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 <em>Fuzzy Supertertiary Interactions within PSD-95 Enable Ligand Binding</em>. 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 <strong>1. Single Molecule Experimental Data</strong> .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 S_PIE&lt;0.1 while AO data were S_PIE&gt;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. <strong>Fluorescence Decay Histograms</strong> 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) <strong>Filtered FCS Curves and Filter Files</strong> 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 <strong>Single Molecule Experimental Data</strong>. 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. <strong>Simulation AV-Derived Distance Values</strong> 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. <strong>5. MFD Histograms</strong> 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. <strong>6. PDA Histograms</strong> Contains time-binned histograms of smFRET data and modeling outputs from PDA fitting.本文件详述了随<em>《PSD-95内的模糊超三级相互作用介导配体结合》</em>一文所开展的实验与分析配套提供的数据文件的文件夹结构。校正参数、研究结果与实验方法详见该论文手稿。 《Sample Reference.xlsx》文件详述了不同荧光共振能量转移（FRET）标记位点变体的命名规范。《RefitDistanceTables.xlsx》则提供了为分类DMD结构而对样本子集开展的所有全局拟合结果对应的距离数据。 压缩文件《PDBDev_adtl_Datasets.zip》包含与该论文手稿向wwPDB-Dev提交的结构数据配套的额外文件。 <strong>1. 单分子实验数据</strong> 文件夹包含.ht3与.ptu格式文件，对应使用Hydra Harp时间相关单光子计数（TCSPC）软硬件与单光子探测器采集的时间标记光子记录。每个样本均设有专属子文件夹。数据选择标准与校正参数详见该论文手稿。仅供体（DO）数据取自S_PIE＜0.1的光子爆发事件，而仅受体（AO）数据取自S_PIE＞0.9的光子爆发事件。 1.1 背景（BG）文件 用于为各样本计算背景信号的背景文件，每个样本对应一个专属子文件夹。 1.2 仪器响应函数（IRF）文件 用于生成荧光衰减直方图分析所需的IRF曲线以及滤波式荧光相关光谱（fFCS）滤波模板的IRF数据文件，每个样本对应一个专属子文件夹。 <strong>荧光衰减直方图数据</strong> 包含供体激发脉冲后各时间分箱内的光子计数数据文件，对应仅供体（DO）、荧光共振能量转移（FRET，DA）以及仪器响应函数（IRF）三类用于荧光衰减直方图分析的曲线数据。 2.1 拟合曲线 用于匹配衰减直方图的拟合曲线，采用xyxy格式存储，字段依次为脉冲后时间延迟、拟合曲线光子计数、时间、残差。 <strong>滤波式荧光相关光谱（fFCS）曲线与滤波文件</strong> 包含每个样本对应的四类fFCS曲线数据：低FRET-高FRET（lohi）、高FRET-低FRET（hilo）、低FRET-低FRET（lolo）以及高FRET-高FRET（hihi），同时包含使用<strong>单分子实验数据</strong>文件夹中的.ht3、.ptu数据与IRF文件，通过Kristine软件生成的滤波文件。 3.1 拟合结果 包含所有样本的拟合曲线与残差数据。.cor格式文件为简单的xy格式文本文件（第三列未启用），.res与.fit格式文件遵循相同格式。 <strong>基于原子向量（AV）的模拟距离数值</strong> 包含DMD模拟得到的结构，以及用于与实验FRET数据进行结构分类比对的染料间距离数值（由AV方法推导得到）。同时包含用于将距离数据与对应结构、FRET对正确关联的参考文件。 4.1 质心（CoM）、AV轮廓与主成分分析（PCA）数据文件 包含所有DMD模拟结构的AV推导距离信息，采用紧凑的npy格式，可通过numpy.load函数加载。文本文件则以xyz格式存储指定结构域的质心坐标。 <strong>5. 多维度分布（MFD）直方图</strong> 包含用于绘制MFD等高线图的文本文件，以及每个样本对应的FRET直线拟合方程。文本文件采用矩阵格式存储，首行与首列分别为X/Y轴刻度值，内部其余数值代表二维直方图的各分箱计数。 <strong>6. 光子分布分析（PDA）直方图</strong> 包含单分子荧光共振能量转移（smFRET）数据的时间分箱直方图，以及通过PDA拟合得到的模型输出结果。