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Mechanisms of secondary structure breakers in soluble proteins

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ABSTRACT

Breaking signals of secondary structure put strong limitations on the tertiary structures of proteins. In addition to proline and glycine clusters, which are well-known secondary structure breakers, clusters of amphiphilic residues were found to be a novel type of secondary structure breaker. These secondary structure breakers were found to depend on specific environmental factors. Such conditions included the average hydrophobicity, the helical periodicity, the density of serine and threonine residues, and the presence of tryptophan and tyrosine clusters. Principal component analysis of environmental factors was conducted in order to identify candidate breakers in the secondary structure breaking regions. Predicted breakers were located in breaking regions with an accuracy of 72%. Taking the loop core into consideration, almost 90% of the predicted breakers were located in the loop segments. When the migration effect of the breaking point was taken into account, the loop segments with the predicted breakers covered two thirds of all loop segments. Herein, the possibility of secondary structure prediction based on secondary structure breakers is discussed. The system of the present method is available at the URL: http://bp.nuap.nagoya-u.ac.jp/sosui/sosuibreaker/sosuibreaker_submit.html.

No MeSH data available.


Flow chart of prediction of secondary structure breakers.
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f3-1_55: Flow chart of prediction of secondary structure breakers.

Mentions: In order to obtain the best fit of the profiles for the potential breakers with typical breakers, the position of the potential breakers was scanned for several residues: 5 residues for glycine clusters and 9 residues for amphiphilic residues. This final step of the prediction improved its accuracy by several percent. A flow chart of prediction of secondary structure breakers is shown in Figure 3, in which the equations for the parameters and a discrimination function given in the next section are related to the corresponding processes.


Mechanisms of secondary structure breakers in soluble proteins
Flow chart of prediction of secondary structure breakers.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036629&req=5

f3-1_55: Flow chart of prediction of secondary structure breakers.
Mentions: In order to obtain the best fit of the profiles for the potential breakers with typical breakers, the position of the potential breakers was scanned for several residues: 5 residues for glycine clusters and 9 residues for amphiphilic residues. This final step of the prediction improved its accuracy by several percent. A flow chart of prediction of secondary structure breakers is shown in Figure 3, in which the equations for the parameters and a discrimination function given in the next section are related to the corresponding processes.

View Article: PubMed Central - PubMed

ABSTRACT

Breaking signals of secondary structure put strong limitations on the tertiary structures of proteins. In addition to proline and glycine clusters, which are well-known secondary structure breakers, clusters of amphiphilic residues were found to be a novel type of secondary structure breaker. These secondary structure breakers were found to depend on specific environmental factors. Such conditions included the average hydrophobicity, the helical periodicity, the density of serine and threonine residues, and the presence of tryptophan and tyrosine clusters. Principal component analysis of environmental factors was conducted in order to identify candidate breakers in the secondary structure breaking regions. Predicted breakers were located in breaking regions with an accuracy of 72%. Taking the loop core into consideration, almost 90% of the predicted breakers were located in the loop segments. When the migration effect of the breaking point was taken into account, the loop segments with the predicted breakers covered two thirds of all loop segments. Herein, the possibility of secondary structure prediction based on secondary structure breakers is discussed. The system of the present method is available at the URL: http://bp.nuap.nagoya-u.ac.jp/sosui/sosuibreaker/sosuibreaker_submit.html.

No MeSH data available.