DOI: 10.7910/dvn/gmeeyl
title: Replication Data for: Protein Secondary Structure in Spider Silk Nanofibrils

description: &lt;p&gt;This dataset contains raw data, processed data, and the codes used for data processing in our manuscript from our Fourier-transform infrared (FTIR) spectroscopy, Nuclear magnetic resonance (NMR), Raman spectroscopy, and X-ray diffraction (XRD) experiments. The data and codes for the fits of our unpolarized Raman spectra to polypeptide spectra is also included. The following explains the folder structure of the data provided in this dataset, which is also explained in the file &lt;b&gt;ReadMe.txt&lt;/b&gt;.&lt;/p&gt;

&lt;p&gt;Browsing the data in "Tree" view is recommended.&lt;/p&gt;

&lt;h2&gt;Folder contents&lt;/h2&gt;

&lt;h3&gt;Codes&lt;/h3&gt;
&lt;ol&gt;
&lt;li&gt;&lt;b&gt;Raman Data Processing:&lt;/b&gt; The MATLAB script file &lt;i&gt;RamanDecomposition.m&lt;/i&gt; contains the code to decompose the sub-peaks across different polarized Raman spectra (&lt;i&gt;XX&lt;/i&gt;, &lt;i&gt;XZ&lt;/i&gt;, &lt;i&gt;ZX&lt;/i&gt;, &lt;i&gt;ZZ&lt;/i&gt;, and &lt;i&gt;YY&lt;/i&gt;), considering a set of pre-determined restrictions. The helper functions used in &lt;i&gt;RamanDecomposition.m&lt;/i&gt; are included in the &lt;i&gt;Helpers&lt;/i&gt; folder. &lt;i&gt;RamanDecomposition.pdf&lt;/i&gt; is a PDF printout of the MATLAB code and output.&lt;/li&gt;
&lt;li&gt;&lt;b&gt;P Value Simulation:&lt;/b&gt;
&lt;ul&gt;
&lt;li&gt;&lt;b&gt;31_helix.ipynb and a_helix.ipynb:&lt;/b&gt; These two Jupyter Notebook files contain the intrinsic &lt;i&gt;P&lt;/i&gt; value simulation for the 31-helix and alpha-helix structures. The simulation results were used to prepare Supplementary Table 4. See more details in the comments contained.&lt;/li&gt;
&lt;li&gt;&lt;b&gt;Vector.py, Atom.py, Amino.py, and Helpers.py:&lt;/b&gt; These python files contains the class definitions used in &lt;i&gt;31_helix.ipynb&lt;/i&gt; and &lt;i&gt;a_helix.ipynb&lt;/i&gt;. See more details in the comments contained.&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;/ol&gt;

&lt;h3&gt;FTIR&lt;/h3&gt;
&lt;ol&gt;
&lt;li&gt;&lt;b&gt;FTIR Raw Transmission.opj:&lt;/b&gt; This Origin data file contains the raw transmission data measured on single silk strand and used for FTIR spectra analysis.&lt;/li&gt;
&lt;li&gt;&lt;b&gt;FTIR Deconvoluted Oscillators.opj:&lt;/b&gt; This Origin data file was generated from the data contained in the previous file using W-VASE software from J. A. Woollam, Inc.&lt;/li&gt;
&lt;li&gt;&lt;b&gt;FTIR Unpolarized MultiStrand Raw Transmission.opj:&lt;/b&gt; This Origin data file contains the raw transmission data measured on multiple silk strands.&lt;/li&gt;
&lt;/ol&gt;
&lt;p&gt;The datasets contained in the first two files above were used to plot Figure 2a-b and the FTIR data points in Figure 4a, and Supplementary Figure 6. The datasets contained in the third file above were used to plot Supplementary Figure 3a.&lt;/p&gt;

&lt;p&gt;The datasets contained in the first two files above were used to plot Figure 2a-b, FTIR data points in Figure 4a, and Supplementary Figure 6.&lt;/p&gt;

&lt;h3&gt;NMR&lt;/h3&gt;
Raw data files of the 13C MAS NMR spectra:
&lt;ol&gt;
&lt;li&gt;&lt;b&gt;ascii-spec_CP.txt:&lt;/b&gt; cross-polarized spectrum&lt;/li&gt;
&lt;li&gt;&lt;b&gt;ascii-spec_DP.txt:&lt;/b&gt; direct-polarized spectrum&lt;/li&gt;
&lt;/ol&gt;
Data is in ASCII format (comma separated values) using the following columns:
&lt;ol&gt;
&lt;li&gt;&lt;b&gt;Data point number&lt;/b&gt;&lt;/li&gt;
&lt;li&gt;&lt;b&gt;Intensity&lt;/b&gt;&lt;/li&gt;
&lt;li&gt;&lt;b&gt;Frequency [Hz]&lt;/b&gt;&lt;/li&gt;
&lt;li&gt;&lt;b&gt;Frequency [ppm]&lt;/b&gt;&lt;/li&gt;
&lt;/ol&gt;

