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

2014 ◽  
Vol 6 (6) ◽  
pp. 1691-1699 ◽  
Author(s):  
Olayinka O. Oshokoya ◽  
Carol A. Roach ◽  
Renee D. JiJi
Keyword(s):  
Multivariate Analysis ◽  
Secondary Structure ◽  
Protein Function ◽  
Resonance Raman ◽  
Protein Secondary Structure ◽  
Secondary Structure Content ◽  
Deep Ultraviolet ◽  
Ultraviolet Resonance Raman ◽  
Β Sheet

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.

scholarly journals Development of advanced chemometric methods for analysis of deep-ultraviolet resonance Raman and circular dichroism spectroscopic data for protein secondary structure determination

2015 ◽  
Author(s):  
◽  
Olayinka Oshokoya
Keyword(s):  
Circular Dichroism ◽  
Secondary Structure ◽  
Least Squares ◽  
Structure Determination ◽  
Spectroscopic Data ◽  
Resonance Raman ◽  
Protein Secondary Structure ◽  
Secondary Structure Content ◽  
Ultraviolet Resonance Raman ◽  
Circular Dichroïsm

Determination of protein secondary structure 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. While NMR and x-ray crystallography can predict placement of each atom in proteins to within an angstrom, optical methods are the preferred techniques for rapid evaluation of protein secondary structure content. Such techniques require calibration data to predict unknown protein secondary structure content where accuracy may be improved with the application of multivariate analysis. We compare protein secondary structure predictions obtained from multivariate analysis of ultraviolet resonance Raman (UVRR) and circular dichroism (CD) spectroscopic data using classical and partial least squares, and multivariate curve resolution-alternating least squares is made. Based on this analysis, the suggested best approach to rapid and accurate secondary structure determination is a combination of both CD and UVRR spectroscopy. While initial studies suggest that a complementary use of spectroscopic data from optical methods such as circular dichroism (CD), infrared (IR) and ultraviolet resonance Raman (UVRR) coupled with multivariate calibration techniques like multivariate curve resolution-alternating least squares (MCR-ALS) is the preferred route for real-time and accurate evaluation of protein secondary structure, further study presents a new strategy for the improvement of secondary structure determination of proteins by fusing CD and UVRR spectroscopic data. Also, a new method for determining the structural composition of each protein is employed, which is based on the relative abundance of the (phi,psi) dihedral angles of the peptide backbone as they correspond to each type of secondary structure. Comparison of the predicted protein secondary structures from MCR-ALS analysis of CD, UVRR and fused data with definitions obtained from dihedral angles of the peptide backbone, yields lower overall root mean squared errors of calibration for helical, sheet, poly-proline II type and total unfolded secondary structures with fused data. Considering that a disadvantage of multivariate calibration methods is the requirement of known concentration or spectral profiles, and second-order calibration methods, such as parallel factor analysis (PARAFAC), do not have such a requirement due to the "second-order advantage", PARAFAC was employed for analysis of UVRR data. An exceptional feature of UVRR spectroscopy is that UVRR spectra are also dependent on excitation wavelength as they are on secondary structure composition. Thus, higher order data can be created by combining protein UVRR spectra of several proteins collected at multiple excitation wavelengths. PARAFAC has been used to analyze UVRR data collected at multiple excitation wavelengths on several proteins to determine secondary structure content.

Use of synchrotron-based FTIR microspectroscopy to determine protein secondary structures of raw and heat-treated brown and golden flaxseeds: A novel approach

2005 ◽  
Vol 85 (4) ◽  
pp. 437-448 ◽  
Author(s):  
P. Yu ◽  
J. J. McKinnon ◽  
H. W. Soita ◽  
C. R. Christensen ◽  
D. A. Christensen
Keyword(s):  
Secondary Structure ◽  
Matrix Protein ◽  
Protein Secondary Structure ◽  
Secondary Structures ◽  
Heat Processing ◽  
Lower Percentage ◽  
Protein Secondary Structures ◽  
Novel Approach ◽  
Α Helix ◽  
Β Sheet

The objectives of the study were to use synchrotron Fourier transform infrared microspectroscopy (S-FTIR) as a novel approach to: (1) reveal ultra-structural chemical features of protein secondary structures of flaxseed tissues affected by variety (golden and brown) and heat processing (raw and roasted), and (2) quantify protein secondary structures using Gaussian and Lorentzian methods of multi-component peak modeling. By using multi-component peak modeling at protein amide I region of 1700–1620 cm-1, the results showed that the golden flaxseed contained relatively higher percentage of α-helix (47.1 vs. 36.9%), lower percentage of β-sheet (37.2 vs. 46.3%) and higher (P < 0.05) ratio of α-helix to β-sheet than the brown flaxseed (1.3 vs. 0.8). The roasting reduced (P < 0.05) percentage of α-helix (from 47.1 to 36.1%), increased percentage of β-sheet (from 37.2 to 49.8%) and reduced α-helix to β-sheet ratio (1.3 to 0.7) of the golden flaxseed tissues. However, the roasting did not affect percentage and ratio of α-helix and β-sheet in the brown flaxseed tissue. No significant differences were found in quantification of protein secondary structures between Gaussian and Lorentzian methods. These results demonstrate the potential of highly spatially resolved S-FTIR to localize relatively pure protein in the tissue and reveal protein secondary structures at a cellular level. The results indicated relative differences in protein secondary structures between flaxseed varieties and differences in sensitivities of protein secondary structure to the heat processing. Further study is needed to understand the relationship between protein secondary structure and protein digestion and utilization of flaxseed and to investigate whether the changes in the relative amounts of protein secondary structures are primarily responsible for differences in protein availability. Key words: Synchrotron, FTIR microspectrosopy, flaxseeds, intrinsic structural matrix, protein secondary structures, protein nutritive value

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