Quantification of protein secondary structure content by multivariate analysis of deep-ultraviolet resonance Raman and circular dichroism spectroscopies

Oshokoya, Olayinka O.; Roach, Carol A.; JiJi, Renee D.

doi:10.1039/c3ay42032a

Cited by 19 publications

(18 citation statements)

References 51 publications

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“…However, conventional Raman spectroscopy lacks the spatial resolution fordetailed characterizations of the peptide nanostructures duelow signal to noise ratios at dilute conditions,and different approaches have been developed to improve the scattering intensities for the analysis. UV resonance Raman spectroscopy, which enhances the frequencies in vibrational amide modes including amide III and C α -H bands were applied to selectively monitor the secondary, tertiary or quaternary organization of the peptides in solution [255][256][257][258]. The relatively low Raman signal of the peptide assemblies wasalso increased via surface-enhanced Raman scattering (SERS) using the localized surface plasmon resonances of the metallic clusters in liquid or solid environments [259,260].…”

Section: Spectroscopic Analysismentioning

confidence: 99%

Self-assembled peptide nanostructures for functional materials

et al. 2016

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Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.

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Section: Spectroscopic Analysismentioning

confidence: 99%

Self-assembled peptide nanostructures for functional materials

et al. 2016

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“…The aromatic amino acid contributions (phenylalanine and tyrosine) were quantitatively subtracted as described by Oshokoya et al [45] Spectra of phenylalanine and tyrosine were subtracted from corresponding protein spectra collected at the same excitation wavelength.…”

Section: Data Preprocessing and Analysismentioning

confidence: 99%

“…[39] Initially, quantification studies of protein secondary structure employing DUVRR focused on univariate calibration methods of single amide modes, [26] but have evolved to include multivariate calibration and multivariate curve resolution methods and other advanced statistical analyses of all observable amide modes. [22,35,36,[40][41][42][43][44][45] In these methods, first order data are decomposed using bilinear models showing that individual protein spectra, x, are a linear combination of the different underlying pure secondary structure motifs, s, and their respective fractional amounts, c (Equation 1);…”

Section: Introductionmentioning

confidence: 99%

“Parallel factor analysis of multi-excitation ultraviolet resonance Raman spectra for protein secondary structure determination”

Oshokoya

JiJi

2015

Analytica Chimica Acta

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Protein secondary structural analysis is important for understanding the relationship between protein structure and function, or more importantly how changes in structure relate to loss of function. The structurally sensitive protein vibrational modes (amide I, II, III and S) in deep-ultraviolet resonance Raman (DUVRR) spectra resulting from the backbone C-O and N-H vibrations make DUVRR a potentially powerful tool for studying secondary structure changes. Experimental studies reveal that the position and intensity of the four amide modes in DUVRR spectra of proteins are largely correlated with the varying fractions of α-helix, β-sheet and disordered structural content of proteins. Employing multivariate calibration methods and DUVRR spectra of globular proteins with varying structural compositions, the secondary structure of a protein with unknown structure can be predicted. A disadvantage of multivariate calibration methods is the requirement of known concentration or spectral profiles. Second-order curve resolution methods, such as parallel factor analysis (PARAFAC), do not have such a requirement due to the "second-order advantage." An exceptional feature of DUVRR spectroscopy is that DUVRR spectra are linearly dependent on both excitation wavelength and secondary structure composition. Thus, higher order data can be created by combining protein DUVRR spectra of several proteins collected at multiple excitation wavelengths to give multi-excitation ultraviolet resonance Raman data (ME-UVRR). PARAFAC has been used to analyze ME-UVRR data of nine proteins to resolve the pure spectral, excitation and compositional profiles. A three factor model with non-negativity constraints produced three unique factors that were correlated with the relative abundance of helical, β-sheet and poly-proline II dihedral angles. This is the first empirical evidence that the typically resolved "disordered" spectrum represents the better defined poly-proline II type structure.

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“…Accordingly, multivariate analysis tools like principal component analysis (PCA), partial least squares (PLS) to latent structures, orthogonal PLS, canonical variate analysis (CVA), extended CVA (ECVA), and others, are widely used as they are efficient, validated, and robust methods for modelling many sorts of biological and chemical data . For example, PLS, PCA, and others, have been applied on spectroscopic data for optimizing the protein secondary structure determination . Furthermore, chemometric tools are used to support the study of protein aggregation, interactions with certain molecules with biological interest, and protein–surfactant interactions .…”

Section: Introductionmentioning

confidence: 99%

“…[27,28] For example, PLS, PCA, and others, have been applied on spectroscopic data for optimizing the protein secondary structure determination. [29][30][31] Furthermore, chemometric tools are used to support the study of protein aggregation, [32] interactions with certain molecules with biological interest, [33] and protein-surfactant interactions. [34] More specifically, CVA has been applied in the characterization of protein folding transition.…”

Section: Introductionmentioning

confidence: 99%

A comprehensive study of protein–mesoporous–macroporous silica interactions by extended canonical variate analysis of Raman spectra

Videira‐Quintela

Prazeres

Ortega-Ojeda

et al. 2019

J Raman Spectroscopy

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Understanding the protein–support interactions is of major importance when manufacturing bionanomaterials to a certain application. These interactions can be the cause for enhanced properties or denaturation phenomena in the target protein. Raman spectroscopy was applied to a bionanomaterial comprehending the protein β‐galactosidase immobilized by physical adsorption into a mesoporous–macroporous silica material, with a nanoporous network consisting of 9‐nm mesopores and 200‐nm macropores. Raman spectra of the bionanomaterial evidenced a complex amount of differences related to the Raman shifts, intensities, band enlargement, appearance of new bands, and overlapping, in comparison with the silica support and the protein spectra. To help in the analysis of the Raman spectra and in the inspection of possible protein–support interactions, ECVA (extended canonical variate analysis) was used as a chemometric complementary tool, dividing the spectra into four segments: 1 (3,100 to 2,800 cm−1), 2 (1,800 to 1,500 cm−1), 3 (1,500 to 1,200 cm−1), and 4 (1,200 to 900 cm−1). Major alterations in the Amide I band (1,800 to 1,500 cm−1) and the amino acid band regions demonstrated possible structure alterations to a non‐native form of the protein β‐galactosidase. Also, other minor alterations were observed in other spectral regions (3,100 to 2,800 cm−1,1,500 to 1,200 cm−1, and 1,200 to 900 cm−1) also representative of protein structure alteration due to protein–support interactions.

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Quantification of protein secondary structure content by multivariate analysis of deep-ultraviolet resonance Raman and circular dichroism spectroscopies

Abstract: Determination of protein secondary structure (α-helical, β-sheet, and disordered motifs) has become an area of great importance in biochemistry and biophysics as protein secondary structure is directly related to protein function and protein related diseases.

Cited by 19 publications

References 51 publications

Self-assembled peptide nanostructures for functional materials

Self-assembled peptide nanostructures for functional materials

“Parallel factor analysis of multi-excitation ultraviolet resonance Raman spectra for protein secondary structure determination”

A comprehensive study of protein–mesoporous–macroporous silica interactions by extended canonical variate analysis of Raman spectra

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