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7 protocols using j 1500 magnetic circular dichroism spectrometer

1

CD Spectroscopy Analysis of Protein-Ligand Interactions

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The Jasco J-1500 magnetic circular dichroism spectrometer (JASCO International CO., Tokyo, Japan) was used to measure CD spectra. Circular dichroism spectra were collected for protein solutions and after adding small portions of analyzed phthalimide analogs. Phosphate buffer was used as a solvent here (pH 7.5), and due to this, physiological parameters were simulated here. The parameters of measurements of CD measurements were as follows: the range was 205–250 nm for BSA and AAG, and 210–250 nm for GG, scan speed rate was equal to 50 nm/min, with a response time of 1 s, path length—10 mm. The concentrations of solution used were 1.0 μM, and 1.0 μM for the proteins and phthalimide analogs, respectively. The molar ratios of proteins and ligands were equal to 1:0, 1:0.5, 1:1, 1:5, and 1:10. The CD Multivariate Calibration Creation and CD Multivariate SSE programs (JASCO International CO., Tokyo, Japan) were used for the analysis of the secondary structure elements. Mean residue molar concentrations of proteins have been included in this analysis.
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2

Circular Dichroism Analysis of Protein-Ligand Interactions

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Circular dichroism (CD) spectra were measured on the Jasco J-1500 magnetic circular dichroism spectrometer (JASCO International CO., Tokyo, Japan) at room temperature with a 10 mm path length. All spectra for the HSA and AAG solutions in the absence and presence of 5a, 5b, and 5c were measured under simulated physiological conditions in pH 7.4, in phosphate buffer as a solvent, and were baseline corrected (the spectrum phosphate buffer was used as a baseline). The spectra were measured in the range of 205–250 nm at a scan rate speed of 50 nm/min, with a response time of 1 s. The concentration of HSA and AAG was 1·10−6 M, while for 5a, 5b, and 5c, it was 1·10−3 M. Experiments were performed to obtain the appropriate protein to compound molar ratios equal to 1:0, 1:0.5, 1:1, 1:1, 1:3, and 1:5. They were respectively added into 3 mL of protein solution successive portions of the solutions of the analyzed compounds. The analysis of the obtained results was performed using the CD Multivariate Calibration Creation and CD Multivariate SSE programs (JASCO International CO., Tokyo, Japan). Protein concentrations were converted here for mean residue molar concentrations.
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3

Circular Dichroism Spectroscopy of Protein-Peptide Interactions

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Circular dichroism (CD) spectroscopy was performed using the Jasco J-1500 magnetic circular dichroism spectrometer (JASCO International CO., Tokyo, Japan). All measurements for the protein solutions in the absence and presence of the analyzed peptides L1, L2, and L3 were made at room temperature under simulated physiological conditions in pH 7.4, in phosphate buffer as a solvent. The phosphate buffer not only controls the stable pH but also imitates the biological environments. However, its use leads to some limitations for CD measurements due to containing NaCl and KCl. The spectra were baseline corrected (phosphate buffer was used as a baseline) and were measured in the range of 205–250 nm at a scan rate speed of 50 nm/min, with a response time of 1 s, and a 10 mm or 5 mm path length for BSA and GGF, respectively. The concentrations of proteins and analyzed peptides were 1 × 10−6 mol/dm3 and 1 × 10−3 mol/dm3, respectively. Experiments were performed with protein to ligand molar ratios: 1:0, 1:0.25, 1:0.5, 1:0.75, 1:1, and 1:1.5. In total, 3 cm3 of a solution of each protein was titrated by successive additions of analyzed peptides. The results were analyzed by CD Multivariate Calibration Creation and CD Multivariate SSE programs (JASCO International CO., Tokyo, Japan), with the conversion of protein concentrations for mean residue molar concentrations.
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4

