Membrane Binding of Recoverin : From Mechanistic Understanding to Biological Functionality

Recoverin is a neuronal calcium sensor involved in vision adaptation that reversibly associates with cellular membranes via its calcium-activated myristoyl switch. While experimental evidence shows that the myristoyl group significantly enhances membrane affinity of this protein, molecular details of the binding process are still under debate. Here, we present results of extensive molecular dynamics simulations of recoverin in the proximity of a phospholipid bilayer. We capture multiple events of spontaneous membrane insertion of the myristoyl moiety and confirm its critical role in the membrane binding. Moreover, we observe that the binding strongly depends on the conformation of the N-terminal domain. We propose that a suitable conformation of the N-terminal domain can be stabilized by the disordered C-terminal segment or by binding of the target enzyme, i.e., rhodopsin kinase. Finally, we find that the presence of negatively charged lipids in the bilayer stabilizes a physiologically functional orientation of the membrane-bound recoverin.Peer reviewe

Ultrafast structure and dynamics in ionic liquids: 2D-IR spectroscopy probes the molecular origin of viscosity

The viscosity of imidazolium ionic liquids increases dramatically when the strongest hydrogen bonding location is methylated. In this work, ultrafast two-dimensional vibrational spectroscopy of dilute thiocyanate ion ([SCN] -) in 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C4C1im][NTf2]) and 1-butyl-2,3- dimethylimidazolium bis(trifluoromethylsulfonyl)imide ([C4C 1C12im][NTf2]) shows that the structural reorganization occurs on a 26 ± 3 ps time scale and on a 47 ± 15 ps time scale, respectively. The results suggest that the breakup of local ion-cages is the fundamental event that activates molecular diffusion and determines the viscosity of the fluids. © 2014 American Chemical Society

Computational approaches to understanding reaction outcomes of organic processes in ionic liquids

This review considers how various computational methods have been applied to explain the changes in reaction outcome on moving from a molecular to an ionic liquid solvent. Initially, different conceptual approaches to modelling ionic liquids are discussed, followed by a consideration of the limitations and constraints of these approaches. A series of case studies demonstrating the utility of computational approaches to explain processes in ionic liquids are considered; some of these address the solubility of species in ionic liquids while others examine classes of reaction where the outcome in ionic liquids can be explained through the application of computational approaches. Overall, the utility of computational methods to explain, and potentially predict, the effect of ionic liquids on reaction outcome is demonstrated

Unfolding of DNA by co-solutes: insights from Kirkwood–Buff integrals and transfer free energies

Many organic co-solutes are known to stabilize or to destabilize native structures of proteins or DNA. Most of these effects can be explained by co-solute binding or exclusion mechanisms. A beneficial approach to study the underlying principles relies on the computation of Kirkwood–Buff integrals, which can be also used to derive detailed expressions for transfer free energies and changes of the chemical equilibrium between the unfolded and the native states. In this article, we use the framework of Kirkwood–Buff theory in order to study the influence of ectoine on the stability of short DNA hairpins. Our results highlight a strong binding of ectoine, which reveals a pronounced destabilization of DNA in good agreement with experimental findings

Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions

Calcium is one of the biologically most important ions; however, its accurate description by classical molecular dynamics simulations is complicated by strong electrostatic and polarization interactions with surroundings due to its divalent nature. Here, we explore the recently suggested approach for effectively accounting for polarization effects via ionic charge rescaling and develop a new and accurate parametrization of the calcium dication. Comparison to neutron scattering and viscosity measurements demonstrates that our model allows for an accurate description of concentrated aqueous calcium chloride solutions. The present model should find broad use in efficient and accurate modeling of calcium in aqueous environments, such as those encountered in biological and technological applications

Complex transitions between dihydrate and anhydrate forms of ectoine - unexpected behavior of a highly hygroscopic compatible solute in the solid state

The crystalline dihydrate of the compatible solute ectoine undergoes a loss of water at ambient conditions and transforms into a highly hygroscopic anhydrate form. This unexpected transition is studied combining single-crystal and powder X-ray, single crystal neutron diffraction measurements and quantum mechanical calculations. Overall, our study provides a rationale for the important uptake and loss of water by ectoine in the solid state