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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.


Three regions around a potential breaker with a length of five residues used for analysis of environmental factors.
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f2-1_55: Three regions around a potential breaker with a length of five residues used for analysis of environmental factors.

Mentions: In order to reveal the difference between the potential breakers in the breaking regions and those in the secondary structure core, a segment around a potential breaker numerated according to the primary features was divided into three regions with a fixed length of five residues (Fig. 2). Then, the averages of various physicochemical parameters in the three regions in Figure 2 were calculated for both the potential breakers in the breaker regions (true data) and those in the secondary structure core (false data). A number of physicochemical properties may contribute to the environmental conditions around the breaking point of secondary structures. Approximately ten types of physicochemical parameters were investigated. Four of these parameters that were selected were found to be different between the true and false data: the average hydrophobicity, the helical periodicity score, the density of small polar residues, and the average A′-index (defined in the Methods). Because these parameters have their own physical meanings, the results of analysis reveal which property supports or hampers the local structures. Moreover, the difference in the environmental parameters may be used to predict secondary structure breakers. The similarity in the profiles of the environmental factors around the potential breakers with the typical profiles of real breakers became a good score to predict the true secondary structure breakers based solely on amino acid sequences.


Mechanisms of secondary structure breakers in soluble proteins
Three regions around a potential breaker with a length of five residues used for analysis of environmental factors.
© Copyright Policy
Related In: Results  -  Collection

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

f2-1_55: Three regions around a potential breaker with a length of five residues used for analysis of environmental factors.
Mentions: In order to reveal the difference between the potential breakers in the breaking regions and those in the secondary structure core, a segment around a potential breaker numerated according to the primary features was divided into three regions with a fixed length of five residues (Fig. 2). Then, the averages of various physicochemical parameters in the three regions in Figure 2 were calculated for both the potential breakers in the breaker regions (true data) and those in the secondary structure core (false data). A number of physicochemical properties may contribute to the environmental conditions around the breaking point of secondary structures. Approximately ten types of physicochemical parameters were investigated. Four of these parameters that were selected were found to be different between the true and false data: the average hydrophobicity, the helical periodicity score, the density of small polar residues, and the average A′-index (defined in the Methods). Because these parameters have their own physical meanings, the results of analysis reveal which property supports or hampers the local structures. Moreover, the difference in the environmental parameters may be used to predict secondary structure breakers. The similarity in the profiles of the environmental factors around the potential breakers with the typical profiles of real breakers became a good score to predict the true secondary structure breakers based solely on amino acid sequences.

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.