Statistical dependence of protein secondary structure on amino acid bigrams

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.

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Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.340120410 ◽

1992 ◽

Vol 12 (4) ◽

pp. 382-399 ◽

Cited By ~ 14

Author(s):

Gregory E. Arnold ◽

A. Keith Dunker ◽

Susan J. Johns ◽

Richard J. Douthart

Keyword(s):

Amino Acid ◽

Secondary Structure ◽

Amino Acid Sequence ◽

Protein Secondary Structure ◽

Conditional Probabilities

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

Canadian Journal of Animal Science ◽

10.4141/a05-004 ◽

2005 ◽

Vol 85 (4) ◽

pp. 437-448 ◽

Cited By ~ 21

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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