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

Mónika Bokor,Ágnes Tantos

doi:10.1021/acs.jproteome.0c00986

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.

Highlights

New recently developed and older sequence-based predictors are widely applied for the characterization and prediction of protein structure and function
The particular predicted protein secondary structures (SSs) are compared with the structural information gained by wide-line nuclear magnetic resonance (NMR) experiments for verification
Calculations to establish the presence of disordered protein regions and disordered binding regions were made for Tb4 and the stabilin-2 cytoplasmic domain (CTD) by IUPred[2] and ANCHOR2, respectively (Figure 1)

Summary

■ INTRODUCTION

New recently developed and older sequence-based predictors are widely applied for the characterization and prediction of protein structure and function. Wide-line 1H NMR experimental results provide unique information on the interactions of proteins with the solvent water in the form of a melting diagram (MD).[4−6] The MDs HeR is measured from MDs as a ratio of the thermal width of the heterogeneous behavior to the thermal distance of the mobile hydration water appearance. We compare SS predictions with wideline 1H NMR experimental results and evaluate the predictions based on their agreement

■ RESULTS AND DISCUSSION

■ METHODS

■ REFERENCES