&lt;h3&gt;Polypeptide Spectrum Fits&lt;/h3&gt;
&lt;ol&gt;
&lt;li&gt;&lt;b&gt;MATLAB scripts (.m files) and Helpers:&lt;/b&gt;
&lt;ul&gt;
&lt;li&gt;The MATLAB script file &lt;i&gt;Raman_Fitting_Process_Part_1.m&lt;/i&gt; and &lt;i&gt;Raman_Fitting_Process_Part_2.m&lt;/i&gt; contains the step-by-step instructions to perform the fitting process of our calculated unpolarized Raman spectrum, using digitized model polypeptide Raman spectra.&lt;/li&gt;
&lt;li&gt;The &lt;i&gt;Helper&lt;/i&gt; folder contains two helper functions used by the above scripts.&lt;/li&gt;
&lt;li&gt;See the scripts for further instruction and information.&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;li&gt;&lt;b&gt;Data&lt;/b&gt;
&lt;ul&gt;
&lt;li&gt;&lt;b&gt;aPA.csv, bPA.csv, GlyI.csv, GlyII.csv files:&lt;/b&gt;
&lt;ul&gt;&lt;li&gt;These csv files contain the digitized Raman spectra of poly-alanine, beta-alanine, poly-glycine-I, and poly-glycine-II.&lt;/li&gt;&lt;/ul&gt;
&lt;/li&gt;
&lt;li&gt;&lt;b&gt;Raman_Exp_Data.mat:&lt;/b&gt;
&lt;ul&gt;
&lt;li&gt;This MATLAB data file contains the processed, polarized Raman spectra obtained from our experiments.&lt;/li&gt;
&lt;li&gt;Variable &lt;i&gt;freq&lt;/i&gt; is the wavenumber information of each collected spectrum. The variables &lt;i&gt;xx&lt;/i&gt;, &lt;i&gt;yy&lt;/i&gt;, &lt;i&gt;zz&lt;/i&gt;, &lt;i&gt;xz&lt;/i&gt;, &lt;i&gt;zx&lt;/i&gt; represent the polarized Raman spectra collected.&lt;/li&gt;
&lt;li&gt;These variables are used to calculate the unpolarized Raman spectrum in &lt;i&gt;Raman_Fitting_Process_Part_2.m&lt;/i&gt;.&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
See the scripts for further instruction and information.
&lt;/ul&gt;
&lt;/li&gt;
&lt;/ol&gt;

&lt;h3&gt;Raman&lt;/h3&gt;
&lt;ol&gt;
&lt;li&gt;&lt;b&gt;Raman Raw Data.mat:&lt;/b&gt;
&lt;ul&gt;
&lt;li&gt;This MATLAB data file contains all the raw data used for Raman spectra analysis. All variables are of MATLAB structure data type. Each variable has fields called &lt;i&gt;Freq&lt;/i&gt; and &lt;i&gt;Raw&lt;/i&gt;, with &lt;i&gt;Freq&lt;/i&gt; contains the wavenumber information of the measured spectra and &lt;i&gt;Raw&lt;/i&gt; contains 5 measured Raman signal strengths.&lt;/li&gt;
&lt;li&gt;Variable &lt;i&gt;XX&lt;/i&gt;, &lt;i&gt;XZ&lt;/i&gt;, &lt;i&gt;ZX&lt;/i&gt;, &lt;i&gt;ZZ&lt;/i&gt;, and &lt;i&gt;YY&lt;/i&gt; were used to plot and sub-peak analysis for Figure 2c-d, Raman data points in Figure 4a, Figure 5b, Supplementary Figure 2, and Supplementary Figure 7.&lt;/li&gt;
&lt;li&gt;Variable &lt;i&gt;WideRange&lt;/i&gt; was used to plot and identify the peaks for Supplementary Figure 3b.&lt;/li&gt;
&lt;/ul&gt;
&lt;/ol&gt;

&lt;h3&gt;X-Ray&lt;/h3&gt;
&lt;ol&gt;
&lt;li&gt;&lt;b&gt;X-Ray.mat:&lt;/b&gt; This MATLAB data file contains the raw X-ray data used for the diffraction analysis in Supplementary Figure 5.&lt;/li&gt;
&lt;/ol&gt;