Hydration of Protein Secondary Structures—The Role in Protein Folding

1993 ◽  
pp. 148-162 ◽  
Author(s):  
C. Y. Sekharudu ◽  
M. Sundaralingam
Keyword(s):  
Protein Folding ◽  
Secondary Structures ◽  
Protein Secondary Structures

scholarly journals An Alternative Approach to Protein Folding

2013 ◽  
Vol 2013 ◽  
pp. 1-10
Author(s):  
Yeona Kang ◽  
Charles M. Fortmann
Keyword(s):  
Protein Folding ◽  
Ab Initio ◽  
Diffusion Model ◽  
Diffusion Theory ◽  
Secondary Structures ◽  
Drift Diffusion Model ◽  
Drift Diffusion ◽  
Desktop Computer ◽  
Tertiary Structures ◽  
Protein Secondary Structures

A diffusion theory-based, all-physicalab initioprotein folding simulation is described and applied. The model is based upon the drift and diffusion of protein substructures relative to one another in the multiple energy fields present. Without templates or statistical inputs, the simulations were run at physiologic and ambient temperatures (including pH). Around 100 protein secondary structures were surveyed, and twenty tertiary structures were determined. Greater than 70% of the secondary core structures with over 80% alpha helices were correctly identified on protein ranging from 30 to 200 amino-acid sequence. The drift-diffusion model predicted tertiary structures with RMSD values in the 3–5 Angstroms range for proteins ranging 30 to 150 amino acids. These predictions are among the best for an allab initioprotein simulation. Simulations could be run entirely on a desktop computer in minutes; however, more accurate tertiary structures were obtained using molecular dynamic energy relaxation. The drift-diffusion model generated realistic energy versus time traces. Rapid secondary structures followed by a slow compacting towards lower energy tertiary structures occurred after an initial incubation period in agreement with observations.

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.

scholarly journals Spectrum of disease-causing mutations in protein secondary structures

2007 ◽  
Vol 7 (1) ◽  
pp. 56 ◽  
Author(s):  
Sofia Khan ◽  
Mauno Vihinen
Keyword(s):  
Secondary Structures ◽  
Protein Secondary Structures

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

JSSPrediction: a Framework to Predict Protein Secondary Structures Using Integration

2006 ◽  
Author(s):  
L. Palopoli ◽  
S.E. Rombo ◽  
F. Terracina ◽  
G. Tradigo ◽  
P. Veltri
Keyword(s):  
Secondary Structures ◽  
Protein Secondary Structures

scholarly journals Impact of residue accessible surface area on the prediction of protein secondary structures

2008 ◽  
Vol 9 (1) ◽  
pp. 357 ◽  
Author(s):  
Amir Momen-Roknabadi ◽  
Mehdi Sadeghi ◽  
Hamid Pezeshk ◽  
Sayed-Amir Marashi
Keyword(s):  
Surface Area ◽  
Secondary Structures ◽  
Accessible Surface Area ◽  
Protein Secondary Structures ◽  
Accessible Surface

Use of information discrepancy measure to compare protein secondary structures

2009 ◽  
Vol 909 (1-3) ◽  
pp. 102-106 ◽  
Author(s):  
Shengli Zhang ◽  
Lianping Yang ◽  
Tianming Wang
Keyword(s):  
Secondary Structures ◽  
Protein Secondary Structures ◽  
Discrepancy Measure
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