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Statistical Analysis of Terminal Extensions of Protein β-Strand Pairs.

Zhang N, Gao S, Zhang L, Ruan J, Zhang T - Adv Bioinformatics (2013)

Bottom Line: However, we found that the best pairing required a terminal alignment, and β-strands tend to pair to make bigger common parts.As a result, 96.97%  of β-strand pairs have a ratio of 25% of the paired common part to the whole length.Interstrand register predictions by searching interacting β-strands from several alternative offsets should comply with this rule to reduce the computational searching space to improve the performances of algorithms.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Tianjin University, Tianjin Key Lab of BME Measurement, Tianjin 300072, China.

ABSTRACT
The long-range interactions, required to the accurate predictions of tertiary structures of β-sheet-containing proteins, are still difficult to simulate. To remedy this problem and to facilitate β-sheet structure predictions, many efforts have been made by computational methods. However, known efforts on β-sheets mainly focus on interresidue contacts or amino acid partners. In this study, to go one step further, we studied β-sheets on the strand level, in which a statistical analysis was made on the terminal extensions of paired β-strands. In most cases, the two paired β-strands have different lengths, and terminal extensions exist. The terminal extensions are the extended part of the paired strands besides the common paired part. However, we found that the best pairing required a terminal alignment, and β-strands tend to pair to make bigger common parts. As a result, 96.97%  of β-strand pairs have a ratio of 25% of the paired common part to the whole length. Also 94.26% and 95.98%  of β-strand pairs have a ratio of 40% of the paired common part to the length of the two β-strands, respectively. Interstrand register predictions by searching interacting β-strands from several alternative offsets should comply with this rule to reduce the computational searching space to improve the performances of algorithms.

No MeSH data available.


Related in: MedlinePlus

Cumulative percentages (CPs) of R, Rt1, and Rt2 calculated from the present dataset. The horizontal axis denotes the percentage of common paired region PL to EL (for curve R) or to SL (for curves Rt1 and Rt2). Points on the R curve denote the cumulative percentages of samples whose R = PL/EL equals or is bigger than the corresponding abscissa value. Points on the Rt1 and Rt2 curves denote the cumulative percentages of samples whose Rt1 = PL/Rt1 or Rt2 = PL/Rt2 equals or is bigger than the corresponding abscissa value, respectively.
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fig4: Cumulative percentages (CPs) of R, Rt1, and Rt2 calculated from the present dataset. The horizontal axis denotes the percentage of common paired region PL to EL (for curve R) or to SL (for curves Rt1 and Rt2). Points on the R curve denote the cumulative percentages of samples whose R = PL/EL equals or is bigger than the corresponding abscissa value. Points on the Rt1 and Rt2 curves denote the cumulative percentages of samples whose Rt1 = PL/Rt1 or Rt2 = PL/Rt2 equals or is bigger than the corresponding abscissa value, respectively.

Mentions: To quantify the pairing common part of paired β-strands, we calculated the cumulative percent of variables R, Rt1, and Rt2 and depicted them in Figure 4.


Statistical Analysis of Terminal Extensions of Protein β-Strand Pairs.

Zhang N, Gao S, Zhang L, Ruan J, Zhang T - Adv Bioinformatics (2013)

Cumulative percentages (CPs) of R, Rt1, and Rt2 calculated from the present dataset. The horizontal axis denotes the percentage of common paired region PL to EL (for curve R) or to SL (for curves Rt1 and Rt2). Points on the R curve denote the cumulative percentages of samples whose R = PL/EL equals or is bigger than the corresponding abscissa value. Points on the Rt1 and Rt2 curves denote the cumulative percentages of samples whose Rt1 = PL/Rt1 or Rt2 = PL/Rt2 equals or is bigger than the corresponding abscissa value, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569888&req=5

fig4: Cumulative percentages (CPs) of R, Rt1, and Rt2 calculated from the present dataset. The horizontal axis denotes the percentage of common paired region PL to EL (for curve R) or to SL (for curves Rt1 and Rt2). Points on the R curve denote the cumulative percentages of samples whose R = PL/EL equals or is bigger than the corresponding abscissa value. Points on the Rt1 and Rt2 curves denote the cumulative percentages of samples whose Rt1 = PL/Rt1 or Rt2 = PL/Rt2 equals or is bigger than the corresponding abscissa value, respectively.
Mentions: To quantify the pairing common part of paired β-strands, we calculated the cumulative percent of variables R, Rt1, and Rt2 and depicted them in Figure 4.

Bottom Line: However, we found that the best pairing required a terminal alignment, and β-strands tend to pair to make bigger common parts.As a result, 96.97%  of β-strand pairs have a ratio of 25% of the paired common part to the whole length.Interstrand register predictions by searching interacting β-strands from several alternative offsets should comply with this rule to reduce the computational searching space to improve the performances of algorithms.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Tianjin University, Tianjin Key Lab of BME Measurement, Tianjin 300072, China.

ABSTRACT
The long-range interactions, required to the accurate predictions of tertiary structures of β-sheet-containing proteins, are still difficult to simulate. To remedy this problem and to facilitate β-sheet structure predictions, many efforts have been made by computational methods. However, known efforts on β-sheets mainly focus on interresidue contacts or amino acid partners. In this study, to go one step further, we studied β-sheets on the strand level, in which a statistical analysis was made on the terminal extensions of paired β-strands. In most cases, the two paired β-strands have different lengths, and terminal extensions exist. The terminal extensions are the extended part of the paired strands besides the common paired part. However, we found that the best pairing required a terminal alignment, and β-strands tend to pair to make bigger common parts. As a result, 96.97%  of β-strand pairs have a ratio of 25% of the paired common part to the whole length. Also 94.26% and 95.98%  of β-strand pairs have a ratio of 40% of the paired common part to the length of the two β-strands, respectively. Interstrand register predictions by searching interacting β-strands from several alternative offsets should comply with this rule to reduce the computational searching space to improve the performances of algorithms.

No MeSH data available.


Related in: MedlinePlus