Fuzzy Supertertiary Interactions within PSD-95 Enable Ligand Binding
This file details the folder structure for the data files provided corresponding to the experiments and analysis performed in Fuzzy Supertertiary Interactions within PSD-95 Enable Ligand Binding. Correction parameters, results, and methods are detailed in the manuscript. The file “Sample Reference.xlsx” details the naming conventions for different FRET labeling site variants. “RefitDistanceTables.xlsx” provides the distances for all global fits of subsets of samples performed for classification of DMD structures. The .zip file "PDBDev_adtl_Datasets.zip" Contains additional files corresponding to submissions of structures from the corresponding manuscript to wwPDB-Dev. Folder 1. Single Molecule Experimental Data .ht3 and .ptu files corresponding to time-tagged photon records collected using single-photon detectors with Hydra Harp TCSPC software and hardware. Folders are provided for each sample. Selection criteria and correction parameters are detailed in the manuscript. DO data were taken from bursts with SPIE<0.1 while AO data were SPIE>0.9. 1.1 BG Background files from which background signals were calculated for each sample. Subfolder for each sample. 1.2 IRF IRF data files used for generation of IRF curves for fluorescence decay histogram analysis and generation of fFCS filters. Subfolder for each sample. Fluorescence Decay Histograms Data files for photon counts in each time bin following donor excitation pulse for Donor-only (DO), FRET (DA), and Instrument Response Function (IRF) curves used in fluorescence decay histogram analysis. 2.1 Fit Curves Curves fit to decay histograms, in xyxy format (time delay after pulse, fit curve counts, time, residual) Filtered FCS Curves and Filter Files Data corresponding to four fFCS curves per sample: low-FRET-high-FRET (lohi), high-FRET-low-FRET (hilo), low-FRET-low-FRET (lolo), and high-FRET-high-FRET (hihi), as well as filter files generated in the Kristine software package using the .ht3 and .ptu data and IRF files from Single Molecule Experimental Data. 3.1 Fits Fit curves and residuals for all samples. .cor files are simple text files in xy format (third column unused). .res, .fit files follow likewise. Simulation AV-Derived Distance Values Structures from DMD simulations and AV-derived interdye distances used for structural classification against experimental FRET data. Also includes references files for associating distances correctly with structures and FRET pairs. 4.1 CoM AV Contours and PCA Data Files contain AV-derived distance information for all simulation structures from DMD, in compact npy format loadable via numpy.load. The text files contain center-of-mass positions in xyz format for the indicated domains. 5. MFD Histograms Contains text files for MFD contour plot data, as well as FRET line equations for each sample. Text files are in matrix representation, with the first row and column being the x/y axis values and all internal values representing a 2D bin. 6. PDA Histograms Contains time-binned histograms of smFRET data and modeling outputs from PDA fitting.
Kubiak, Jakub; Hamilton, George; Sanabria, Hugo; Bowen, Mark E.; Changcheng, Zhang; Hao, Yan; Ding, Feng; Welcome, Franceine S.; Saikia, Nabanita; Wu, Fang; Basak, Sujit; Seidel, Claus A.M. (2022), "Fuzzy Supertertiary Interactions within PSD-95 Enable Ligand Binding", Zenodo, doi: 10.5281/zenodo.7063094