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

scholarly journals Protein secondary structures (α-helix and β-sheet) at a cellular level and protein fractions in relation to rumen degradation behaviours of protein: a new approach

2005 ◽  
Vol 94 (5) ◽  
pp. 655-665 ◽  
Author(s):  
Peiqiang Yu
Keyword(s):  
Nutritive Value ◽  
Secondary Structures ◽  
Cellular Level ◽  
Heat Processing ◽  
Molecular Chemistry ◽  
New Approach ◽  
Ftir Microspectroscopy ◽  
Protein Secondary Structures ◽  
Α Helix ◽  
Β Sheet

Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the α-helix and β-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of β-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution (∼10 μm). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of α-helixes and β-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P<0·05) the percentage of α-helixes (from 47·1 % to 36·1 %: S-FTIR absorption intensity), increased the percentage of β-sheets (from 37·2 % to 49·8 %: S-FTIR absorption intensity) and reduced the α-helix to β-sheet ratio (from 0·3 to 0·7) in the golden flaxseeds, which indicated a negative effect of the roasting on protein values, utilisation and bioavailability. These results were proved by the Cornell Net Carbohydrate Protein System in situ animal trial, which also revealed that roasting increased the amount of protein bound to lignin, and well as of the Maillard reaction protein (both of which are poorly used by ruminants), and increased the level of indigestible and undegradable protein in ruminants. The present results demonstrate the potential of highly spatially resolved synchrotron-based infrared microspectroscopy to locate ‘pure’ protein in feed tissues, and reveal protein secondary structures and digestive behaviour, making a significant step forward in and an important contribution to protein nutritional research. Further study is needed to determine the sensitivities of protein secondary structures to various heat-processing conditions, and to quantify the relationship between protein secondary structures and the nutrient availability and digestive behaviour of various protein sources. Information from the present study arising from the synchrotron-based IR probing of the protein secondary structures of protein sources at the cellular level will be valuable as a guide to maintaining protein quality and predicting digestive behaviours.

Multicomponent Peak Modeling of Protein Secondary Structures: Comparison of Gaussian with Lorentzian Analytical Methods for Plant Feed and Seed Molecular Biology and Chemistry Research

2005 ◽  
Vol 59 (11) ◽  
pp. 1372-1380 ◽  
Author(s):  
Peiqiang Yu
Keyword(s):  
Secondary Structure ◽  
Nutritive Value ◽  
Secondary Structures ◽  
Plant Seed ◽  
Relative Percentage ◽  
Protein Secondary Structures ◽  
Ft Ir ◽  
Ir Microspectroscopy ◽  
Α Helix ◽  
Β Sheet

The objective of this study was to compare Gaussian and Lorentzian multicomponent peak modeling methods in quantification of protein secondary structures of various plant seed and feed tissues within intact tissue at a cellular and subcellular level using the advanced synchrotron light sourced Fourier transform infrared (FT-IR) microspectroscopy (S-FTIR). This experiment was performed at the beamline U10B at the National Synchrotron Light Source (NSLS) in Brookhaven National Laboratory (BNL), U.S. Dept of Energy (NSLS-BNL, NY). The results show that in the comparison of the Gaussian and Lorentzian multi-peak modeling methods, the Gaussian method is more accurate for fitting multi-peak curves of protein secondary structures than the Lorentzian method, with higher modeling R2 values (0.92 versus 0.89, P < 0.05). There were no large differences ( P > 0.05) in the quantification of the relative percentage of α-helices, β-sheets, and others in protein secondary structures of the plant seed tissues, with averages of 30.2%, 40.4%, and 29.4%, respectively. However, there are significant differences ( P < 0.05) in the quantification of the ratios of β-sheet to α-helix (1.42 versus 1.60; SEM = 0.058) in protein secondary structures of the plant seed tissues. With synchrotron FT-IR microspectroscopy, the ultrastructural–chemical makeup and nutritive characteristics could be revealed at a high spatial resolution. Synchrotron-based FT-IR microspectroscopy revealed that the secondary structure of protein differed between the plant seed tissues in terms of relative percentage and ratio of protein secondary structures (α-helix and β-sheet) within cellular dimensions. The results also show that the flaxseed tissues contained higher ( P < 0.05) percentage of α-helix (38.6 versus 24.0%) and β-sheet (45.3 versus 36.9%), lower ( P < 0.05) percentage of other secondary structures (16.1% versus 39.0%), and higher ( P < 0.05) ratios of α-helix to β-sheet (0.90 versus 0.69) than the winterfat seed tissues. It must be mentioned that the relative percentages of protein secondary structure may not reflect the true secondary structure. However, the purpose of modeling the relative percentage of secondary structure was to detect the variety of differences among seed/feed/plant tissues and their relation to nutritive value and digestive behavior. The results demonstrate the potential of highly spatially resolved synchrotron-based FT-IR microspectroscopy to reveal protein secondary structures of the plant seed/feed tissues. Further study is needed to quantify the relationship between protein secondary structures and nutrient availability and digestive behavior of various varieties of plant seed tissues. Information from the infrared probing of protein secondary structures can be valuable as a guide to maintaining protein nutritive value and quality for animal and human use.