Circular Dichroism Analysis of Protein-Ligand Interactions

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Circular dichroism (CD) spectra were measured on a Jasco J-1500 magnetic circular dichroism spectrometer (Jasco International Co., Tokyo, Japan). Human serum albumin (HSA) and α-1-acid glycoprotein (AAG) powders were purchased from Sigma Aldrich. All measurements for the protein solutions in the absence and presence of the analyzed pyrrolo[3,4-c]pyrrole analogues 7a7n were made under simulated physiological conditions in pH 7.4 in phosphate buffer (in tablets, Sigma Aldrich) as a solvent at room temperature. The spectra were measured in the range of 205–250 nm at a scan rate of 50 nm/min, with a response time of 1 s and 10 mm path length. All of them were baseline-corrected (phosphate buffer was used as a baseline). The concentration of proteins was 1 × 10−6 mol/dm3, while for the analyzed compounds 7a7n, the concentration was equal to 1 × 10−3 mol/dm3. Experiments were performed with protein-to-ligand molar ratios of 1:0, 1:0.5, 1:1, 1:1, 1:3, and 1:5. A solution of each protein (3 cm3) was titrated by successive additions of analyzed compounds. The analysis of obtained results was made by CD Multivariate Calibration Creation and CD Multivariate SSE programs (Jasco International Co., Tokyo, Japan), with the conversion of protein concentrations for mean residue molar concentrations.
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5

Circular Dichroism Spectroscopy Analysis

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Circular dichroism (CD) spectra were measured on a Jasco J-1500 magnetic circular dichroism spectrometer (JASCO International CO., Tokyo, Japan). All of the measurements for the BSA, AAG, and GG solutions in the absence and presence of the analyzed compounds were made at room temperature under simulated physiological conditions at pH 7.4 in phosphate buffer as a solvent. The CD spectra were measured in the range of 205–250 nm for BSA and AAG and 210–250 for GG at a scan rate speed of 50 nm/min with a response time of 1 s and a 10 mm path length. All spectra were baseline-corrected. The concentrations of BSA, AAG, and GG were 1 × 10−6 mol/dm3. For the analyzed compounds F1, F2, F3, and F4, the concentration was equal to 1×10−3 mol/dm3. Experiments were performed on each analyzed compound in molar protein-to-ligand ratios equal to 1:0, 1:0.5, 1:1, 1:5, and 1:10, and 2 cm3 of a solution of each protein was titrated by successive additions of solutions of the analyzed compounds to give final molar ratios. The percentage content of the secondary structure elements of the analyzed proteins was obtained by CD Multivariate Calibration Creation and CD Multivariate SSE programs (JASCO International CO., Tokyo, Japan). For this purpose, the protein concentrations were converted to mean residue molar concentrations.
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6

Spectroscopic Characterization of Peptide Complexes

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Visible spectra of complexes for the P1 and P2 systems were recorded at 25 °C on a Varian Cary 50 Bio spectrophotometer (Varian Inc., Palo Alto, CA, USA) in the 300–800 nm range. Circular dichroism and magnetic circular dichroism spectra were recorded on a Jasco J-1500 magnetic circular dichroism spectrometer (Jasco, Japan, Tokyo) in the range of 230–800 nm at 25 °C for all of the synthetic peptides that were analyzed. Spectra were collected at a scan rate speed of 100 nm min−1 with a response time of 1 s. A path length of 10 mm was used in both the UV-Vis and CD methods. MCD spectra were measured with the use of a Permanent Magnet PM-491 accessory and collected at a scan rate speed of 100 nm min−1 with response time of 1 s, with a 5 mm path length and in a magnetic field of +1.6 T, in the N/S field direction. MCD spectra were also recorded for the previously reported BCS ligand [13 (link)], in the same conditions described above. All spectroscopic measurements were collected in the 2.5–10 pH range, in increments of a half unit. The ligand concentration was 7 × 10−4 mol/L and solutions were prepared in 0.3 mol/L KCl. Sample volumes were 2.0 mL. The pH values were established using a Mettler Toledo pH-meter by adding small amounts of concentrated KOH and HCl solutions.
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7

Spectroscopic Characterization of Complexes

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Visible spectra of complexes were recorded at 25 °C on Varian Carry 50 Bio spectrophotometer. The electron paramagnetic resonance (EPR) spectra were recorded on Bruker ELEXSYS E500 CW-EPR, X-Band spectrometer, equipped with ER 036TM NMR Teslameter and E 41 FC frequency counter. The EPR simulated spectra and all EPR parameters were obtained by the Biomolecular EPR Spectroscopy Software of Wilfred R. Hagen (Hagen 2009 ). Circular dichroism (CD) spectra were recorded on Jasco J-1500 magnetic circular dichroism spectrometer in 230–800 nm range. The same concentrations were used for both spectroscopic and potentiometric studies.
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