Position-specific propensities of amino acids in the β-strand

Abstract

Background: Despite the importance of β-strands as main building blocks in proteins, the propensity of amino acid in β-strands is not well-understood as it has been more difficult to determine experimentally compared to α-helices. Recent studies have shown that most of the amino acids have significantly high or low propensity towards both ends of β-strands. However, a comprehensive analysis of the sequence dependent amino acid propensities at positions between the ends of the β-strand has not been investigated.

Results: The propensities of the amino acids calculated from a large non-redundant database of proteins are found to be highly position-specific and vary continuously throughout the length of the β-strand. They follow an unexpected characteristic periodic pattern in inner positions with respect to the cap residues in both termini of β-strands; this periodic nature is markedly different from that of the α-helices with respect to the strength and pattern in periodicity. This periodicity is not only different for different amino acids but it also varies considerably for the amino acids belonging to the same physico-chemical group. Average hydrophobicity is also found to be periodic with respect to the positions from both termini of β-strands.

Conclusions: The results contradict the earlier perception of isotropic nature of amino acid propensities in the middle region of β-strands. These position-specific propensities should be of immense help in understanding the factors responsible for β-strand design and efficient prediction of β-strand structure in unknown proteins.

Figure 1

Occurrence Frequency of β-strands. Frequency of occurrence of a given strand length in the non-redundant protein database. A Gaussian curve is fitted to the plot. This fit has a center at 4.2 residues, a width of 4.9 residues and an amplitude of 2650 occurrences.

Figure 2

Position-Specific Propensities from N-terminus. Position-specific propensities for each amino acid in the first 10 strand positions from the N-terminus. Position-wise propensities for each β-strands are calculated and standard errors of the data are plotted as error bars.

Figure 3

Position-Specific Propensities from C-terminus. Position-specific propensities for each amino acid in the first 10 strand positions from the C-terminus. Position-wise propensities for each β-strands are calculated and standard errors of the data are plotted as error bars.

Figure 4

Position-Specific Average Hydrophobicity. Average hydrophobicity plotted against position from the cap residues in strands. Position-specific hydrophobicity for each β-strands are calculated and standard error of the data are plotted as error bars.