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23 protocols using spectra manager 2 software

1

Circular Dichroism Thermal Unfolding Protocol

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Circular dichroism (CD) measurements were performed using a JASCO J-810 spectropolarimeter (JASCO Inc., Easton, MD, USA) equipped with a Peltier temperature control system containing a quartz cell (path length 0.2 cm). Prior to each measurement, the peptides were thermally annealed: peptide solutions in water (2 × 10−7 M) were pre-heated at 80 °C for 5 min and slowly cooled to 4 °C, then incubated for 24 h. The peptide solutions were transferred to a CD cell and equilibrated for 30 min at 37 °C. A scan speed of 50 nm/min was used, and four scans per sample were acquired. A reference spectrum containing deionized water was subtracted from the final peptide spectrum.
Thermal unfolding curves were obtained by monitoring the decrease in ellipticity in a 25–80 °C temperature range (dependent on the peptide) at a wavelength where the CD spectra show a positive maximum (224 nm) at a heating rate of 10 °C/h. The derivative of the plotted unfolding curve was calculated using the JASCO Spectra Manager II software (JASCO Inc.). The minimum of the derivative indicates the steepest slope of the unfolding process and determines the helix-to-coil transition temperature (Tm) under the described conditions. All experiments were performed in duplicate or triplicate.
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2

Circular Dichroism Analysis of Peptides

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Circular dichroism (CD) measurements were performed using a JASCO J-810 spectropolarimeter (JASCO Inc., Easton, MD, USA) equipped with a Peltier temperature control system containing a quartz cell (path length 0.2 cm). Prior to each measurement, the peptides were thermally annealed: peptide solutions in 0.1X Phosphate Buffer (PBS) (1× 10−4 M) were pre-heated at 80°C for 10 min and slowly cooled to 4°C, then incubated for 24 h. To record the spectra, the peptide solutions were transferred to a CD cell and equilibrated for 30 min at initial scan temperature. A scan speed of 50 nm/min was used, and 4 scans per sample were acquired. A reference spectrum containing buffer was subtracted from the final peptide spectrum.
Thermal unfolding curves were obtained by monitoring the decrease in ellipticity in a 10-80°C temperature range (dependent on the peptide) at a wavelength where the CD spectra show a positive maximum (224 nm) at a heating rate of 0.1°C/min. The derivative of the plotted unfolding curve was calculated using the JASCO Spectra Manager II software (JASCO Inc.). The minimum of the derivative indicates the steepest slope of the unfolding process and determines the helix-to-coil transition temperature (Tm) under the described conditions. All experiments were performed in duplicate or triplicate.
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3

Circular Dichroism Analysis of SGT1 Proteins

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The protein samples for CD measurements were dialyzed overnight against a 10-mM sodium phosphate buffer (pH 7.5) at 4°C. Following dialysis, the sample was centrifuged at 14000 rpm for 30 minutes at 4°C and filtered through a 0.1-µm filter. CD measurements were conducted at room temperature using diluted protein samples (c = 10–47 µM) and a Jasco J-815 spectropolarimeter (Jasco, Japan) with a 0.02 cm cell length path. For full-length SGT1 (c = 12 µM) a total of six scans, ranging from 176 nm to 280 nm, were collected. CD data for TPR-CS (c = 10.4 µM), CS-SGS (12.8 µM) were collected from 190 nm to 280 nm. CS domain from barley SGT1 protein (c = 47 µM) and CS domain of SGT1a from Arabidopsis thalina (46.7 µM) CS domain form were studied from 205 nm to 280 nm. All CD data were collected at a 50 nm/sec scanning speed and 1 nm band-width. Buffer subtraction and spectra deconvolution procedures were conducted using the Jasco Spectra Manager II software and using CDSSTR module on Dichroweb server [35] (link), [36] (link).
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4

Circular Dichroism Spectroscopy of Proteins

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CD spectra were collected using a Jasco J-1500 spectropolarimeter (Jasco, Tokyo, Japan) equipped with a Peltier thermostatic unit set at 20 °C using 0.1 mm optical length quartz cells and driven by a JASCO Spectra Manager II software. The protein concentration was 5 µM in 10 mM K2HPO4 buffered at pH 7. The spectral scans were collected between 250 and 180 nm, 0.5 nm data pitch, 8 s DIT, bandwidth 2 nm, at 50 nm/min scanning speed. Each spectrum was the result of 3 averaged accumulations. Secondary structure estimation was performed by using the Dichroweb server [24 (link)]. All CD spectra were corrected for buffer background. Far‐UV CD signal changes at 220 nm were monitored as a function of increasing temperature from 20 to 90 °C, with steps of 5 °C and with an equilibration time of 1 s at each temperature before recording the measurement. The thermal transitions were analyzed with the CalFitter algorithm [25 (link)].
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5

