Secondary Structures of Proteins: A Comparison of Models and Experimental Results

Abstract

Secondary structure predictions of proteins were compared to experimental results by wide-line 1H NMR. IUPred2A was used to generate predictions of disordered protein or binding regions. Thymosin-β4 and the stabilin-2 cytoplasmic domain were found to be mainly disordered, in agreement with the experimental results. α-Synuclein variants were predicted to be disordered, as in the experiments, but the A53T mutant showed less predicted disorder, in contrast with the wide-line 1H NMR result. A disordered binding site was found for thymosin-β4, whereas the stabilin-2 cytoplasmic domain was indicated as such in its entire length. The last third of the α-synuclein variant's sequence was a disordered binding site. Thymosin-β4 and the stabilin-2 cytoplasmic domain contained only coils and helices according to five secondary structure prediction methods (SPIDER3-SPOT-1D, PSRSM, MUFold-SSW, Porter 5, and RaptorX). β-Sheets are present in α-synucleins, and they extend to more amino acid residues in the A53T mutant according to the predictions. The latter is verified by experiments. The comparison of the predictions with the experiments suggests that helical parts are buried.