Delineating the effect of mutations on the conformational dynamics of N-terminal domain of TDP-43

Abstract

The structural integrity of N-terminal domain (NTD) of TAR DNA-binding protein-43 (TDP-43) is essential for the biological functions of TDP-43 involved in neurodegenerative diseases. Here, we used all-atom molecular dynamics (MD) simulations to understand the folding, dynamics and conformational stability of four variants of NTD, the wild type (WT) and three mutants (L27A, L28A and V31R). The deleterious and destabilizing nature of NTD mutants were predicted on DynaMut and SAAFEC server. Results show that predicted mutations modulate the conformational stability and flexibility of NTD. The effect of mutations on the conformational dynamics of NTD was studied through the free-energy landscape (FEL), essential dynamics (ED), hydrogen-bonds and intermolecular contact map. We observed that the mutations disrupt the intermolecular interactions between the dimeric NTD besides affecting the long-range intramolecular contacts, resulting in a less compact structure. ED essentially provides the collective motion of protein and we observed that the mutation increased the overall motions of the protein which might result in protein dysfunction. FEL shows the different conformational transitions of WT and mutants which revealed the structural basis of protein destabilization and unfolding due to mutation. We find that L28A has most of the deleterious effect compared to other two mutations, L27A and V31R. These results obtained here are well correlated with reported experimental studies which show the disruption of protein folding, stability and function with these mutations. Hence this computational study describes the structural details to unravel the mutant effects at the atomistic resolution and has implications for understanding the TDP-43's physiological and pathological role.