Comparison of protein secondary structure calculation methods based on infrared spectra deconvolution

Андреевич, Усольцев Дмитрий; Евгеньевна, Ситникова Вера; Николаевна, Носенко Татьяна; Олегович, Олехнович Роман; Валерьевна, Успенская Майя

doi:10.17586/2226-1494-2019-19-4-586-593

Cited by 4 publications

(2 citation statements)

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“…The analysis of the second derivative, the FSD method, and curve fitting, applied in analyzing the protein spectra, gives reasonable results for the protein secondary structure [19], consistent with each other and with X-ray data [20]. Besides, the second derivative, despite the subjectivity of determining the baseline for the derivative of the spectrum [21], has enormous advantages (it separates the components of amide I without any arbitrary input factors, such as the band half-width and enhancement factor) and gives a more accurate result [22].…”

Section: Introductionmentioning

confidence: 54%

“…The protein spectra used for analysis were obtained by subtracting the spectra of an aqueous solution using Opus 7.0 software. The secondary structure was determined by decomposing the second derivative of the amide I band in the OriginPro 2015 software (OriginLab Corporation, Northampton, MA, USA), by the method described in [20,22]. All second derivatives were multiplied by −1 for easy decomposition.…”

Section: Methodsmentioning

confidence: 99%

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Systematic FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin under Various Denaturation Conditions

et al. 2019

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Human serum albumin (HSA) is the most abundant protein in blood plasma. HSA is involved in the transport of hormones, fatty acids, and some other compounds, maintenance of blood pH, osmotic pressure, and many other functions. Although this protein is well studied, data about its conformational changes upon different denaturation factors are fragmentary and sometimes contradictory. This is especially true for FTIR spectroscopy data interpretation. Here, the effect of various denaturing agents on the structural state of HSA by using FTIR spectroscopy in the aqueous solutions was systematically studied. Our data suggest that the second derivative deconvolution method provides the most consistent interpretation of the obtained IR spectra. The secondary structure changes of HSA were studied depending on the concentration of the denaturing agent during acid, alkaline, and thermal denaturation. In general, the denaturation of HSA in different conditions is accompanied by a decrease in α-helical conformation and an increase in random coil conformation and the intermolecular β-strands. Meantime, some variation in the conformational changes depending on the type of the denaturation agent were also observed. The increase of β-structural conformation suggests that HSA may form amyloid-like aggregates upon the denaturation.

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