Gold Nanoparticles Synthesized in the Presence of Peptides - UV-Vis Spectra, Fluorescence, USAXS, Electron Microscopy

Content Summary: Data from experiments in which gold nanoparticles were synthesized in the presence of peptides using a liquid-handling robot. Samples were analyzed using UV-Vis spectroscopy, fluorescence emission, USAXS, TEM, and SEM. Notebooks for loading and plotting data Code for synthesizing samples using an OT2 Opentrons liquid-handling robot. README: /Data Contains all UV-Vis, electron microscopy, fluorescence, and SAXS data for gold nanoparticles synthesized in the presence of peptides and HEPES. /Data/2021_12_30_Prepared_UV_Vis_Data The primary portion of the experimental dataset. UV-Vis spectroscopy data collected on a Biotek Epoch 2 microplate spectrophotometer 24 hours after samples were synthesized using a liquid handling robot (Opentrons OT2). The 4x4x4_SI.csv file is the compilation of all sample information: Concentrations (M) of peptide, HAuCl4, and HEPES UID – unique ID based on date of synthesis, sample position, and peptide which was used to synthesize the sample. Peptide names: Z2: RMRMKMK; MZ2: myristoylated - RMRMKMK; MZ2R: myristoylated - KMKMRMR; PZ2: palmitoylated – RMRMKMK; Z2M6I: RMRMKIK; Z2M246I: RIRIKIK; AG3: AYSSGAPPMPPF. Each sample’s UID is a key to match with UV-Vis measurement result stored in the {UID}.txt files. Each of these files contains the wavelength, absorbance, and absorbance after subtraction of a water measurement. /Data/2022_02_13_AuPeptide_Kinetics Measurement_Data.xlsx and Measurement_Times.xlsx contain UV-Vis spectra at several time points for each well measured, and the time corresponding to each time step, respectively. See /Notebooks/UV_Vis_Kinetics.ipynb for data plotting and sample concentration information. /Data/ElectronMicroscopy Scanning electron microscopy and transmission electron microscopy results of gold nanoparticles formed from the reduction of HAuCl4 in the presence or absence of different peptides. Fig A, B, C, D, E/F were prepared in the presence of Z2, Z2M6I, Z2M246I, no peptide, and MZ2R, respectively. /Data/Fluorescence Pyrene fluorescence data collected in the presence of different concentrations of lipidated peptides (MZ2, MZ2R, and PZ2) for estimation of the peptide critical micelle concentration. /Data/SAXS SAXS data of a high concentration of MZ2 which was fit using a cylindrical model form factor. The evaluated model is also shared in this directory. /Data/USAXS Similarly to the UV-Vis data directory, the USAXS_SI.csv file contains sample information for all of the USAXS measurements. The dsm_rg.csv file contains the output of AUTORG evaluated on the desmeared data after subtraction of a flat background at high-q. /DSM_Nexus, DSM_sub_AUTORG, and SMR_Nexus contain the