The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease.

The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro's susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of an Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrate a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild type enzyme. We show that other point mutations also significantly shift the equilibrium towards this state by altering conformational free energies. Unique avenues of SARS-CoV-2 research can be explored by understanding how H163 modulates this equilibrium.

Cohesiveness and Nondiffusive Rotational Jump Dynamics of Protic Ionic Liquid from Dispersion-Corrected FPMD Simulations.

We have investigated the liquid phase of an ionic liquid (IL), methylammonium formate (MAF), through the first principles molecular dynamics simulations using van der Waals (vdW) corrected exchange and correlation functionals of the density functional theory. The simulations were carried out to obtain a comparative study of various properties of the MAF using two different generalized gradient approximation functionals (Becke-Lee-Yang-Parr (BLYP) and Perdew-Burke-Ernzerhof (PBE)) along with three types of dispersion corrections (D2, D3, and dispersion-corrected atom-centered one-electron potentials), and two values of the plane-wave cutoff (300 and 600 Ry). We have evaluated the effects of various electronic parameters in describing the hydrogen-bonded structure and dynamical properties of MAF by performing 10 sets of molecular dynamics simulations. Thermodynamic properties are found to be sensitive to the details of electronic structure calculations. Our results of PBE functionals with the semiempirical vdW method provide the best agreement with experimental density. The overall density predictions match the cohesive energy trends, and the calculations incorporating dispersion forces exhibit enhanced intermolecular interactions within the hydrogen-bonded IL framework. All of the vdW-corrected BLYP functionals, mainly the dispersion-corrected atom-centered one-electron potential (DCACP) method, illustrate a well-defined structure of liquid MAF. To look into the dynamical perspective of the hydrogen-bond descriptions, we elucidate two possible mechanistic pathways of the hydrogen-bond jump events between the counterions. The hydrogen-bond breaking and forming mechanism along with the collision dynamics can be best described by incorporating dispersion interactions alongside the exchange and correlation functionals within the Kohn-Sham scheme. The rattling dynamics of ions are observed for dispersion-corrected functionals. Hence, an accurate representation of the delicately balanced interactive forces within ionic liquids is a necessary step toward a better description of its thermophysical and structural properties along with the associated ionic dynamics.

Conformational Free-Energy Landscapes of Alanine Dipeptide in Hydrated Ionic Liquids from Enhanced Sampling Methods.

Understanding the interaction of the ionic liquid (IL) with protein is vital to find the origin of the conformational changes of proteins in these alternative solvents. Here, we performed biased molecular dynamics simulations of alanine dipeptide (ADP), a widely used model for protein backbone structure, in water and two hydrated ionic liquids (ILs): 80% (w/w) 1-ethyl-3-methylimidazolium acetate ([EMIm][Ac]) and 80% (w/w) choline dihydrogen phosphate ([Cho][DHP]). We employed three different biasing methods, metadynamics (metaD), well-tempered metadynamics (WT-metaD), and adaptive biasing force (ABF), to construct the free-energy landscapes of the ADP conformations using the backbone dihedral angles (ϕ and ψ) as the collective variables. The calculations were also performed in water; the free-energy landscapes of ADP in water obtained from three methods are similar and agree well with the previously reported results. In hydrated [EMIm][Ac], α-planar conformation emerges as a minimum, which is comparable to that of α and ß conformations corresponding to α-helix and ß-sheet-like conformations of proteins. Investigation of corresponding conformations suggests that the imidazolium ring of [EMIm] cation is stacked with the amide bonds of ADP. Acetate anion makes hydrogen bonds with the amide hydrogens of the ADP. The amide-π stacking interaction is the driving force for α-planar conformation to become one of the minimum energy conformations in this IL, which destabilizes the protein conformation. However, α and ß conformations are more stable in hydrated [Cho][DHP] compared to α-planar and ß-planar conformations; therefore, this IL stabilizes the protein conformation. These findings are in good correlation with the previous study of proteins in these ILs. Our study helps to understand the interaction of proteins with the ionic entities and their stability in ILs.

