DOI: 10.5281/zenodo.8039199
title: Protein sizing with 15-nm conical biological nanopore YaxAB

description: 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:<br> [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. <br> 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 YaxA<sub>d40</sub>B Figure 2: I/V curves and reverse potential of YaxAB and YaxA<sub>d40</sub>B Figure 3: Protein capture by YaxA<sub>d40</sub>B Figure 4 and Figure S25-S26: Depleted serum capture and titrated CRP capture by YaxA<sub>d40</sub>B Figure S7: I/V curves of reverse potential experiments of YaxAB, YaxA<sub>d40</sub>B, YaxA<sub>d40</sub>B RRR, YaxA<sub>d40</sub>B NNN Figure S8: Current distributions of YaxA<sub>d40</sub>B RRR and YaxA<sub>d40</sub>B NNN FIgure S12: Protein capture by YaxAB FIgure S13: Protein capture by YaxA<sub>d40</sub>B Figure S14-S17, and S19-S21: Voltage-dependent protein capture by YaxA<sub>d40</sub>B Figure S18: Protein capture by YaxA<sub>d40</sub>B with different unitary conductance Figure S23: Concentration-dependent protein capture by YaxA<sub>d40</sub>B Figure S24: Mixed protein capture by YaxA<sub>d40</sub>B with different unitary conductance Figure S26: CRP capture in absence/presence of depleted serum by YaxA<sub>d40</sub>B matlab_script_protein_capture_SAP: Matlab script used to obtain event data in scatter plots Data_MD: Folder containing structures and<strong> </strong>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 (<strong>yaxab-codine.pdb</strong>) and YaxA_{D40}B (<strong>yaxab-d40.pdb</strong>) Figure 2 (MD) - <strong>1)</strong> FORTRAN source code to obtain the axial-symmetric maps and resistance-per -length profile from the VMD Volmap density maps .dx (<strong>dx2radial.zip</strong>); <strong>2)</strong> VMD TCL script to compute the velocity map from the MD trajectories (.dcd) and FORTRAN code (<strong>get_vField.zip</strong>). Figure 3 (MD) - FORTRAN and bash codes to obtain the protein-pore resistance from the VMD Volmap occupancy 3D maps (<strong>Hindrance-Yax.zip</strong>) Figure S2 (MD) - VMD TCL script for MODELLER (<strong>Modella.tcl</strong>) and output PDB for the initial YaxAB nanopore model (<strong>yaxab-codine-init_MODELLER.pdb</strong>) Figure S4 (MD) - VMD TCL scripts to obtain the ionic fluxes, EOF and charge maps .dx (<strong>EFIELD_analysis.zip</strong>). The filtered map is obtained by the <strong>dx2radial </strong>FORTRAN<strong> </strong>program. Figure S5 (MD) - Nothing to upload<br> <br> Figure S6 (MD) - PDBs of mutated pores (<strong>yaxab-RRR.pdb</strong>, <strong>yaxab-NNN.pdb</strong>) Figure S22 (MD) - Analysis of the resistance were performed with <strong>dx2radial </strong>program; nothing additional to update.