Higher peptide nonplanarity (ω) close to protein carboxy-terminal and its positive correlation with ψ dihedral-angle is evolved conferring protein thermostability

Abstract

BackgroundThermostability conferred by ensembles of several weak-interactions results in compactness-rigidity in proteins that impairs their flexibility/function. Understanding of protein's structural modification under stress is important. MethodIn this study, randomly selected 54 nonhomologous and variedly thermostable (0–20 °C/21–40 °C/41–60 °C/61–80 °C/81–100 °C) proteins were investigated to elucidate their thermostability utilizing multiple bioinformatics-tools. Important physico-chemical factors/peptide-nonplanarity(ω) and Ramachandran-plot were analyzed from the proteins’ PDB-structure by SPSS-programme. ResultOur ANOVA results suggest that temperature exerted significant and periodic influences on ω (F = 5.81/p = 0.0001) and ψ (F = 6.52/p = 0.0001) dihedral-angles in proteins where peptide nonplanarity obviously favored thermostability. The Pearson-correlation and further goodness of-fit model from ordinal-regression analysis suggest that nonplanarity is increasingly abundant in protein carboxy-terminal (χ2 = 37.9/p = 0.0001) at higher temperatures. Moreover, the ω is found to be highly correlated with ψ (r = 0.289/p = 0.0001) but not ɸ (r = −0.071/p = 0.365) which is supported by the regression-analysis (R2 = 0.085/F = 7.623/p < 0.001). Consistent and paradoxical decrease in the protein-size is linked to protein-thermostability. Hydrophobicity/hydrophilicity/protein phosphorylation and iso-electric point/charge were found to be grossly increasing with the protein-thermostability. However, outlier/disallowed residue-number (mean ± SD) was lower in moderate- and hyper-thermostable proteins, indicating temperature as a better purifying naturalselection-pressure to generate consistent allelic-fitness. ConclusionsIn the current study, irrespective to the protein homology, nonplanarity has been demonstrated as a significant determinant of protein-thermostability