Interaction of the tau fibrils with the neuronal membrane.

Tau proteins are recently gaining a lot of interest due to their active role in causing a range of tauopathies. Molecular mechanisms underlying the tau interaction with the neuronal membrane are hitherto unknown and difficult to characterize using experimental methods. Using the cryo-EM structure of the tau-fibrils we have used atomistic molecular dynamics simulation to model the tau fibril and neuronal membrane interaction using explicit solvation. The dynamics and structural characteristics of the tau fibril with the neuronal membrane are compared to the tau fibril in the aqueous phase to corroborate the effect of the neuronal membrane in the tau structure. Tau fibrils have been modelled using CHARMM-36m force field and the six component neuronal membrane composition is taken from the earlier simulation results. The timescale conceivable in our molecular dynamics simulations is of the order of microseconds which captures the onset of the interaction of the tau fibrils with the neuronal membrane. This interaction is found to impact the tau pathogenesis that finally causes neuronal toxicity. Our study initiates the understanding of tau conformational ensemble in the presence of neuronal membrane and sheds the light on the significant tau-membrane interactions.

Understanding the screening effect of aqueous DES on the IDPs: A molecular dynamics simulation study using amyloid ß42 monomer.

Deep eutectic solvents (DESs) have emerged as the promising replacement to the ionic liquids in solvent engineering for bio-compatibility. We aim to understand the effect of aqueous deep eutectic solvents on the conformation of intrinsically disordered proteins (IDPs). In this context, we have studied the effect on amyloid beta (Aß42) monomer in the hydrated DES composed of tetrabutylammonium chloride and ethylene glycol in a 3:1 ratio using all-atom molecular dynamics simulations. DES is found to effectively screen the interaction of four zones of the amyloid beta monomer with water. Water molecules and the DES constituents modulate the local protein-solvent interactions, in the solvation shell of the protein. In addition, the aqueous DES medium conserves the secondary structure of the Aß42 monomer by increasing the intramolecular hydrogen bonding and D23-K28 salt-bridge interactions when compared to the pure water medium. The current study provides insights into the impact of DES in stabilizing an IDP, at molecular level. We envisage the hindered aggregation of the amyloid beta structures in DES medium over the pure water medium due to the screening of hydrophobic intramolecular interactions.

Understanding the conformational changes in the influenza B M2 ion channel at various protonation states.

The characterization of influenza (A/B M2) ion channels is very important as they are potential binding sites for the drugs. We report the all-atom molecular dynamics study of the influenza B M2 ion channel in the presence of explicit solvent and lipid bilayers using the high resolution solid-state NMR structures. The importance of the various protonation states of histidine in the activation of the ion channel is discussed. The conformational changes at the closed and the open structures clearly show that the increase in tilt angle is necessary for the activation of the ion channel. Additionally, the free energy surfaces of the eight systems show the importance of the protonation state of the histidine residues in the activation of the influenza B M2 ion channel. The protonation of the histidine residues increases the tilt angle and the intra-helix distance which is evident from the superimposition of the structures corresponding to the maxima and the minima in the free energy landscape. The findings imply differences in the singly protonated and double protonated conformational states of BM2 ion channel and provide insights to help further studies of these ion channels as the drug targets for the influenza virus.

Anatomy of Classical Boron-Boron Bonding: Overlap and sp Dissonance.

Classical bonding is predominantly understood using the insipid spn hybridization for σ-bonds as well as π bonds and their delocalized variants. Because hybridization ignores intricate differences in the energy and size of valence atomic orbitals, its naïve application to classically bonded boron atoms leads to numerous surprises in bond strengths, frontier MOs/bands, and even geometry. Here we show that the sp dissonance caused by size mismatch between the valence s and p orbitals of boron plays a crucial role in its bonding, subtly distinct from that of carbon and silicon. Unlike the heavier p block elements, boron prefers to actively engage its compact 2s orbitals in bonding. This leads to the overreach of p-p σ-type overlap that reduces its magnitude in the entire B─B bonding range. Consequently, the π-type overlap remains substantial, making its electronic structure visibly distinct in saturated and unsaturated regimes. The deltahedral frameworks offer a compromise by breaking this symmetry-enforced dichotomy of classical σ- and π-type bonding and following alternate electron counts that suit the electron deficiency of the boron. The pathological anatomy of classical B─B σ-bonding also explains the origins of puzzling metallic character and disorder in their classical boride networks even with ideal electron count, unlike deltahedral borides. The implications of sp dissonance are illustrated in classical boron networks of various hybridizations, explaining the unusual preference for unique sp3 lattice with strained four-membered rings in CrB4, origins of observed σ holes in MgB2 that lead to its superconducting nature, and the absence of Peierls distortion in LiB.

Helix-coil transition and conformational deformity in Aß42-monomer: a case study using the Zn2+ cation.

The metal ions (like Fe2+, Zn2+, Cu2+) are known to influence the amyloid beta (Aß) aggregation. In this study, we have examined the conformational and dynamical changes during the coordination of Aß-monomer with the Zn2+ ion using all-atom molecular dynamics (MD) simulations using explicit solvent models. We have probed the unfolding of the full-length Aß42 monomer both inclusive and exclusive of the Zn2+ cation, with 1:1 ratio of the peptide and the Zn2+ cation. The inclusion of the Zn2+ cation shows differential intra-peptide interactions which has been probed using various analyses. The Helix - Coil transition of the wild type Aß42 monomer is studied using the steered molecular dynamics simulations by taking the end-to-end C-α distance across the peptide. This gives an idea of the unequal intra - peptide and peptide - water interactions being found across the length of the Aß monomer. The transition of an α-helix dominated wild-type (WT) Aß structure to the unfolded coil structure gives significant evidence of the intra-peptide hydrogen bonding shifts in the presence of the Zn2+ cation. This accounts for the structural and the dynamical variations that take place in the Aß monomer in the presence of the Zn2+ cation to mimic the conditions/environment at the onset of fibrillation.Communicated by Ramaswamy H. Sarma.

The effect of external salts on the aggregation of the multiheaded surfactants: All-atom molecular dynamics studies.

Tailoring the molecular design of the surfactants leads to changes in the aggregation properties. The role of external salts on the aggregation properties of the multiheaded surfactants is investigated using molecular dynamics simulations. The multiheaded surfactants show differential aggregation properties on addition of external salts, as reported earlier from experimental studies. We have modelled the multiheaded surfactants to study the effect of external salts (potassium bromide and sodium salicylate) at three different concentrations using the all-atom modelling and explicit solvation. The influence of external salts on the hydration and aggregation propensity, hydrogen bonding, and the structural characteristics of the surfactant aggregates are probed using various analyses across the four groups of multiheaded surfactants. The larger salicylate ion masks the repulsion between the cationic head groups and acts as an effective promoter of aggregation.