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32 protocols using peakfit 4

1

Quantifying Crystallinity via XRD Analysis

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The XRD analysis of samples was carried out using an X-ray powder diffractometer (D8, Bruker, Germany), operated at 40 kV and 40 mA. Samples were manually packed tightly onto the glass sample holder, and data collected over an angular range from 2θ = 4° to 35° with a step of 0.02° [14 (link)]. Their relative crystallinity was calculated as the ratio of the corresponding crystalline peak area to the total diffraction area, wherein the crystalline peak area and amorphous area were separated by PeakFit 4.0 software (Systat Software Inc., San Jose, CA, USA) following a published method [17 (link)].
Relative crystallinity =Crystalline peak area Crystalline peak area+amorphous area
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2

Raman Spectroscopy for Drug-Alkalizer Interactions

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Raman was used as complement to FTIR for a more direct characterization of the molecular details of the interaction between the drug and the alkalizers. Raman spectroscopy was recorded on a Renishaw (Renishaw, London, UK) inVia laser micro-Raman spectrometer using a 785 nm laser source with power of 300 mW. Samples were placed on an aluminum plate in front of a 50 × objective lens. The acquisition time for each spectrum was 10 s. A Raman spectrum was obtained in the spectral range of 3500–200 cm−1. The spectral data was first pre-processed using WiRE software (Wire Swiss, Zug, Switzerland) and the peak position was deconvoluted and analyzed using PeakFit 4.0 software (Systat Software, San Jose, CA, USA).
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3

FT-IR Analysis of Heat-Treated Silk

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The FT-IR spectroscopy was performed for the silk subjected to different heat treatments (30–90 °C). In this experiment, an autoimage attenuated total reflectance Fourier transform infrared spectroscopic (ATR-FT-IR) microscopy system (Perkin Elmer, Llantrisant, UK) was used to probe the silk samples. The resolution of the mercury cadmium telluride (MCT) detector was 4 cm−1, and the operation condition of the scan number was 128. After the FT-IR spectra were obtained, software PeakFit® 4.11 (Systat Software) was used for further FT-IR spectrum deconvolution and secondary structure analysis.
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4

Cuticle and Cutin Structural Analysis

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XRD diffraction patterns were obtained with an X'Pert Pro (Malvern PANalytical) automated diffractometer using Ge(111)-monochromated CuKa radiation and an X'Celerator detector. Diffractograms were recorded between 5°and 45°(2u) in 0.017°steps at 45 kV and 35 mA for 30 min. Isolated cuticle and cutin samples were placed on an aluminum support adapting them to the goniometer in a u to 2u configuration. The position and the FWHM of peaks were determined after fitting using the software PeakFit 4.11 (Systat Software). The basal spacing d, the average separation between polymer chains in the cuticles, was calculated from the rearrangement of Bragg's diffraction equation: d 5 ½ðl=sin uÞ;
where l is the wavelength of radiation (;1.54 Å) and u is the diffraction maximum angle. The FWHM parameter was calculated by difference of the basal spacings for the strong maximum at half-height intensity.
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5

HPLC-based CPAF Activity Assay

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HPLC-based CPAF activity assays were conducted as described previously at room temperature in a buffer containing 50 mM Tris (pH 7.5), 150 mM NaCl, and 5 mM DTT with CPAF (1 nM) and varying concentrations of 1 (0.23–1.50 mM) in a total volume of 100 μL.22 (link) Michaelis–Menten kinetic parameters were determined following peak integration using PeakFit 4.11 (Systat Software) and analysis in GraphPad Prism (GraphPad Software) using eq 1.
ν=Vmax[S]Km+[S]
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6

Infrared Spectroscopy Analysis of Molecular Structure

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Secondary structure analysis of samples was performed as described by Luo et al. [14] with slight modification. Briefly, freeze-dried powder sample and KBr (2:100) were mixed, compressed, then scanned in the range of 4000–400 cm−1 at a speed of 4 cm−1 using a Vertex 70 Fourier infrared spectrometer (Bruker Co., Ltd., Ettlingen, Germany). Peakfit 4.11 (Systat Software Inc., San Jose, CA) was used to analyze the data of 1600–1700 cm−1 (amide I band).
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7

Capillary Electrophoresis Separation Technique

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The electrophoretic separations were carried out using a P/ACE MDQ instrument (Beckman Instruments, Fullerton, CA, USA). The capillary in this system was maintained at 25°C during the separation, which was performed in most experiments at an applied potential of −30 kV (i.e., in the reversed polarity mode). This system used 60.2 cm × 50 μm I.D. fused silica capillaries (Polymicro Technologies, Phoenix, AZ, USA) with an effective length to the detector of 50 cm. Absorbance detection was carried out at 200 nm, and the CE data were collected by using 32 Karat software 7.0 from Beckman. These data were analyzed by utilizing Peakfit 4.12 software (Systat Software, San Jose, CA, USA).
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8

Oligomeric Protein Analysis by SEC

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Protein oligomers were analysed using size-exclusion chromatography. Samples were loaded on a Superdex 200 Increase 10/300 (GE Healthcare, Piscataway, NJ, USA) column pre-equilibrated with carbonate buffer at 0.75 ml min -1 . Protein samples intended for small-angle X-ray scattering (SAXS) were prepared by collecting fractions corresponding to each oligomer population and concentrated to 5 mg ml -1 , using an Amicon Centrifugal Filters 3 K (Millipore, Cork, Ireland). The supernatant was centrifuged at 15 000g for 30 min to remove possible aggregates and stored at -80 °C. Protein oligomers were re-analysed under the same SEC conditions to assess the structural stability upon separation. The hydrodynamic radius (R h ) was obtained using a protein standard (GE Healthcare, Piscataway, NJ, USA), and the relative amounts of oligomeric forms were calculated by Gaussian deconvolution of the obtained size-exclusion chromatograms using the Peakfit 4.12 software (Systat Software Inc.) and applying a residual method to resolve the overlapped peaks.
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9

Disulfide Bond and Aromatic Amino Acid Analysis

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The conformation of disulfide bonds and aromatic amino acid SFFCNs was analyzed using confocal Raman spectroscopy (RFT-6000FT, JASCO, Europe) (Wang et al., 2020 (link), Wang et al., 2020 (link)). The spectra were acquired within the range of 400–3500 cm−1 using a 1064 nm laser with a resolution of 1 cm−1. Baseline correction was performed using Origin v8.0 (Origin Lab Inc., MA, USA), followed by normalization based on the peak phenylalanine at 1003 cm−1. Raman spectra before and after normalization (Fig. S2). The spectral region ranging from 490 to 560 cm−1 was subjected to S—S conformation analysis using Peak-fit 4.12 software (Systat Software, Chicago, USA) with the application of deconvolution techniques.
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10

Haem Secondary Structure Analysis

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The secondary structure of haem (5 mg/mL) was analysed using VERTEX 70 FTIR spectroscopy (BRUKER, Karlsruhe, Germany). The dispersion medium was deionised water. Scanning was performed using a scanning infrared spectrometer at points between 400 and 4000 cm−1. Subsequently, data between 1600 and 1700 cm−1 were extracted for a Gaussian fit using Peakfit 4.12 software (Systat Software Inc., California, USA). The contents of the α-helix, β-sheet, β-turn and random coil were then calculated (Zhao, et al., 2021 (link)).
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