Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis

Abstract

We employed mutual information (MI) analysis to detect motions affecting the mechanical resistance of the human-engineered protein Top7. The results are based on the MI analysis of pair contact correlations measured in steered molecular dynamics (SMD) trajectories and their statistical dependence on global unfolding. This study is the first application of the MI analysis to SMD forced unfolding, and we furnish specific SMD recommendations for the utility of parameters and options in the TimeScapes package. The MI analysis provided a global overview of the effect of perturbation on the stability of the protein. We also employed a more conventional trajectory analysis for a detailed description of the mechanical resistance of Top7. Specifically, we investigated 1) the hydropathy of the interactions of structural segments, 2) the H₂O concentration near residues relevant for unfolding, and 3) the changing hydrogen bonding patterns and main chain dihedral angles. The results show that the application of MI in the study of protein mechanical resistance can be useful for the engineering of more resistant mutants when combined with conventional analysis. We propose a novel mutation design based on the hydropathy of residues that would stabilize the unfolding region by mimicking its more stable symmetry mate. The proposed design process does not involve the introduction of covalent crosslinks, so it has the potential to preserve the conformational space and unfolding pathway of the protein.

Keywords: molecular dynamics analysis; mutual information (MI); protein design and engineering; protein unfolding pathway; steered molecular dynamics (SMD).