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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.


Levels of averages of four kinds of properties, <H(l)>, <HPS(l)>, <ST(l)>, and <A′(l)>, in three regions were compared between potential breakers in secondary structure core (SSC) and breaking regions (BR). The potential breakers glycine (a) and amphiphilic peaks (b) showed similar patterns despite average hydrophobicity.
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f6-1_55: Levels of averages of four kinds of properties, <H(l)>, <HPS(l)>, <ST(l)>, and <A′(l)>, in three regions were compared between potential breakers in secondary structure core (SSC) and breaking regions (BR). The potential breakers glycine (a) and amphiphilic peaks (b) showed similar patterns despite average hydrophobicity.

Mentions: The averages of the four physicochemical properties surrounding the potential breakers were plotted in histograms for glycine residues (Fig. 6a) and amphiphilic clusters (Fig. 6b).The propertiesare averaged over alldataineach dataset, therefore, a general trend can be obtained from the histograms. The hydrophobicity of the segments surrounding the potential breakers in the breaking region is lower than in the secondary structure core. Similarly, the helical periodicity in the breaking region is lower than that in the secondary structure core. These statistical trends seem physically reasonable. Because most disordered segments stick to the outside of proteins, the hydrophobicity of disordered segments must be low in order to have an affinity for water, and the periodicity due to the local order in the secondary structure region is lost in the loop region. The small polar residues, serine and threonine, are found with higher frequency in the breaking region than in the secondary structure core. This type of residue is thought to have the same effect as glycine, because of the small size of the side chains. Further, bulky amino acids with polar groups, such as tryptophan and tyrosine, are also more abundant in the breaking region. The bulkiness of the side chain may hinder ordering of the structure due to an excluded volume effect.


Mechanisms of secondary structure breakers in soluble proteins
Levels of averages of four kinds of properties, <H(l)>, <HPS(l)>, <ST(l)>, and <A′(l)>, in three regions were compared between potential breakers in secondary structure core (SSC) and breaking regions (BR). The potential breakers glycine (a) and amphiphilic peaks (b) showed similar patterns despite average hydrophobicity.
© Copyright Policy
Related In: Results  -  Collection

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

f6-1_55: Levels of averages of four kinds of properties, <H(l)>, <HPS(l)>, <ST(l)>, and <A′(l)>, in three regions were compared between potential breakers in secondary structure core (SSC) and breaking regions (BR). The potential breakers glycine (a) and amphiphilic peaks (b) showed similar patterns despite average hydrophobicity.
Mentions: The averages of the four physicochemical properties surrounding the potential breakers were plotted in histograms for glycine residues (Fig. 6a) and amphiphilic clusters (Fig. 6b).The propertiesare averaged over alldataineach dataset, therefore, a general trend can be obtained from the histograms. The hydrophobicity of the segments surrounding the potential breakers in the breaking region is lower than in the secondary structure core. Similarly, the helical periodicity in the breaking region is lower than that in the secondary structure core. These statistical trends seem physically reasonable. Because most disordered segments stick to the outside of proteins, the hydrophobicity of disordered segments must be low in order to have an affinity for water, and the periodicity due to the local order in the secondary structure region is lost in the loop region. The small polar residues, serine and threonine, are found with higher frequency in the breaking region than in the secondary structure core. This type of residue is thought to have the same effect as glycine, because of the small size of the side chains. Further, bulky amino acids with polar groups, such as tryptophan and tyrosine, are also more abundant in the breaking region. The bulkiness of the side chain may hinder ordering of the structure due to an excluded volume effect.

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.