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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.


An illustrated example of β-strand pairing in a β-sheet (PDB code: 1HZT). (a) The sketch of the tertiary structure of the protein produced by using RASMOL. Protein 1HZT is an α/β protein with 10 β-strands numbered from 1 to 10, forming seven different strand pairs. (b) The sequences of the 10 β-strands with their initial and ending residue numbers. (c) The 10 β-strands in the linear primary sequence. (d) An example of a β-strand partnership graph. The pairing is between strands “B3” and “B4,” with the light gray box representing the common pairing part.
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fig1: An illustrated example of β-strand pairing in a β-sheet (PDB code: 1HZT). (a) The sketch of the tertiary structure of the protein produced by using RASMOL. Protein 1HZT is an α/β protein with 10 β-strands numbered from 1 to 10, forming seven different strand pairs. (b) The sequences of the 10 β-strands with their initial and ending residue numbers. (c) The 10 β-strands in the linear primary sequence. (d) An example of a β-strand partnership graph. The pairing is between strands “B3” and “B4,” with the light gray box representing the common pairing part.

Mentions: The β-sheets, where two or more β-strands are arranged in a specific conformation, are illustrated in Figure 1(a), by a protein example (PDB code 1HZT). Adjacent strands, or the so-called strand pairs, can either run in the same (parallel) or in the opposite (antiparallel) direction styles. In protein 1HZT, there are 3 β-sheets called A, B, and C, formed by 10 different β-strands numbered from 1 to 10, making 7 different β-strand pairs, respectively. The 10 β-strands can be named by the β-sheet each belongs to and the index numbers in the order of partnership. For example, the 3 β-strands forming β-sheet A can be called “A1,” “A2,” and “A3,” while other 4 β-strands forming β-sheet B can be called “B1,” “B2,” “B3,” and “B4,” respectively. “A1-A2,” “A2-A3,” “B1-B2,” “B2-B3,” and “B3-B4” are all β-strand pairs. Sequences of the 10 β-strands with their initial and ending residue numbers are also given in Figure 1(b).


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

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

An illustrated example of β-strand pairing in a β-sheet (PDB code: 1HZT). (a) The sketch of the tertiary structure of the protein produced by using RASMOL. Protein 1HZT is an α/β protein with 10 β-strands numbered from 1 to 10, forming seven different strand pairs. (b) The sequences of the 10 β-strands with their initial and ending residue numbers. (c) The 10 β-strands in the linear primary sequence. (d) An example of a β-strand partnership graph. The pairing is between strands “B3” and “B4,” with the light gray box representing the common pairing part.
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Related In: Results  -  Collection

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

fig1: An illustrated example of β-strand pairing in a β-sheet (PDB code: 1HZT). (a) The sketch of the tertiary structure of the protein produced by using RASMOL. Protein 1HZT is an α/β protein with 10 β-strands numbered from 1 to 10, forming seven different strand pairs. (b) The sequences of the 10 β-strands with their initial and ending residue numbers. (c) The 10 β-strands in the linear primary sequence. (d) An example of a β-strand partnership graph. The pairing is between strands “B3” and “B4,” with the light gray box representing the common pairing part.
Mentions: The β-sheets, where two or more β-strands are arranged in a specific conformation, are illustrated in Figure 1(a), by a protein example (PDB code 1HZT). Adjacent strands, or the so-called strand pairs, can either run in the same (parallel) or in the opposite (antiparallel) direction styles. In protein 1HZT, there are 3 β-sheets called A, B, and C, formed by 10 different β-strands numbered from 1 to 10, making 7 different β-strand pairs, respectively. The 10 β-strands can be named by the β-sheet each belongs to and the index numbers in the order of partnership. For example, the 3 β-strands forming β-sheet A can be called “A1,” “A2,” and “A3,” while other 4 β-strands forming β-sheet B can be called “B1,” “B2,” “B3,” and “B4,” respectively. “A1-A2,” “A2-A3,” “B1-B2,” “B2-B3,” and “B3-B4” are all β-strand pairs. Sequences of the 10 β-strands with their initial and ending residue numbers are also given in Figure 1(b).

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.