: Percentage of particles falling under the trimer distribution (%)
- stdev-t: Standard deviation of trimer replicates (%)
- tetramer: Percentage of particles falling under the tetramer distribution (%)
- stdev-q: Standard deviation of tetramer replicates (%)
- pentamer: Percentage of particles falling under the pentamer distribution (%)
- stdev-p: Standard deviation of pentamer replicates (%)
- hexamer: Percentage of particles falling under the hexamer distribution (%)
- stdev-h: Standard deviation of hexamer replicates (%)
FigureS6
20241209_10uMRho-10uMATP_IST30.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241209_10uMRho-10uMATP_IST50.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241209_10uMRho-10uMATP_IST100.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241209_10uMRho-10uMATP_IST150.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241209_10uMRho-10uMATP_IST200.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
FigureS7
20241212_10uMRho-100uMATP_IST75
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
FigureS8
20241222_10uMRho-0uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-1uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-3uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-5uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-7uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-20uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-40uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
20241222_10uMRho-100uMATP_IST75.txt
- Header: 7 lines summarizing acquisition parameters and the file structure
- Mass: Mass-to-charge ratio of ions detected (m/z, Th)
- Intensity: Measure of ion abundance (intensity units)
rho_fitting_example.py
- Description: Script used to fit ATP-bound populations of +32 charge state of the Rho hexamer. Includes an example to generate synthetic experiments (lines 10-17). Initial parameters are provided to
itc_model.set_paramsin units of kilojoules per mole.