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

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

Photoswitching of Azobenzene-Based Reverse Micelles above and at Subzero Temperatures As Studied by NMR and Molecular Dynamics Simulations

We designed and studied the structure, dynamics, and photochemistry of photoswitchable reverse micelles (RMs) composed of azobenzene-containing ammonium amphiphile <b>1</b> and water in chloroform at room and subzero temperatures by NMR spectroscopy and molecular dynamics simulations. The NMR and diffusion coefficient analyses showed that micelles containing either the <i>E</i> or <i>Z</i> configuration of <b>1</b> are stable at room temperature. Depending on the water-to-surfactant molar ratio, the size of the RMs remains unchanged or is slightly reduced because of the partial loss of water from the micellar cores upon extensive <i>E</i> → <i>Z</i> or <i>Z</i> → <i>E</i> photoisomerization of the azobenzene group in <b>1</b>. Upon freezing at 253 or 233 K, <i>E</i>-<b>1</b> RMs partially precipitate from the solution but are redissolved upon warming whereas <i>Z</i>-<b>1</b> RMs remain fully dissolved at all temperatures. Light-induced isomerization of <b>1</b> at low temperatures does not lead to the disintegration of RMs remaining in the solution; however, its scope is influenced by a precipitation process. To obtain a deeper molecular view of RMs, their structure was characterized by MD simulations. It is shown that RMs allow for amphiphile isomerization without causing any immediate significant structural changes in the micelles

The complex nature of calcium cation interactions with phospholipid bilayers

Understanding interactions of calcium with lipid membranes at the molecular level is of great importance in light of their involvement in calcium signaling, association of proteins with cellular membranes, and membrane fusion. We quantify these interactions in detail by employing a combination of spectroscopic methods with atomistic molecular dynamics simulations. Namely, time-resolved fluorescent spectroscopy of lipid vesicles and vibrational sum frequency spectroscopy of lipid monolayers are used to characterize local binding sites of calcium in zwitterionic and anionic model lipid assemblies, while dynamic light scattering and zeta potential measurements are employed for macroscopic characterization of lipid vesicles in calcium-containing environments. To gain additional atomic-level information, the experiments are complemented by molecular simulations that utilize an accurate force field for calcium ions with scaled charges effectively accounting for electronic polarization effects. We demonstrate that lipid membranes have substantial calcium-binding capacity, with several types of binding sites present. Significantly, the binding mode depends on calcium concentration with important implications for calcium buffering, synaptic plasticity, and protein-membrane association.publishedVersionPeer reviewe

How Hydrogen Bonds Influence the Mobility of Imidazolium-Based Ionic Liquids. A Combined Theoretical and Experimental Study of 1-n-Butyl-3-methylimidazolium Bromide

The virtual laboratory allows for computer experiments that are not accessible via real experiments. In this work, three previously obtained charge sets were employed to study the influence of hydrogen bonding on imidazolium-based ionic liquids in molecular dynamics simulations. One set provides diffusion coefficients in agreement with the experiment and is therefore a good model for real-world systems. Comparison with the other sets indicates hydrogen bonding to influence structure and dynamics differently. Furthermore, in one case the total charge was increased and in another decreased by 0.1 e. Both the most acidic proton as well as the corresponding carbon atom were artificially set to zero, sequentially and simultaneously. In the final setup a negative charge was placed on the proton in order to introduce a barrier for the anion to contact the cation via this most acidic hydrogen atom. The following observations were made: changing the hydrogen bonding ability strongly influences the structure while the dynamic properties, such as diffusion and viscosity, are only weakly changed. However, the introduction of larger alterations (stronger hydrogen bonding and antihydrogen bonding) also strongly influences the diffusion coefficients. The dynamics of the hydrogen bond, ion pairing, and the ion cage are all affected by the level of hydrogen bonding. A change in total charges predominantly influences transport properties rather than structure. For ion cage dynamics with respect to transport porperties, we find a good correlation and a weak or no correlation for the ion pair or the hydrogen bond dynamics, respectively. Nevertheless, the hydrogen bond does influence ion cage dynamics. Therefore, we confirm that ionic liquids rather consist of loosely interacting counterions than of discrete ion pairs. Hydrogen bonding affects the properties only in a secondary or indirect manner