Dependence of alpha-helical and beta-sheet amino acid propensities on the overall protein fold type

Abstract

BackgroundA large number of studies have been carried out to obtain amino acid propensities for α-helices and β-sheets. The obtained propensities for α-helices are consistent with each other, and the pair-wise correlation coefficient is frequently high. On the other hand, the β-sheet propensities obtained by several studies differed significantly, indicating that the context significantly affects β-sheet propensity.ResultsWe calculated amino acid propensities for α-helices and β-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 α-helix propensities do not differ significantly by fold, but β-sheet propensities are diverse and depend on the fold. The propensities calculated for exposed sites and buried sites are similar for α-helix, but such is not the case for the β-sheet propensities. We also found some fold dependence on amino acid frequency in β-strands. Folds with a high Ser, Thr and Asn content at exposed sites in β-strands tend to have a low Leu, Ile, Glu, Lys and Arg content (correlation coefficient = −0.90) and to have flat β-sheets. At buried sites in β-strands, the content of Tyr, Trp, Gln and Ser correlates negatively with the content of Val, Ile and Leu (correlation coefficient = −0.93). "All-β" proteins tend to have a higher content of Tyr, Trp, Gln and Ser, whereas "α/β" proteins tend to have a higher content of Val, Ile and Leu.ConclusionsThe α-helix propensities are similar for all folds and for exposed and buried residues. However, β-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 β-strands. Furthermore, the correlations we detected suggest that amino acid composition is related to folding properties such as the twist of a β-strand or association between two β sheets.

From the Sequence to the Conformation of the Unabridged Transmembrane Domains TM1 and TM2 of the cASIC1a Ion Channel – A Parallel Tempering Approach

“…4. This is in accordance with common knowledge that glycine resists undergoing a-helical folding [16], while also indicating that formation of a filter ring by G443 in the trimer, by the way of the extended, belt-like conformation of the triad G443-A444-S445, also requires cooperation in the trimer. Admittedly, our observations as to the discontinuous TM2 transmembrane domain of the cASIC1a complex with MitTx suffer from the limited T-REMD simulation under Fig.…”

Hydrolyzing Proficiency of Keratinases in Feather Degradation

“…Other amino acids like arginine, tyrosine, methionine, phenylalanine isoleucine, leucine, lysine, cysteine and aspartic acid were present in very less amount (7-33 lM/ml) in both hydrolyzed product (supplementary Table 1). As tyrosine, tryptophan, glutamine and serine have negative correlation with valine, isoleucine and leucine in b-sheet, therefore concentration of different amino acids in degraded product indicate the site of action of keratinase for hydrolyzation of the exposed sites in B. subtilis RSE163 and RSE165 strains respectively [26]. Results of amino acid profiling elucidated the clear evidences in support of the characteristic behavior of two different keratinases on hydrolysis of feather keratin by showing discrepancy in the concentration of the amino acids analyzed from the hydrolyzed feather from two strains.…”

Fractals and self-organized criticality in proteins

“…5-7). depending on the charge depth from the globular surface, and β strand propensities especially cannot be assigned reliably to individual aa [19,20]. Aggregation is a non-linear property (concentration dependent, or dye enhanced), and linearizing it with respect to multiple factors involves risks which are brought out by more careful study.…”