Limits...
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 number of amino acid clusters to that of all amino acid residues: proline (a), glycine (b), and amphiphilic residues (c). The plot for leucine and isoleucine is shown in all graphs for comparison with potential breakers.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC5036629&req=5

f5-1_55: Ratio of number of amino acid clusters to that of all amino acid residues: proline (a), glycine (b), and amphiphilic residues (c). The plot for leucine and isoleucine is shown in all graphs for comparison with potential breakers.

Mentions: The maximum number of proline and glycine residues in the histograms is located in the loop region, whereas that of leucine and isoleucine is located in the secondary structure core. The shape of the histogram of amphiphilic residues is very similar to that for all of the residues. The histograms of various amino acids are determined by two factors: the histogram of all residues and the ratio for a type of amino acid at all positions. Figures 5a–c show the ratios of four types of amino acids at every position. These values were calculated by dividing the number of a type of amino acid by the total number of residues. As a control for secondary structure breakers, the ratio of leucine and isoleucine in all three graphs for proline (Fig. 5a), glycine (Fig. 5b), and the amphiphilic residues (Fig. 5c) was plotted. The ordinate on the right side indicates the ratio of leucine and isoleucine.


Mechanisms of secondary structure breakers in soluble proteins
Ratio of number of amino acid clusters to that of all amino acid residues: proline (a), glycine (b), and amphiphilic residues (c). The plot for leucine and isoleucine is shown in all graphs for comparison with potential breakers.
© Copyright Policy
Related In: Results  -  Collection

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

f5-1_55: Ratio of number of amino acid clusters to that of all amino acid residues: proline (a), glycine (b), and amphiphilic residues (c). The plot for leucine and isoleucine is shown in all graphs for comparison with potential breakers.
Mentions: The maximum number of proline and glycine residues in the histograms is located in the loop region, whereas that of leucine and isoleucine is located in the secondary structure core. The shape of the histogram of amphiphilic residues is very similar to that for all of the residues. The histograms of various amino acids are determined by two factors: the histogram of all residues and the ratio for a type of amino acid at all positions. Figures 5a–c show the ratios of four types of amino acids at every position. These values were calculated by dividing the number of a type of amino acid by the total number of residues. As a control for secondary structure breakers, the ratio of leucine and isoleucine in all three graphs for proline (Fig. 5a), glycine (Fig. 5b), and the amphiphilic residues (Fig. 5c) was plotted. The ordinate on the right side indicates the ratio of leucine and isoleucine.

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.