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Secondary structure estimation software

Manufactured by Jasco

The Secondary Structure Estimation software is a tool designed to analyze the secondary structure of proteins. It provides quantitative information about the secondary structural elements, such as alpha-helices and beta-sheets, present in a given protein sequence or structure.

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5 protocols using secondary structure estimation software

1

Structural Analysis of Nc-aD Virus-Like Particles

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The percentage of protein secondary structures present in the Nc-aD VLPs produced in Sf9 and E. coli was estimated using CD spectroscopy. Purified Nc-aD VLPs (10 µM; 400 µL) were loaded into a quartz cuvette (0.1 cm path length) and scanned with a circular dichroism (CD) spectrometer (JASCO J-815, Japan) at a speed of 100 nm/min at 20 °C. The CD spectrum was collected from wavelengths 190–240 nm. Measurements were done in triplicates. Collected data were analysed using the JASCO secondary structure estimation software [22 (link),45 (link)]. The absorption reading for Nc-aD was corrected by subtracting the absorption reading of the sodium phosphate sample buffer. Measurements of the secondary structures at interval temperatures ranging from 20 to 100 °C were also performed from wavelengths 240 to 190 nm.
To determine the melting temperature (Tm) of Nc-aD VLPs, the samples were prepared as described above for the secondary structure estimation. The samples were subjected to thermal denaturation over a temperature gradient of 20–100 °C, and increment of temperature was maintained at a constant rate of 1 °C/min. Ellipticity and absorbance were recorded using the CD spectrometer (JASCO J-815, Japan), and the spectra were analysed using the JASCO Denaturation Analysis Programme.
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2

Protein Conformational Changes in BSA Microbubbles

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The stabilities of native and denatured BSA shelled microbubbles depend heavily on the protein shell morphologies, which in turn depends on the secondary structures of the proteins. In order to understand the changes in the protein secondary structures during heating, Circular Dichroism (CD) spectroscopy (JASCO J 815) was used. 2 μM solutions of BSA were prepared and used in experiments. The samples were scanned in a 1 mm path length cell, in the wavelength range of 190-320 nm, with 1 nm bandwidth and 3 accumulations during each run, at room temperature. Each sample was tested 3 times to estimate the statistical uncertainties. The data obtained was then analyzed using the JASCO Secondary Structure Estimation software to find the % alpha helix and % beta sheet in different BSA formulations.
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3

Circular Dichroism Spectroscopy of Proteins

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Circular dichroism (CD) spectra were recorded on a model J-810 spectropolarimeter (JASCO) using the Spectra Manager control software package (JASCO). CD spectra were recorded in NaCl 137 mM, KCl 2.7 mM, Na2HPO4 10 mM, KH2PO4 1.8 mM (pH 7.4) in 1-mm quartz glass precision cells at room temperature in a wavelength range of 260–200 nm with 1.0 nm bandwidth, using the continuous-mode setting, with 1.0 sec response and a scan speed of 50 nm/min. Three spectra were averaged; spectra were background-corrected against pure buffer. For normalization, the final protein concentrations were determined by UV/Vis-spectroscopy using pure buffer for background correction. Deconvolution of the data was performed using the Jasco Secondary Structure Estimation software by the reference CD (Yang-Us).
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4

Circular Dichroism Spectroscopy for Protein Secondary Structure

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ECD spectra were recorded on a Jasco J-815 spectrometer (Jasco Corporation, Tokyo, Japan) equipped with the 150 W xenon lamp in the range of 190–340 nm using quartz cell of 0.01, 0.1 and 1 cm path length at room temperature. All spectra reported here (both for protein and protein with some amount of SDS) were recorded using a standard sensitivity, a scanning speed of 50 nm min-1, a step size of 0.1 nm, a bandwidth of 1 nm, a response time of 1 s, and an accumulation of 5 scans. Baseline correction was achieved by subtracting the spectrum of phosphate-buffered saline (PBS) as a solvent recorded under the same conditions. The reported mean residue ellipticity values were expressed in the unit of deg cm2 dmol-1. They were obtained using a molecular mass of each relevant protein and a total number of amino acids. For estimation of the secondary structural composition the ECD spectra were submitted to the Jasco Secondary Structure Estimation (SSE) software based on the Principle Component Regression method. The multivariate analysis allowed us to obtain quantitative data of helix, sheet and random coil contents from ECD spectra.
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5

β-Lactoglobulin Structural Analysis

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The sample of β-LG (0.3 mg/mL) was suspended in 0.09% citrate buffer at pH = 3.0, 5.0, and 7.0, respectively. Far UV circular dichroism (UV–CD) was performed using J-815 spectrometer (JASCO, Cremella (LC), Italy). The experimental conditions were as follows: sensitivity: high, response: 1 sec, band width: 1 nm, scanning speed: 50 nm/min, accumulation: 10, data pitch: 0.2 nm. All data were background-corrected against citrate buffer in certain pH. All data were acquired in the range from 300 to 190 nm at room temperature using the quartz cell with a path length of 0.02 cm. For estimation of the secondary structural composition, the ECD spectra were submitted to the JASCO Secondary Structure Estimation (SSE) software based on the Principal Component Regression method (PCR). The multivariate analysis allowed us to obtain quantitative data of α-helix, β-sheet, turns, and random coil contents from experimental CD spectra.
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