desmeared, desmeared with background subtraction, and smeared versions of the USAXS data, respectively. /Notebooks Notebooks for plotting the shared data and estimating the CMC from the fluorescence data. See /Notebooks/environment.yml for packages necessary to execute the notebooks here and in /Synthesis_Protocol. We recommend installing this environment by using: conda env create -f /environment.yml Refer to https://github.com/SasView/sasmodels and the first cell of /Notebooks/USAXS.ipynb for specific instructions on how to complete installation of the sasmodels module (sasmodels will be installed by Pip if you correctly use the shared environment.yml file). /Figures Figures generated from /Notebooks. /Synthesis_Protocol Please read the instructions within /Synthesis_Procol/Example.ipynb. In short, this folder contains the code used to synthesize the samples in this dataset using an OT2 Opentrons liquid handling robot.内容摘要：本数据集源自使用液体处理机器人在多肽存在条件下合成金纳米颗粒的实验数据。实验样品采用紫外-可见（UV-Vis）光谱法、荧光发射光谱、超小角X射线散射（USAXS）、透射电子显微镜（TEM）以及扫描电子显微镜（SEM）进行表征分析。本数据集包含用于数据加载与绘图的Jupyter笔记本代码，以及使用Opentrons OT2液体处理机器人合成样品的代码。 自述文件（README）：/Data 目录包含在多肽与4-羟乙基哌嗪乙磺酸（HEPES）存在条件下合成的金纳米颗粒的全部紫外-可见光谱、电子显微镜、荧光以及小角X射线散射（SAXS）数据。 /Data/2021_12_30_Prepared_UV_Vis_Data：该目录为实验数据集的核心部分。使用Opentrons OT2液体处理机器人合成样品24小时后，采用Biotek Epoch 2微孔板分光光度计采集紫外-可见光谱数据。4x4x4_SI.csv文件汇总了全部样品信息：多肽、氯金酸（HAuCl4）以及HEPES的浓度（单位：mol/L）；唯一标识符（UID, Unique ID）：基于合成日期、样品位置以及合成所用多肽生成的唯一标识。多肽名称及序列如下：Z2: RMRMKMK；MZ2: 肉豆蔻酰化-RMRMKMK；MZ2R: 肉豆蔻酰化-KMKMRMR；PZ2: 棕榈酰化-RMRMKMK；Z2M6I: RMRMKIK；Z2M246I: RIRIKIK；AG3: AYSSGAPPMPPF。每个样品的UID为匹配对应紫外-可见光谱测量结果的键值，测量结果存储于{UID}.txt文件中，每个文件包含波长、吸光度以及扣除空白水测量值后的吸光度数据。 /Data/2022_02_13_AuPeptide_Kinetics：该目录下的Measurement_Data.xlsx与Measurement_Times.xlsx分别存储了各检测孔在多个时间点的紫外-可见光谱数据，以及对应每个时间步的采集时间。数据绘图与样品浓度信息可参考/Notebooks/UV_Vis_Kinetics.ipynb文件。 /Data/ElectronMicroscopy：该目录包含通过氯金酸还原制备的金纳米颗粒的扫描电子显微镜与透射电子显微镜表征结果，实验分别在不同多肽存在或不存在的条件下进行。图A、B、C、D、E/F分别对应添加Z2、Z2M6I、Z2M246I、无多肽以及MZ2R的实验组。 /Data/Fluorescence：该目录包含在不同浓度的脂化多肽（MZ2、MZ2R与PZ2）存在条件下采集的芘荧光光谱数据，用于估算多肽的临界胶束浓度（CMC）。 /Data/SAXS：该目录包含高浓度MZ2的小角X射线散射（SAXS）数据，该数据采用圆柱模型形状因子进行拟合，本次评估所用的模型文件也存储于该目录中。 /Data/USAXS：该目录与紫外-可见光谱数据目录结构类似，其中USAXS_SI.csv文件包含所有超小角X射线散射（USAXS）测量的样品信息。dsm_rg.csv文件存储了AUTORG软件对扣除高q区间平背景后的去弥散散射数据的评估结果。/DSM_Nexus、DSM_sub_AUTORG以及SMR_Nexus目录分别存储了USAXS数据的去弥散版本、扣除背景后的去弥散版本以及带弥散的原始版本。 /Notebooks：该目录包含用于绘制共享数据图表以及通过荧光光谱数据估算临界胶束浓度的Jupyter笔记本代码。可参考/Notebooks/environment.yml文件获取运行本目录以及/Synthesis_Protocol目录下笔记本所需的依赖包。我们推荐通过以下命令创建并配置运行环境：`conda env create -f /environment.yml`。如需安装sasmodels模块的详细说明，请参考https://github.com/SasView/sasmodels链接以及/Notebooks/USAXS.ipynb文件的首个代码单元格（若正确使用本目录提供的environment.yml文件，sasmodels模块将通过Pip自动完成安装）。 /Figures：该目录存储通过/Notebooks目录下代码生成的全部图表。 /Synthesis_Protocol：请先阅读/Synthesis_Protocol/Example.ipynb文件中的操作说明。简言之，该目录包含使用Opentrons OT2液体处理机器人合成本数据集所用样品的代码。