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.


Histograms of four types of amino acid clusters as a function of position relative to termini of secondary structures: proline (a), glycine (b), amphiphilic residues (c), and leucine and isoleucine (d). A histogram of all residues is also plotted as a control (e).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC5036629&req=5

f4-1_55: Histograms of four types of amino acid clusters as a function of position relative to termini of secondary structures: proline (a), glycine (b), amphiphilic residues (c), and leucine and isoleucine (d). A histogram of all residues is also plotted as a control (e).

Mentions: Proline and glycine are well-known secondary structure breakers4,6. Furthermore, amphiphilic residues are known to form clusters at disordered regions of soluble proteins7,8 as well as at the ends of transmembrane helices1,2,11. Figures 4a, 4b, and 4c show histograms of the locations of proline, glycine, and clusters of amphiphilic residues around the termini of secondary structures, respectively. The histograms of hydrophobic residues, leucine and isoleucine, and all residues are shown in Figures 4d and 4e as control data. As can be seen in the figures, all histograms have a bell shape. The histogram showing all of the residues is related to the length of the secondary structures and the loop regions. Analysis was only conducted on secondary structures longer than seven residues. Further, a residue was counted only once at the terminal position of the nearest secondary structure. Therefore, the number of all residues at positions −2 to 0 was constant at 11,314. The number of residues was observed to gradually decrease on the negative side beyond position −3, according to the length distribution of the secondary structures, and on the positive side depending on the length distribution of the loop regions.


Mechanisms of secondary structure breakers in soluble proteins
Histograms of four types of amino acid clusters as a function of position relative to termini of secondary structures: proline (a), glycine (b), amphiphilic residues (c), and leucine and isoleucine (d). A histogram of all residues is also plotted as a control (e).
© Copyright Policy
Related In: Results  -  Collection

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

f4-1_55: Histograms of four types of amino acid clusters as a function of position relative to termini of secondary structures: proline (a), glycine (b), amphiphilic residues (c), and leucine and isoleucine (d). A histogram of all residues is also plotted as a control (e).
Mentions: Proline and glycine are well-known secondary structure breakers4,6. Furthermore, amphiphilic residues are known to form clusters at disordered regions of soluble proteins7,8 as well as at the ends of transmembrane helices1,2,11. Figures 4a, 4b, and 4c show histograms of the locations of proline, glycine, and clusters of amphiphilic residues around the termini of secondary structures, respectively. The histograms of hydrophobic residues, leucine and isoleucine, and all residues are shown in Figures 4d and 4e as control data. As can be seen in the figures, all histograms have a bell shape. The histogram showing all of the residues is related to the length of the secondary structures and the loop regions. Analysis was only conducted on secondary structures longer than seven residues. Further, a residue was counted only once at the terminal position of the nearest secondary structure. Therefore, the number of all residues at positions −2 to 0 was constant at 11,314. The number of residues was observed to gradually decrease on the negative side beyond position −3, according to the length distribution of the secondary structures, and on the positive side depending on the length distribution of the loop regions.

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.