scholarly journals Ifosfamide toxicity to the retina and the possible roles of lecithin and quercetin in albino rats

2018 ◽  
Vol 7 (2) ◽  
pp. 800
Author(s):  
Rehab Ahmed ◽  
Eman Aly ◽  
Sherif Mahmoud ◽  
Sahar Awad ◽  
Gehan Kamal
Keyword(s):  
Oxidative Stress ◽  
Side Effects ◽  
Secondary Structure ◽  
Combined Treatment ◽  
Protein Secondary Structure ◽  
Tail Length ◽  
Albino Rats ◽  
Drug Induced ◽  
Α Helix ◽  
Β Sheet

Background: During cancer chemotherapy, drug-induced oxidative stress can limit therapeutic efficiency and cause a number of side effects. Objectives: Our study aimed to characterize the side effects of an alkylating agent chemotherapy ifosfamide to the retina and if the supplementation of lecithin and or quercetin can diminish its oxidative stress by means of comet assay and FTIR.Methods: Seventy female albino rats divided as control, rats given orally quercetin or lecithin, rats injected with ifosfamide, rats given quercetin or lecithin and in combination of them with ifosfamide injection.Results: Lecithin and quercetin groups indicate a normal comet parameters and distribution of protein secondary structure components content of β-turn, α-helix and β-sheet. After Ifosfamide injection, all comet parameters and β-Turns content were significant increase (p˂0.05) with the same context significant decrease (p˂0.05) of α-helix was observed. Lecithin or quercetin reduces the effect of ifosfamide injection in tail length and percentage tailed DNA. Combined treatment gives more protection against DNA damage. Lecithin role is cleared in returning the normal distribution of β-turn, α-helix, β-sheet and lack of protective effect of quercetin regarding the protein secondary structure of retina was observed.Conclusion: We suggest using lecithin and quercetin in combined treatment to reduce the oxidative stress due to ifosfamide.

FTIR Analysis of Conformational Changes in the Secondary Structure of Ovalbumin: Effect of pH and Cosolvent Sugar-free Natura

2020 ◽  
Vol 8 (1) ◽  
pp. 78-83
Author(s):  
P. Agalya ◽  
◽  
V. Velusamy
Keyword(s):  
Secondary Structure ◽  
Conformational Changes ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Secondary Structures ◽  
Structural Elements ◽  
Random Coils ◽  
Protein Secondary Structures ◽  
Derivative Analysis ◽  
Influence Of Ph

a-helix, þ-sheet, þ-turns, and random coils are the three-dimensional local segments that constitute a protein secondary structure. Molecular vibrations of proteins are sensitive to structural organizations of peptide chains hence Fourier Transform infrared (FTIR) spectroscopy is one of the recognized techniques for the identification of protein secondary structures. However, the lower frequency region of FTIR especially the amide VI bands (in the region 590-490cm-1) is little studied for proteins. Further, the effect of sugar-free natura on ovalbumin stability is not yet studied to our knowledge. The present study examines the conformational changes in the secondary structure of ovalbumin (OVA) protein under the influence of pH variations (2, 5, 7, 9, and 12) and also cosolvent sugar-free Natura (SFN) inclusion. From the primary absorption spectra of the amide VI bands, the second derivative analysis is furnished to quantify the secondary structural elements of protein thereby conformational changes are analyzed. From obtained results, it is found that conformational changes occur between two major secondary structures of a-helix and þ-sheet of OVA due to variation of pH and inclusion of cosolvent. Also, the results confirm that the denaturation of OVA in the presence of SFN irrespective of pH.

scholarly journals Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration

2021 ◽  
Author(s):  
Joëlle De Meutter ◽  
Erik Goormaghtigh
Keyword(s):  
Secondary Structure ◽  
Protein Secondary Structure ◽  
Protein Microarrays ◽  
Ftir Spectra ◽  
Partial Least Square ◽  
Least Square ◽  
Partial Least Square Regression ◽  
Disordered Structures ◽  
Α Helix ◽  
Β Sheet

AbstractFTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.

