Role of a high centrality residue in protein dynamics and thermal stability

Evolutionary rewiring of the dynamic network underpinning allosteric epistasis in NS1 of influenza A virus

Viral proteins frequently mutate to evade or antagonize host innate immune responses, yet the impact of these mutations on the molecular energy landscape remains unclear. Epistasis, the intramolecular communications between mutations, often renders the combined mutational effects unpredictable. Nonstructural protein 1 (NS1) is a major virulence factor of the influenza A virus (IAV) that activates host PI3K by binding to its p85β subunit. Here, we present the deep analysis for the impact of evolutionary mutations in NS1 that emerged between the 1918 pandemic IAV strain and its descendant PR8 strain. Our analysis reveal how the mutations rewired inter-residue communications which underlies long-range allosteric and epistatic networks in NS1. Our findings show that PR8 NS1 binds to p85β with approximately 10-fold greater affinity than 1918 NS1 due to allosteric mutational effects. Notably, these mutations also exhibited long-range epistatic effects. NMR chemical shift perturbation and methyl-axis order parameter analyses revealed that the mutations induced long-range structural and dynamic changes in PR8 NS1, enhancing its affinity to p85β. Complementary MD simulations and graph-based network analysis uncover how these mutations rewire dynamic residue interaction networks, which underlies the long-range epistasis and allosteric effects on p85β-binding affinity. Significantly, we find that conformational dynamics of residues with high betweenness centrality play a crucial role in communications between network communities and are highly conserved across influenza A virus evolution. These findings advance our mechanistic understanding of the allosteric and epistatic communications between distant residues and provides insight into their role in the molecular evolution of NS1.

Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics

Dynamics-driven allostery provides important insights into the working mechanics of proteins, especially enzymes. In this study, we employ this paradigm to answer a basic question: in enzyme superfamilies, where the catalytic mechanism, active sites, and protein fold are conserved, what accounts for the difference in the catalytic prowess of the individual members? We show that when subtle changes in sequence do not translate to changes in structure, they do translate to changes in dynamics. We use sequentially diverse PTP1B, TbPTP1, and YopH as representatives of the conserved protein tyrosine phosphatase (PTP) superfamily. Using amino acid network analysis of group behavior (community analysis) and influential node dominance on networks (eigenvector centrality), we explain the dynamic basis of the catalytic variations seen between the three proteins. Importantly, we explain how a dynamics-based blueprint makes PTP1B amenable to allosteric control and how the same is abstracted in TbPTP1 and YopH.

Exploring the molecular mechanism of cold-adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network

Psychrophilic proteases have attracted enormous attention in past decades, due to their high catalytic activity at low temperatures in a wide range of industrial processes, especially in the detergent and leather industries. Among them, H5 is an alkaline protease mutant, which featuring psychrophilic-like behavior, but the reasons that H5 with higher activity at low temperatures are still poorly understood. Herein, the molecular dynamics (MD) simulations combined with residue interaction network (RIN) were utilized to investigate the mechanisms of the cold-adaption of mutant H5. The results demonstrated that two loops involved in the substrate binding G100-S104 and S125-S129 in H5 had higher mobility, and the distance enlargement between the two loops modulated the substrate's accessibility compared with wild type counterpart. Besides, H5 enhanced conformational flexibility by weakening salt bridges and increasing interaction with the solvent. In particular, the absence of Lys251-Asp197-Arg247 salt bridge network may contribute to the structural mobility. Based on the free energy landscape and molecular mechanics Poisson-Boltzmann surface area of the wild type and H5, it was elucidated that H5 possessed a large population of interconvertible conformations, resulting in the weaker substrate binding free energy. The calculated RIN topology parameters such as the average degree, average cluster coefficient, and average path length further verified that the mutant H5 attenuated residue-to-residue interactions. The investigation of the mechanisms by which how the residue mutation affects the stability and activity of enzymes provides a theoretical basis for the development of cold-adapted protease.

Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics

Dynamics-driven allostery provides important insights into the working mechanics of proteins, especially enzymes. In this study we employ this paradigm to answer a basic question: in enzyme superfamilies where the catalytic mechanism, active sites and protein fold are conserved, what accounts for the difference in the catalytic prowess of the individual members? We show that when subtle changes in sequence do not translate to changes in structure, they do translate to changes in dynamics. We use sequentially diverse PTP1B, TbPTP1, and YopH as the representatives of the conserved Protein Tyrosine Phosphatase (PTP) superfamily. Using amino acid network analysis of group behavior (community analysis) and influential node dominance on networks (eigenvector centrality), we explain the dynamic basis of catalytic variations seen between the three proteins. Importantly, we explain how a dynamics-based blueprint makes PTP1B amenable to allosteric control and how the same is abstracted in TbPTP1 and YopH.