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Mechanisms of secondary structure breakers in soluble proteins

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.


Ratio of the number of predicted secondary structure breakers to that of all amino acid residues after discrimination by primary component analysis: glycine (a) and amphiphilic residues (b). The plot for proline is shown in both graphs. A combination of the three types of predicted breakers is also plotted (c).
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f7-1_55: Ratio of the number of predicted secondary structure breakers to that of all amino acid residues after discrimination by primary component analysis: glycine (a) and amphiphilic residues (b). The plot for proline is shown in both graphs. A combination of the three types of predicted breakers is also plotted (c).

Mentions: Results of the discrimination of potential breakers are shown in Figure 7. A profile of the ratio of proline around the termini of the secondary structure is plotted as the standard profile of the breaker. The profiles of both glycine and amphiphilic peaks after discrimination in Figures 7a and 7b are very similar to that of proline, strongly suggesting that the effect of the environmental parameters are substantial for the final local structures. The profile of unified secondary structure breakers is plotted in Figure 7c. Approximately 10% of all residues at each position in the loop region have the activity to break the secondary structure.


Mechanisms of secondary structure breakers in soluble proteins
Ratio of the number of predicted secondary structure breakers to that of all amino acid residues after discrimination by primary component analysis: glycine (a) and amphiphilic residues (b). The plot for proline is shown in both graphs. A combination of the three types of predicted breakers is also plotted (c).
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Related In: Results  -  Collection

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

f7-1_55: Ratio of the number of predicted secondary structure breakers to that of all amino acid residues after discrimination by primary component analysis: glycine (a) and amphiphilic residues (b). The plot for proline is shown in both graphs. A combination of the three types of predicted breakers is also plotted (c).
Mentions: Results of the discrimination of potential breakers are shown in Figure 7. A profile of the ratio of proline around the termini of the secondary structure is plotted as the standard profile of the breaker. The profiles of both glycine and amphiphilic peaks after discrimination in Figures 7a and 7b are very similar to that of proline, strongly suggesting that the effect of the environmental parameters are substantial for the final local structures. The profile of unified secondary structure breakers is plotted in Figure 7c. Approximately 10% of all residues at each position in the loop region have the activity to break the secondary structure.

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.