Helix-coil transition and conformational deformity in Aβ42-monomer: a case study using the Zn2+ cation

The metal ions (like Fe2+, Zn²⁺, Cu2+) are known to influence the amyloid beta (Aβ) aggregation. In this study, we have examined the conformational and dynamical changes during the coordination of Aβ-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 Aβ₄₂ 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 Aβ42 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 Aβ monomer. The transition of an α-helix dominated wild-type (WT) Aβ 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 Aβ monomer in the presence of the Zn2+ cation to mimic the conditions/environment at the onset of fibrillation.Communicated by Ramaswamy H. Sarma.

Key Factors Determining Efficiency of Liquid-Liquid Extraction: Implications from Molecular Dynamics Simulations of Biphasic Behaviors of CyMe4-BTPhen and Its Am(III) Complexes

CyMe₄-BTPhen (2,9-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzotriazin-3-yl)-1,10-phenanthroline, denoted as L) has been considered as a promising extractant in lanthanide(III)/actinide(III) separation. Vast endeavors in its application put forward a compelling need on the understanding of the underlying mechanism in the liquid-liquid extraction. To address the issue of its dynamics in biphasic systems, we carried out molecular dynamics (MD) simulations of L and its complexes with a heavy f-block metal ion, americium(III) (Am³⁺) in "oil"/water binary solvents. Two types of organic phases have been considered, differing in the presence of octanol in the bulk n-dodecane or not, and the distribution of the solutes and their interfacial behaviors have been investigated. Two of the key factors that determine the efficiency of a liquid-liquid extraction protocol were delineated and discussed, that is, the appropriate ligand to enhance the lipophilicity of AmL complexes and appropriate way to form ion pairs to minimize the attraction between the complexes and aqueous phase. The simulations showed that the charge states of both ligand and AmL complexes were strongly correlated with their phase behavior, and the migration of neutral species was driven by van der Waals interactions while that of charged species by electrostatic interactions, indicating stronger lipophilicity of the former than the latter. The presence of octanol facilitated the migration of the ligand from the interface to the organic phase via hydrogen bond between its polar head and the ligand or the AmL complexes and constituted a polar core in the organic phase. This work bridged the widely used liquid-liquid extraction technique in chemistry to a fundamental chemical concept, that is, minimization of hydrophilicity and maximization of lipophilicity to facilitate phase transfer from the aqueous phase to the organic phase, and is expected to improve the understanding of dynamics of ligands and their complexes with metal ions and to contribute to the development of efficient protocols for phase transfer of target species.

The effect of solvent heterogeneity on the solvation and complexation of alkali cations by 18-crown-6: a simulation study in the 90 : 10 chloroform/methanol mixture

Although chloroform is in excess over methanol in the mixture, the predicted ion binding affinities and selectivities are more “methanol-like” than “chloroform-like”.