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.

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 1 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 E or Z configuration of 1 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 E → Z or Z → E photoisomerization of the azobenzene group in 1.

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.

Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization.

Calcium represents a key biological signaling ion with the EF-hand loops being its most prevalent binding motif in proteins. We show using molecular dynamics simulations with umbrella sampling that including electronic polarization effects via ionic charge rescaling dramatically improves agreements with experiment in terms of the strength of calcium binding and structures of the calmodulin binding sites. The present study thus opens way to accurate calculations of interactions of calcium and other computationally difficult high-charge-density ions in biological contexts.

Exploring Ion-Ion Interactions in Aqueous Solutions by a Combination of Molecular Dynamics and Neutron Scattering.

Recent advances in computational and experimental techniques have allowed for accurate description of ion pairing in aqueous solutions. Free energy methods based on ab initio molecular dynamics, as well as on force fields accounting effectively for electronic polarization, can provide quantitative information about the structures and occurrences of individual types of ion pairs. When properly benchmarked against electronic structure calculations for model systems and against structural experiments, in particular neutron scattering, such force field simulations represent a powerful tool for elucidating interactions of salt ions in complex biological aqueous environments.

Accounting for Electronic Polarization Effects in Aqueous Sodium Chloride via Molecular Dynamics Aided by Neutron Scattering.

Modeled ions, described by nonpolarizable force fields, can suffer from unphysical ion pairing and clustering in aqueous solutions well below their solubility limit. The electronic continuum correction takes electronic polarization effects of the solvent into account in an effective way by scaling the charges on the ions, resulting in a much better description of the ionic behavior. Here, we present parameters for the sodium ion consistent with this effective polarizability approach and in agreement with experimental data from neutron scattering, which could be used for simulations of complex aqueous systems where polarization effects are important.

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.

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.

Performance of quantum chemically derived charges and persistence of ion cages in ionic liquids. A molecular dynamics simulations study of 1-n-butyl-3-methylimidazolium bromide.

We carried out classical molecular dynamics simulations with a standard and two quantum chemistry based charge sets to study the ionic liquid 1-n-butyl-3-methylimidazolium bromide, [C(4)C(1)im][Br]. We split the cation up into different charge groups and found that the total charge and the charge distribution in the imidazolium ring are completely different in the three systems while the total charge of the butyl chain is much better conserved between the methods. For comparison, the spatial distribution functions and the radial distribution functions as well as different time correlation functions were calculated.