Circular Dichroism Spectroscopy of Protein

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CD spectra (200–260 nm) were recorded at 20°C and at a scanning speed of 50 nm/min on a J‐1500 CD spectrophotometer (Jasco, Tokyo, Japan) fitted with a quartz cell (0.1 cm path length). The protein concentration was 1 mg/ml in 5 mM 3‐(morpholin‐4‐yl)propane‐1‐sulfonic acid (MOPS; pH 7.6), 25 mM KCl. For measurements with Ca2+, equal volumes of the protein buffer solution and the same buffer supplemented with 0.5 mM CaCl2 were mixed, resulting in a protein concentration of 0.5 mg/ml. Each spectrum was the average of five successive scans. The graphs were smoothed using the integrated function of Spectra Manager II software (Jasco). Secondary structure was predicted using the JWMVS‐529 multivariate SSE analysis program (Jasco).
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6

Characterization of Magnetite Nanocomposites

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FTIR spectroscopy was used to highlight the formation of magnetite in the synthesized samples. FTIR spectra were recorded using an FTIR spectrometer (Jasco FTIR 6300, JASCO Int. Co., Ltd., Tokyo, Japan) equipped with a Golden Gate Specac ATR (KRS5 lens), in the range of 4000–400 cm−1 (32 scans for each point at a spectral resolution of 4 cm−1). The deconvolution of the FTIR spectra was carried using the Jasco spectrum analysis software program (Spectra Manager II software from Jasco Inc., Tokyo, Japan).
The evaluation of the phase composition of the samples was performed using X-ray diffraction analyses, with a Rigaku SmartLab (Rigaku Corp., Tokyo, Japan), operated at 45 kV and 200 mA, with CuKα radiation (1.54059 Å), working in parallel beam configuration (2θ/θ scan mode), with the diffractograms being recorded in the range of 5–90° (2θ). The individual components were identified using the Rigaku Data Analysis Software PDXL 2 database provided by ICDD.
To investigate the morphology and dimensions of the nanostructured thin layers (obtained composites), the samples were sectioned using a diamond disc placed on a support and were introduced into an FEI Electron Microscope (SEM) (Hillsboro, OR, USA). The obtained images were recorded using secondary electron beams at an energy of 30 kV.
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7

FTIR Spectroscopy for Material Analysis

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FTIR spectra were performed with the JASCO 6200 spectrophotometer (JASCO, Pfungstadt, Germany) which has an attenuated total reflectance (ATR) accessory. Measurements were performed in the range 4000–600 cm−1 with a 0.5 cm−1 resolution and a well-plate sampler. The results were analyzed using the Spectra Manager II software (Version 2, JASCO).
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8

Photophysical Characterization of Emitters

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Steady-state PL emission and PL excitation spectra were measured with a spectrofluorometer (JASCO FP-8500) utilizing a Xenon arc lamp with a power of 150 W. PLQE was measured using the same spectrofluorometer equipped with a 100 mm integrating sphere (ILF-835) coated with barium sulfate and the value was calculated using Jasco SpectraManager II software. A correction for taking account of absorption from the scattered light (i.e., indirect configuration) was performed in order to rule out the possibility of overestimating the PLQE when measuring highly scattering powder samples56 (link),57 (link). Confocal PL mapping was performed using an XperRam 200 (Nanobase Inc.) instrument with a 405-nm laser excitation source and a diffraction-limited laser spot size of ~1 μm. Temperature-dependent PL measurements were conducted using the same equipment (XperRam 200, Nanobase Inc.), with the temperature controlled by liquid N2.
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9

Fourier Transform Infrared Spectroscopy

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IR spectra were recorded on a Jasco FT/IR 4100LE spectrometer (Groß-Umstadt, Germany) equipped with a MIRacleTM single reflection ATR device from PIKE Technologies (Fitchburg, WI, USA). Samples were directly placed on the ATR crystal. Data recording and analysis was done with Spectra Manager® II software from Jasco.
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10

Fabrication and Optical Characterization of C-dot Films

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C-dots (250 mg) were dissolved in toluene (5 ml). The solution (5 ml) was mixed with the 10% poly(methyl methacrylate) solution in anisole (5 ml). The mixture was vortexed for 10 min and air bubbles were removed. The mixture (0.5 ml) was then dropped onto 18 mm × 18 mm cover glasses and kept undisturbed for 24 h on a flat table. Once the solvent was evaporated completely, the resulting films were peeled off from the cover glasses and placed over 280–320 nm InGaN light-emitting diodes by using adhesive tapes. Emission spectra were recorded on a Minolta CS2000 spectroradiometer with a Keithley 236 sourcemeter. Internal quantum yields were recorded on a Jasco FP-8500 fluorometer equipped with a 100 mm integrating sphere setup (ILF-835) and calculated by using Jasco Spectra Manager II Software.
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