Using long-range contact number information for protein secondary structure prediction

2014 ◽  
Vol 07 (05) ◽  
pp. 1450052 ◽  
Author(s):  
Yonge Feng ◽  
Liaofu Luo
Keyword(s):  
Secondary Structure ◽  
Long Range ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Protein Secondary Structure ◽  
Secondary Structures ◽  
Negative Influence ◽  
Protein Secondary Structure Prediction ◽  
Contact Number ◽  
Protein Secondary Structures

In this paper, we first combine tetra-peptide structural words with contact number for protein secondary structure prediction. We used the method of increment of diversity combined with quadratic discriminant analysis to predict the structure of central residue for a sequence fragment. The method is used tetra-peptide structural words and long-range contact number as information resources. The accuracy of Q3 is over 83% in 194 proteins. The accuracies of predicted secondary structures for 20 amino acid residues are ranged from 81% to 88%. Moreover, we have introduced the residue long-range contact, which directly indicates the separation of contacting residue in terms of the position in the sequence, and examined the negative influence of long-range residue interactions on predicting secondary structure in a protein. The method is also compared with existing prediction methods. The results show that our method is more effective in protein secondary structures prediction.

scholarly journals Statistical dependence of protein secondary structure on amino acid bigrams

2006 ◽  
Vol 12 (1) ◽  
pp. 82-85
Author(s):  
Miodrag Zivkovic ◽  
Sasa Malkov ◽  
Snezana Zaric ◽  
Milena Vujosevic-Janicic ◽  
Jelena Tomasevic ◽  
...  
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Amino Acid Sequence ◽  
Protein Secondary Structure ◽  
Data Bank ◽  
Secondary Structures ◽  
Statistical Dependence ◽  
Conditional Probabilities ◽  
Protein Secondary Structures ◽  
Protein Data Bank Database

The statistical dependence of protein secondary structure on amino acid bigram frequencies was studied. Proteins in the PDBSELECT subset of the Protein Data Bank database were investigated. Protein secondary structures were determined using DSSP software. The conditional probabilities of protein secondary structures were calculated and presented. The results on bigrams show the frequencies of all the possible bigrams in all secondary structure types. These results elucidate some factors important for the prediction of the secondary structures of proteins based on the amino acid sequence.

Influence of the secondary structure on the AIE-related emission behavior of an amphiphilic polypeptide containing a hydrophobic fluorescent terminal and hydrophilic pendant groups

2016 ◽  
Vol 7 (1) ◽  
pp. 153-163 ◽  
Author(s):  
Li-Yang Lin ◽  
Po-Chiao Huang ◽  
Deng-Jie Yang ◽  
Jhen-Yan Gao ◽  
Jin-Long Hong
Keyword(s):  
Secondary Structure ◽  
Secondary Structures ◽  
Random Coil ◽  
Emission Behavior ◽  
Α Helix ◽  
Β Sheet

AIE-related emission of polypeptide containing an AIE-active terminal is correlated with secondary structures (α-helix, β-sheet and random coil) of the peptide chains.

scholarly journals Protein Secondary Structure Prediction With a Reductive Deep Learning Method

2021 ◽  
Vol 9 ◽  
Author(s):  
Zhiliang Lyu ◽  
Zhijin Wang ◽  
Fangfang Luo ◽  
Jianwei Shuai ◽  
Yandong Huang
Keyword(s):  
Deep Learning ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Protein Secondary Structure ◽  
Secondary Structures ◽  
Resonance Spectroscopy ◽  
Data Set ◽  
X Ray Crystallography ◽  
Protein Secondary Structures

Protein secondary structures have been identified as the links in the physical processes of primary sequences, typically random coils, folding into functional tertiary structures that enable proteins to involve a variety of biological events in life science. Therefore, an efficient protein secondary structure predictor is of importance especially when the structure of an amino acid sequence fragment is not solved by high-resolution experiments, such as X-ray crystallography, cryo-electron microscopy, and nuclear magnetic resonance spectroscopy, which are usually time consuming and expensive. In this paper, a reductive deep learning model MLPRNN has been proposed to predict either 3-state or 8-state protein secondary structures. The prediction accuracy by the MLPRNN on the publicly available benchmark CB513 data set is comparable with those by other state-of-the-art models. More importantly, taking into account the reductive architecture, MLPRNN could be a baseline for future developments.

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