Desolvation Energy Explains Partitioning of Client Proteins into Condensates

Membraneless organelles are cellular compartments that form by liquid-liquid phase separation of one or more components. Other molecules, such as other proteins and nucleic acids, will distribute between the cytoplasm and the liquid compartment in accordance with the thermodynamic drive to lower the free energy of the system. The resulting distribution colocalizes molecular species, to carry out a diversity of functions. Two factors could drive this partitioning: the difference in solvation between the dilute versus dense phase, and intermolecular interactions between the client and scaffold proteins. Here, we develop a set of knowledge-based potentials that allow for the direct comparison between desolvation energy and pairwise interaction energy terms, and use these to examine experimental data from two systems: protein cargo dissolving within phase-separated droplets made from FG repeat proteins of the nuclear pore complex, and client proteins dissolving within phase-separated FUS droplets. We find close agreement between desolvation energies of the client proteins and the experimentally determined values of the partition coefficients, while pairwise interaction energies between client and scaffold show weaker correlations. These results show that client stickiness is sufficient to explain differential partitioning of clients within these two phase-separated systems without taking into account the composition of the condensate. This suggests that selective trafficking of client proteins to distinct membraneless organelles requires recognition elements beyond the client sequence composition.

Intrinsic basis of thermostability of prolyl oligopeptidase from Pyrococcus furiosus

Salt-bridges play a key role in the thermostability of proteins adapted in stress environments whose intrinsic basis remains to be understood. We find that the higher hydrophilicity of PfP than that of HuP is due to the charged but not the polar residues. The primary role of these residues is to enhance the salt-bridges and their ME. Unlike HuP, PfP has made many changes in its intrinsic property to strengthen the salt-bridge. First, the desolvation energy is reduced by directing the salt-bridge towards the surface. Second, it has made bridge-energy more favorable by recruiting energetically advantageous partners with high helix-propensity among the six possible salt-bridge pairs. Third, ME-residues that perform intricate interactions have increased their energy contribution by making major changes in their binary properties. The use of salt-bridge partners as ME-residues, and ME-residues' overlapping usage, predominant in helices, and energetically favorable substitution are some of the favorable features of PfP compared to HuP. These changes in PfP reduce the unfavorable, increase the favorable ME-energy. Thus, the per salt-bridge stability of PfP is greater than that of HuP. Further, unfavorable target ME-residues can be identified whose mutation can increase the stability of salt-bridge. The study applies to other similar systems.

Vitamin D is a New Promising Inhibitor to the Main Protease (Mpro) of COVID-19 by Molecular Docking

In this study, vitamin D has shown greater efficacy of binding with Mpro of COVID-19 compared to the recently recommended drugs. The docking study was simulated to streamline interaction effects of Vitamin D, Remdesivir, Chloroquine, Hydroxychloroquine, Aspirin, and Azithromycin complexes with the active site of Mpro. Vitamin D is found to have the highest potential interaction in terms of total H-bond, van der Waal, torsional, and desolvation energy which were the lowest among all the selected drugs. The hydroxyl group of vitamin D and the thiol group of Mpro cysteine had played a leading role in increasing Vitamin D binding and stability with the Mpro pocket by contribution to the inception of three hydrogen bonds. The study recommend that vitamin D can be added to the COVID-19 treatment protocol, which may have the desired effect on viral replication inhibition and decreases mortality.

Molecular modeling of electrolyte and polysulfide ions for lithium-sulfur batteries

The operation of a lithium-sulfur (Li-S) battery involves the transport of Li+ ions and soluble sulfides mostly in the form of solvated ions. Key challenges in the development of Li-S battery technology are the diffusion of Li+ in micropores filled with sulfur and eliminating the “shuttling” of polysulfides. Ion dimensions in solvated and desolvated forms are key parameters determining the diffusion coefficient and the rate of transport of such ions, while constrictivity effects due to the effect of pore size compared to ion size control both transport and filling of the pores. We present molecular simulations to determine the solvation parameters of electrolyte ions and sulfides S22−, S42−, S62−, and S82− in two different electrolyte systems: LiTFSI in DOL/DME and LiPF6 in EC/DMC. The calculated parameters include the coordination number and the geometrically optimized model and dimensions, using the van der Waals surface approach, of the solvated and desolvated ions. The desolvation energy of the electrolyte ions is also calculated. Such data is useful for the modeling and design of the pore sizes of cathode host materials to be able to accommodate the different sulfides while minimizing their “shuttling” between cathode and anode.

Suppressing lithium dendrite formation by slowing its desolvation kinetics

A higher desolvation energy barrier and slower lithium electrodeposition kinetics tends to inhibit dendrite formation.