Protein sizing with 15-nm conical biological nanopore YaxAB

This dataset belongs to the article: "Protein sizing with 15-nm conical biological nanopore YaxAB" and contains the raw electrophysiology data of protein capture by YaxAB, conductance distributions and reverse potential experiments. A Matlab script describing the analysis is also added. This dataset also includes the molecular dynamics simulations and analysis (see below)

The Data_exp.zip contains experimental files; Data_MD.zip contains MD simulation files. 

For Data_exp.zip:

- Each electrophysiology file contains measurement info as follows:
[Date of measurement]_[Buffer conditions]_[Pore type]_[added analyte(s)]_[operator initials]

- Each electrophys trace is accompannied by Excel file with Clampfit analysis in Sheet1 (named [voltage], with the columns corresponding to: Trace; Search; Level; State; Event Start Time (ms); Event End Time (ms); Amplitude (pA); Amp S.D. (pA); Dwell Time (ms); Inst. Freq. (Hz); Interevent Interval (ms); [empy]; open pore current (pA)

- This Excel file was analyzed with inhouse Matlab script (matlab_script_protein_capture_SAP); and event data (Ires, dwell time, Amp S.D.) was used in scatter plots. 

Data_exp_zip: Folder containing raw electrophysiology data and result after Clampfit analysis, with each folder containing the following:

Figure 1: Current distributions of YaxAB and YaxAd40B

Figure 2: I/V curves and reverse potential of YaxAB and YaxAd40B

Figure 3: Protein capture by YaxAd40B

Figure 4 and Figure S25-S26: Depleted serum capture and titrated CRP capture by YaxAd40B

Figure S7: I/V curves of reverse potential experiments of YaxAB, YaxAd40B, YaxAd40B RRR, YaxAd40B NNN

Figure S8: Current distributions of YaxAd40B RRR and YaxAd40B NNN

FIgure S12: Protein capture by YaxAB

FIgure S13: Protein capture by YaxAd40B

Figure S14-S17, and S19-S21: Voltage-dependent protein capture by YaxAd40B

Figure S18: Protein capture by YaxAd40B with different unitary conductance

Figure S23: Concentration-dependent protein capture by YaxAd40B

Figure S24: Mixed protein capture by YaxAd40B with different unitary conductance

Figure S26: CRP capture in absence/presence of depleted serum by YaxAd40B

matlab_script_protein_capture_SAP: Matlab script used to obtain event data in scatter plots 

Data_MD: Folder containing structures and MD analysis script and tools. Trajectories are not uploaded as they are more than 2Tb of data and can be easily reproduced using the provided files and described methods.

Figure 1 (MD) - PDBs of the modeled didecameric YaxAB (yaxab-codine.pdb) and YaxA_{D40}B (yaxab-d40.pdb)

Figure 2 (MD) - 1) FORTRAN source code to obtain the axial-symmetric maps and resistance-per -length profile from the VMD Volmap density maps .dx (dx2radial.zip); 2) VMD TCL script to compute the velocity map from the MD trajectories (.dcd) and FORTRAN code (get_vField.zip).

Figure 3 (MD) - FORTRAN and bash codes to obtain the protein-pore resistance from the VMD Volmap occupancy 3D maps (Hindrance-Yax.zip)

Figure S2 (MD) - VMD TCL script for MODELLER (Modella.tcl) and output PDB for the initial YaxAB nanopore model (yaxab-codine-init_MODELLER.pdb)

Figure S4 (MD) - VMD TCL scripts to obtain the ionic fluxes, EOF and charge maps .dx (EFIELD_analysis.zip). The filtered map is obtained by the dx2radial FORTRAN program.

Figure S5 (MD) - Nothing to upload

Figure S6 (MD) - PDBs of mutated pores (yaxab-RRR.pdb, yaxab-NNN.pdb)

Figure S22 (MD) - Analysis of the resistance were performed with dx2radial program; nothing additional to update.