The influence of salt on processes involving aqueous proteins - Hofmeister effects

Using computer simulations we investigate the effect of specific salt ions on protein association (precipitation), denaturation, and on enzymatic activity (e.g., of HIV protease and horseradish peroxidase). As an illustrative example, our coarse-grained model of lysozyme correctly predict the reversal of Hofmeister series at the isoelctric point. Namely, for low pH, iodide is more efficient than chloride for assiciating lysozymes in water, while it is the other way around at high pH.

Binding of ions to proteins, polypeptides, and amino acids

By means of molecular dynamics and ab initio calculations we are ordering biologically relevant cations and anions in terms of their affinity to the protein surface. Simple alkali cations exhibit a propensity for the carboxylate of aspartate and glutamate and for the amide oxygen of the backbone. In both cases binding is stronger for small cations (sodium) than larger ones (potassium). For anions the situation is more complex and the lessons we are learning from the halide series are as follows. Smaller halides (flouride and chloride) interact more strongly with positively charged side chains of arginine, lysine, and protonated histidine that heavier halides (bromide and iodide).

The latter, however, exhibit an affinity for the non-polar regions of protein surface, similarly as we observed at the water/air interface. The ion-specific Hofmeister effects thus seem to be due to several physical phenomena - ion-pairing, segregation at non-polar surfaces, and others. Among the others, we are investigating the effect of ion aggregation in solution which "steals" them from the surface. This is particularly pertinent to complex molecular ions and multivalent ions, a prime example being guanidinium sulfate.

Phospholipid membranes in silico

We investigate affinities of biologically relevant ions for lipid membranes in aqueous salt solutions by means of molecular dynamics simulations, in direct connection with fluorescence spectroscopy measurements. The simulations reveal, e.g., that sodium is attracted to the headgroup region with its concentration being maximal in the vicinity of the phosphate groups. Potassium and cesium, however, do not preferentially adsorb to the membrane. Similarly, halide anions do not exhibit a strong affinity for the lipid headgroups but merely compensate the positive charge of the sodium counter-cations. Nevertheless, larger halides such as bromide and iodide penetrate deeper into the headgroup region toward the boundary with the hydrophobic alkyl chain. Addition of alkali halide salts modifies physical properties of the bilayer including the electronic density profiles, the electrostatic potential, and the area per lipid headgroup.

We also perform molecular dynamics simulations of a multicomponent asymmetric bilayer in mixed aqueous solutions of sodium and potassium chloride. Due to the geometry of the system there are two aqueous solution regions: one mimicking intracellular region and one extracellular. Ion specific effects are observed at the membrane/aqueous solution interface. Namely, at equal concentrations of sodium and potassium, sodium ions are more strongly adsorbed to carbonyl groups of the lipid head groups and a significant concentration excess of potassium is needed for this ion to overwhelm in abundance sodium at the membrane. These simulations represent a step toward modeling of realistic biological membranes at physiological conditions.

Additionally, we simulate the effects of oxidation of the acyl chains of phospholipids on local and global membrane properties. Oxidative attacks are known to result, among others, in loss of the plasma membrane phospholipid asymmetry, which is a key early event in programmed cell death (apoptosis). Simulation results show that oxidatively modified phosphatidylcholines introduce major changes in biophysical properties of lipid bilayers including reorientation of acyl chains and creation of pores. An important consequence of these changes is also fast inter-bilayer diffusion ('flip-flop') of membrane phospholipids and rapid loss of lipid asymmetry,

Direct and indirect radiation damage to DNA in aqueous solutions

We are approaching the basic physics and chemistry of radiation-induced damage in water. The indirect effects are due to water ionization which we follow by ab initio molecular dynamics. In particular we follow the ultrafast dynamics of both the cationic hole and excess electron created in water upon photoionization. In the realm of direct radiation damage we are attempting to accurately establish vertical ionization potentials of aqueous components of DNA and proteins by means of ab initio calculations employing a non-equilibrium polarizable continuum model.