%0 Journal Article
%T Dependence of ¦Á-helical and ¦Â-sheet amino acid propensities on the overall protein fold type
%A Kazuo Fujiwara
%A Hiromi Toda
%A Masamichi Ikeguchi
%J BMC Structural Biology
%D 2012
%I BioMed Central
%R 10.1186/1472-6807-12-18
%X We calculated amino acid propensities for ¦Á-helices and ¦Â-sheets for 39 and 24 protein folds, respectively, and addressed whether they correlate with the fold. The propensities were also calculated for exposed and buried sites, respectively. Results showed that ¦Á-helix propensities do not differ significantly by fold, but ¦Â-sheet propensities are diverse and depend on the fold. The propensities calculated for exposed sites and buried sites are similar for ¦Á-helix, but such is not the case for the ¦Â-sheet propensities. We also found some fold dependence on amino acid frequency in ¦Â-strands. Folds with a high Ser, Thr and Asn content at exposed sites in ¦Â-strands tend to have a low Leu, Ile, Glu, Lys and Arg content (correlation coefficient = £¿0.90) and to have flat ¦Â-sheets. At buried sites in ¦Â-strands, the content of Tyr, Trp, Gln and Ser correlates negatively with the content of Val, Ile and Leu (correlation coefficient = £¿0.93). "All-¦Â" proteins tend to have a higher content of Tyr, Trp, Gln and Ser, whereas "¦Á/¦Â" proteins tend to have a higher content of Val, Ile and Leu.The ¦Á-helix propensities are similar for all folds and for exposed and buried residues. However, ¦Â-sheet propensities calculated for exposed residues differ from those for buried residues, indicating that the exposed-residue fraction is one of the major factors governing amino acid composition in ¦Â-strands. Furthermore, the correlations we detected suggest that amino acid composition is related to folding properties such as the twist of a ¦Â-strand or association between two ¦Â sheets.In 1974, Chou and Fasman published the calculated frequency of occurrence and conformational propensity of each amino acid in the secondary structures of 15 proteins, consisting of 2473 amino acid residues [1]. Since then, a vast number of protein structures have been determined and classified to reflect both structural and evolutionary relatedness [2,3]. SCOP classification (Structural Classification of Protein) is
%U http://www.biomedcentral.com/1472-6807/12/18