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Biomedical subjects

Lubos Vrbka

Publications and source records attributed to Lubos Vrbka.

7 recordsLinked to original sources

Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces.

For a series of different proteins, including a structural protein, enzyme, inhibitor, protein marker, and a charge-transfer system, we have quantified the higher affinity of Na+ over K+ to the protein surface by means of molecular dynamics simulations and conductivity measurements. Both approaches show that sodium binds at least twice as strongly to the protein surface than potassium does with this effect being present in all proteins under study. Different parts of the protein exterior are responsible to a varying degree for the higher surface affinity of sodium, with the charged carboxylic groups of aspartate and glutamate playing the most important role. Therefore, local ion pairing is the key to the surface preference of sodium over potassium, which is further demonstrated and quantified by simulations of glutamate and aspartate in the form of isolated amino acids as well as short oligopeptides. As a matter of fact, the effect is already present at the level of preferential pairing of the smallest carboxylate anions, formate or acetate, with Na+ versus K+, as shown by molecular dynamics and ab initio quantum chemical calculations. By quantifying and rationalizing the higher preference of sodium over potassium to protein surfaces, the present study opens a way to molecular understanding of many ion-specific (Hofmeister) phenomena involving protein interactions in salt solutions.

Animals↗

Homogeneous freezing of water starts in the subsurface.

Molecular dynamics simulations of homogeneous ice nucleation in extended aqueous slabs show that freezing preferentially starts in the subsurface. The top surface layer remains disordered during the freezing process. The subsurface accommodates better than the bulk the increase of volume connected with freezing. It also experiences strong electric fields caused by oriented surface water molecules, which can enhance ice nucleation. Our computational results shed new light on the experimental controversy concerning the bulk vs surface origin of homogeneous ice nucleation in water droplets. This has important atmospheric implications for the microphysics of formation of high altitude clouds.

Journal Article↗

Selected biologically relevant ions at the air/water interface: a comparative molecular dynamics study.

Interfacial behavior of selected biologically and technologically relevant ions is studied using molecular dynamics simulations employing polarizable potentials. Propensities of choline, tetraalkylammonium (TAA), and sodium cations, and sulfate and chloride anions for the air/water interface are analyzed by means of density profiles. Affinity of TAA ions for the interface increases with their increasing hydrophobicity. Tetramethylammonium favors bulk solvation, whereas cations with propyl and butyl chains behave as surfactants. The choice of counter-anions has only a weak effect on the behavior of these cations. For choline, sodium, chloride and sulfate, the behavior at the air/water interface was compared to the results of our recent study on the segregation of these ions at protein surfaces. No analogy between these two interfaces in terms of ion segregation is found.

Air↗

Specific ion effects at protein surfaces: a molecular dynamics study of bovine pancreatic trypsin inhibitor and horseradish peroxidase in selected salt solutions.

The distribution of sodium, choline, sulfate, and chloride ions around two proteins, horseradish peroxidase (HRP) and bovine pancreatic trypsin inhibitor (BPTI), is investigated by means of molecular dynamics simulations with the aim to elucidate ion adsorption at the protein surface. Although the two proteins under investigation are very different from each other, the ion distributions around them are remarkably similar. Sulfate is always strongly attached to the proteins, choline shows a significant, but unspecific, propensity for the protein surfaces, and sodium ions have a weak surface affinity, while chloride has virtually no preference for the protein surface. In mixtures of all four ion species in protein solutions, the resulting distributions are almost a superposition of the distributions of sodium sulfate and choline chloride, except that sodium partially replaces choline close to the proteins. The present simulations support a picture of ions interacting with individual ionic and polar amino acid groups rather than with an averaged protein surface. The results thus show how subtle the so-called Hofmeister and electroselectivity effects are in salt solution of proteins, making all simplified interaction models questionable.

Amino Acids↗

Aqueous ionic and complementary zwitterionic soluble surfactants: molecular dynamics simulations and sum frequency generation spectroscopy of the surfaces.

An aqueous ionic surfactant, 1-dodecyl-4-(dimethylamino)pyridinium (DMP) bromide, and the corresponding zwitterion 2-[4-(dimethylamino)pyridinio]dodecanoate (DPN) were explored by means of molecular dynamics (MD) simulations and, for the ionic system, by infrared-visible sum frequency generation (IR-vis SFG). The molecular structure of the interfacial layer was investigated for the ionic and zwitterionic systems as a function of surfactant concentration, both in water and in salt (KF or KBr) solutions, by MD simulations in a slab geometry. The buildup of the surface monolayer and a sublayer was monitored, and density and orientational profiles of the surfactants were evaluated. The difference between the ionic and zwitterionic systems and the effect of the added salt were analyzed at the molecular level. The results of MD simulations were compared to those of nonlinear optical spectroscopy measurements. IR-vis SFG was employed to study the DMP ionic surfactant in water and upon addition of simple salts. The influence of added salts on the different molecular moieties at the interface was quantified in detail experimentally.

Ions↗

Brine rejection from freezing salt solutions: a molecular dynamics study.

The atmospherically and technologically very important process of brine rejection from freezing salt solutions is investigated with atomic resolution using molecular dynamics simulations. The present calculations allow us to follow the motion of each water molecule and salt ion and to propose a microscopic mechanism of brine rejection, in which a fluctuation (reduction) of the ion density in the vicinity of the ice front is followed by the growth of a new ice layer. The presence of salt slows down the freezing process, which leads to the formation of an almost neat ice next to a disordered brine layer.

Biophysics↗

Interior and interfacial aqueous solvation of benzene dicarboxylate dianions and their methylated analogues: A combined molecular dynamics and photoelectron spectroscopy study.

Aqueous solvation of benzene dicarboxylate dianions (BCD(2-)) was studied by means of photoelectron spectroscopy and molecular dynamics simulations. Photoelectron spectra of hydrated o- and p-BCD(2-) with up to 25 water molecules were obtained. An even-odd effect was observed for the p-BCD(2-) system as a result of the alternate solvation of the two negative charges. However, the high polarizability of the benzene ring makes the two carboxylate groups interact with each other in p-BCD(2-), suppressing the strength of this even-odd effect compared with the linear dicarboxylate dianions linked by an aliphatic chain. No even-odd effect was observed for the o-BCD(2-) system, because each solvent molecule can interact with the two carboxylate groups at the same time due to their proximity. For large solvated clusters, the spectral features of the solute decreased while the solvent features became dominant, suggesting that both o- and p-BCD(2-) are situated in the center of the solvated clusters. Molecular dynamics simulations with both nonpolarizable and polarizable force fields confirmed that all three isomers (o-, m-, and p-BCD(2-)) solvate in the aqueous bulk. However, upon methylation the hydrophobic forces overwhelm electrostatic interactions and, as a result, the calculations predict that the tetramethyl-o-BCD(2-) is located at the water surface with the carboxylate groups anchored in the liquid and the methylated benzene ring tilted away from the aqueous phase.

Anions↗