Thermophysical Properties and Angular Jump Dynamics of Water: A Comparative DFT and DFT-Dispersion-Based Molecular Dynamics Study.

We present the first-principles molecular dynamics simulations of water molecules using two different levels of density functional theory within the Kohn-Sham scheme, namely, Becke-Lee-Yang-Parr (BLYP) and Perdew-Burke-Ernzerhof (PBE) with dispersion corrections such as D2 as well as D3 versions of Grimme dispersion correction and dispersion-corrected atom-centered potential. Our aim is to provide a comparative study of these functionals in explaining the thermophysical and structural properties along with nondiffusive jump dynamics of water molecules concerning the experimental data. The hydrogen bonding phenomenon is dependent on polarity, bonding, as well as nonbonding interactions, which requires thorough parametrization. Since hydrogen bonding is responsible for several properties in the water, we investigate the effect of dispersion corrections on the hydrogen bond jump dynamics. BLYP and PBE functionals are well-known for overestimating the spatial structure and underestimating the density and diffusivity. Thus, dispersion corrections are introduced to generate a well-structured and adequately dense equilibrated liquid water system. Here, we have reported the density values of water obtained from different density functionals and also verified the trend with other thermophysical phenomena such as compressibility and cohesive energy. The behavior of simulated water systems is further explained by analyzing various structural properties and hydrogen bond jump dynamics.

Conformational dynamics of amyloid-ß (16-22) peptide in aqueous ionic liquids.

Molecular dynamics simulations of amyloid-ß (16-22) peptide dimer in water as well as at two different experimentally studied concentrations of hydrated ionic liquids (ILs), ethylammonium mesylate (EAM), ethylammonium nitrate (EAN), and triethylammonium mesylate (TEAM), were carried out employing an umbrella sampling method. We used the average Ψ angle of the peptide backbone as the reaction coordinate to observe the conformational changes of a peptide dimer. Secondary structural element values were calculated for the peptide dimer along the reaction coordinate to see the transition of the peptide dimer between ß-sheet and α-helix conformations. We observe the ß-sheet conformation as the global minimum on the free energy surfaces in both EAM and EAN ILs at both the concentrations and at a low concentration of TEAM. However, we observe α-helix conformation as the global minimum at a high concentration of TEAM. Our results are in good correlation with the experimental findings. We calculated the average number of intramolecular and intermolecular hydrogen bonds of α-helix and ß-sheet conformations in all solutions, and they are in correlation with the secondary structure element values. To understand the peptide-IL interactions, atom-atom radial distribution functions of cation, anion, and water around amide oxygen and hydrogen atoms were calculated. The solvent-accessible surface area of the peptide dimer was calculated to understand the exposure of the peptide towards the solvent during conformational changes. Finally, van der Waals (vdW) and Coulomb interaction energies were calculated between peptide-cation, peptide-anion, and peptide-water to understand the stability of conformations in different concentrations. We find that the TEA cation has more vdW interaction energy compared to Coulomb interaction energy with peptide in 70% (w/w) TEAM, which mimics a membrane-like environment to induce α-helix conformation rather than ß-sheet conformation.

Nondiffusive Rotational Jump Dynamics in Ethyl Ammonium Nitrate.

We examine the hydrogen bond jump mechanism in ionic liquid, ethyl ammonium nitrate (EAN), using classical molecular dynamics simulations. Hydrogen bond jump in EAN can occur through two different nondiffusive rotational jump mechanisms: N-H bond of ethyl ammonium can switch its hydrogen bond between two oxygen atoms of the same nitrate ion or it can break its hydrogen bond with the oxygen of a nitrate ion to form a new hydrogen bond with the oxygen atom of another nitrate ion. We observe the average magnitude of the jump angle of 30° in the first mechanism, whereas the jump angle for the second mechanism is 70°. The in-plane rotation of nitrate ion facilitates the H-bond switch in the first mechanism, whereas the rotation of the ammonium group of cation around the C-N bond facilitates the H-bond switch in the second mechanism. The jump angle observed in the second mechanism qualitatively agrees with experimentally observed large jump angle. We also investigate the effect of temperature on this nondiffusive rotational dynamics of ionic liquid to observe the changes in the jump angle and its distributions.

