Mechanistic Insights into the Protection Effect of Argonaute-RNA Complex on the HCV Genome

Advances in Computational Intelligence-Based Methods of Structure and Function Prediction of Proteins

Proteins serve as the building blocks of life and play essential roles in almost every cellular process [...].

Probing the conformational dynamics of an Ago-RNA complex in water/methanol solution

Argonaute (Ago) proteins mediate target recognition guiding miRNA to bind complementary mRNA primarily in the seed region. However, additional pairing can occur beyond the seed, forming a supplementary duplex that can contribute to the guide-target affinity. In order to shed light on the connection, between protein-RNA interactions and miRNA-mRNA seed and supplementary duplex mobility, we carried out molecular dynamics simulations at the microsecond time-scale using a different approach compared to the ones normally used. Until now, theoretical investigations with classical MD on Ago-RNA complexes have been focused primarily on pure water solvent, which mimics the natural environment of biological molecules. Here, we explored the conformational space of a human Ago2 (hAgo2) bound to the seed + supplementary miRNA-mRNA duplex, using the solvent environment as a molecular probe. MD simulations have been performed in a mixture of water/MeOH at a molar ratio of 70 : 30 as well as in pure water for comparison. Our findings revealed that the mixed solvent promotes protein RNA association, principally enhancing salt-linkages between basic amino acid side-chains and acidic phosphates of the sugar-phosphate backbone. The primary effect registered was the restriction of supplementary duplex flexibility and the stabilization of the miRNA 3' terminus. Interestingly, we observed that the influence of the solvent appears to have almost no impact on the conformation of the seed duplex.

Designing drugs and chemical probes with the dualsteric approach

Traditionally, drugs are monovalent, targeting only one site on the protein surface. This includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric sites, respectively. Orthosteric drugs are good in potency, whereas allosteric drugs have better selectivity and are solutions to classically undruggable targets. However, it would be difficult to simultaneously reach high potency and selectivity when targeting only one site. Also, both kinds of monovalent drugs suffer from mutation-caused drug resistance. To overcome these obstacles, dualsteric modulators have been proposed in the past twenty years. Compared to orthosteric or allosteric drugs, dualsteric modulators are bivalent (or bitopic) with two pharmacophores. Each of the two pharmacophores bind the protein at the orthosteric and an allosteric site, which could bring the modulator with special properties beyond monovalent drugs. In this study, we comprehensively review the current development of dualsteric modulators. Our main effort reason and illustrate the aims to apply the dualsteric approach, including a "double win" of potency and selectivity, overcoming mutation-caused drug resistance, developments of function-biased modulators, and design of partial agonists. Moreover, the strengths of the dualsteric technique also led to its application outside pharmacy, including the design of highly sensitive fluorescent tracers and usage as molecular rulers. Besides, we also introduced drug targets, designing strategies, and validation methods of dualsteric modulators. Finally, we detail the conclusions and perspectives.

Decoding the deactivation mechanism of R192W mutation of ZAP-70 using molecular dynamics simulations and binding free energy calculations

CONTEXT

ZAP-70 (zeta-chain-associated protein of 70 kDa), serving as a critical regulator for T cell antigen receptor signaling, represents an attractive therapeutic target for autoimmunity disease. How the mechanistical mechanism of ZAP-70 to a human autoimmune syndrome-associated R192W mutation remains unclear. The results indicated that the R192W mutation of ZAP-70 clearly affected the conformational flexibility of the N-terminal ITAM-Y2P. Structural analysis unveiled that the R192W mutation of ZAP-70 caused the exposure of the N-terminal ITAM-Y2P to the solvent. MM-GBSA binding free energy calculations exhibited that the R192W mutation decreased the binding affinity of ITAM-Y2P to the ZAP-70 mutant. Residue-based free energy decomposition further revealed that the protein-peptide interaction networks involving electrostatic interactions provide significant contributions for complex formation. The energy unfavorable residues include Arg43, Arg192, Tyr240, and Lys244 from ZAP-70 and Asn301, Leu303, pY304, and pY315 from ITAM-Y2P in the R192W mutant. Our obtained results may help the understanding of the deactivation mechanism of ZAP-70 induced by the R192W mutation.

METHODS

In the work, multiple replica molecular dynamics simulations and molecular mechanics-generalized Born surface area (MM-GBSA) method were performed to reveal the doubly phosphorylated ITAMs (ITAM-Y2P)-mediated deactivation mechanism of ZAP-70 induced by the R192W mutation.