Association of Nucleobases in Hydrated Ionic Liquid from Biased Molecular Dynamics Simulations.

We employed metadynamics-based classical molecular dynamics simulations to methylated adenine-thymine (mA-mT) and guanine-cytosine (mG-mC) base pairs to see favorable conformations in various concentrations of hydrated 1-ethyl, 3-methyl imidazolium acetate. We investigated various stacked and hydrogen-bonded conformations of association of base pairs through appropriately chosen collective variables. Stacked conformations more favored in water for both base pairs, whereas Watson-Crick (WC) hydrogen-bonding conformations are favored in pure and hydrated ionic liquids (ILs) except for 0.75 mol fraction IL. We observe that EMIm cations surround the base pairs in WC conformations creating a kind of hydrophobic cavity and protect the hydrogen bonds between base pairs. However, the five-membered heteroaromatic rings of cations stack with the nucleobases in the cation-base-cation (π-π-π) model, which resembles the base-base-base stacking in a DNA duplex. Interestingly, from additional simulations of 0.5 mol fraction hydrated choline dihydrogen phosphate IL, we observe that the stacked conformations become more favored than the WC conformation due to the absence of π-bonds in cations. The calculated values of relative solubility of base pairs in pure and hydrated ionic liquids compared to those in pure water correlate well with the free energy values of WC and stacked conformations.

Biosolvation Nature of Ionic Liquids: Molecular Dynamics Simulation of Methylated Nucleobases in Hydrated 1-Ethyl-3-methylimidazolium Acetate.

Solvation free energies of methylated nucleobases were calculated in pure and hydrated 1-ethyl-3-methylimidazolium acetate, [Emim][Ac], ionic liquid, and pure water using classical molecular dynamics simulations using multistate Bennett's acceptance ratio method. The calculated solvation free energies in pure water were compared with the previous experimental and theoretical findings and found to be in agreement. We observe that the solvation free energy of methylated nucleobases is more in the pure ionic liquid compared to that in the pure water and on changing the mole fraction of water in the ionic liquid, the solvation free energy decreases gradually. Comparing the Coulombic and van der Waals contribution to the solvation free energy, electrostatic contribution is more compared to that of the latter for all nucleobases. To obtain the atomistic details and explain the solvation mechanism, we calculated radial distribution functions (RDFs), spatial distribution functions (SDFs), and stacking angle distribution of cations to the nucleobases. From RDFs and SDFs, we find that the acetate anions of the ionic liquid are forming strong hydrogen bonds with the amine hydrogen atoms of the nucleobases. These hydrogen bonds contribute to the major part of the Coulombic contribution to the solvation free energy. Stacking of cations to the nucleobases is primarily due to the van der Waals contribution to the solvation free energy.

Hopping-mediated anion transport through a mannitol-based rosette ion channel.

Artificial anion selective ion channels with single-file multiple anion-recognition sites are rare. Here, we have designed, by hypothesis, a small molecule that self-organizes to form a barrel rosette ion channel in the lipid membrane environment. Being amphiphilic in nature, this molecule forms nanotubes through intermolecular hydrogen bond formation, while its hydrophobic counterpart is stabilized by hydrophobic interactions in the membrane. The anion selectivity of the channel was investigated by fluorescence-based vesicle assay and planar bilayer conductance measurements. The ion transport by a modified hopping mechanism was demonstrated by molecular dynamics simulation studies.