Jan Heyda

Molecular Mechanisms of Ion-Specific Effects on Proteins

The specific binding sites of Hofmeister ions with an uncharged 600-residue elastin-like polypeptide, (VPGVG)(120), were elucidated using a combination of NMR and thermodynamic measurements along with molecular dynamics simulations. It was found that the large soft anions such as SCN(-) and I(-) interact with the polypeptide backbone via a hybrid binding site that consists of the amide nitrogen and the adjacent α-carbon. The hydrocarbon groups at these sites bear a slight positive charge, which enhances anion binding without disrupting specific hydrogen bonds to water molecules. The hydrophobic side chains do not contribute significantly to anion binding or the corresponding salting-in behavior of the biopolymer. Cl(-) binds far more weakly to the amide nitrogen/α-carbon binding site, while SO(4)(2-) is repelled from both the backbone and hydrophobic side chains of the polypeptide. The Na(+) counterions are also repelled from the polypeptide. The identification of these molecular-level binding sites provides new insights into the mechanism of peptide-anion interactions.

The Molecular Origin of Like-Charge Arginine−Arginine Pairing in Water

Molecular dynamics simulations show significant like-charge pairing of guanidinium side chains in aqueous poly-arginine, while this effect is absent in aqueous poly-lysine containing ammonium-terminated side chains. This behavior of the guanidinium group is revealed also by protein database searches, having important biochemical implications. Combination of molecular dynamics simulations with explicit solvent and ab initio calculations employing a polarizable continuum model of water allows one to rationalize the formation of contact ion pairs between guanidinium cations in terms of individual interactions at the molecular level.

Reversal of the hofmeister series: specific ion effects on peptides.

Ion-specific effects on salting-in and salting-out of proteins, protein denaturation, as well as enzymatic activity are typically rationalized in terms of the Hofmeister series. Here, we demonstrate by means of NMR spectroscopy and molecular dynamics simulations that the traditional explanation of the Hofmeister ordering of ions in terms of their bulk hydration properties is inadequate. Using triglycine as a model system, we show that the Hofmeister series for anions changes from a direct to a reversed series upon uncapping the N-terminus. Weakly hydrated anions, such as iodide and thiocyanate, interact with the peptide bond, while strongly hydrated anions like sulfate are repelled from it. In contrast, reversed order in interactions of anions is observed at the positively charged, uncapped N-terminus, and by analogy, this should also be the case at side chains of positively charged amino acids. These results demonstrate that the specific chemical and physical properties of peptides and proteins play a fundamental role in ion-specific effects. The present study thus provides a molecular rationalization of Hofmeister ordering for the anions. It also provides a route for tuning these interactions by titration or mutation of basic amino acid residues on the protein surface.

Ion specificity at the peptide bond: molecular dynamics simulations of N-methylacetamide in aqueous salt solutions.

Affinities of alkali cations and halide anions for the peptide group were quantified using molecular dynamics simulations of aqueous solutions of N-methylacetamide using both nonpolarizable and polarizable force fields. Potassium and, more strongly, sodium exhibit an affinity for the carbonyl oxygen of the amide group, while none of the halide anions shows any appreciable attraction for the amide hydrogen. Heavier halides, however, interact with the hydrophobic methyl groups of N-methylacetamide. Using the present results for a model of the peptide bond we predict that the destabilizing effect of weakly hydrated Hofmeister ions, such as bromide or iodide, is not due to direct interactions with the backbone but rather due to attraction to hydrophobic regions of the protein.

Sensing Solvents with Ultrasensitive Porous Poly(ionic liquid) Actuators

We introduced a new concept for fabricating solvent stimulus polymer actuators with unprecedented sensitivity and accuracy. This was accomplished by integrating porous architectures and electrostatic complexation gradients in a poly(ionic liquid) membrane that bears ionic liquid species for solvent sorption. In contact with 1.5 mol% of acetone molecules in water, the actuator membrane (1 mm x 20 mm x 30 um) bent into a closed loop. While the interaction between solvents and the polymer drives the actuation, the continuous gradient in complexation degree combined with the porous architecture optimizes the actuation, giving it a high sensitivity and even the ability to discriminate butanol solvent isomers. The membrane is also capable of cooperative actuation. The design concept is easy to implement and applicable to other polyelectrolyte systems, which substantially underpins their potentials in smart and sensitive signaling microrobotics/devices.

Attractive interactions between side chains of histidine-histidine and histidine-arginine-based cationic dipeptides in water.

Molecular dynamics simulations of histidine-based dipeptides in water show that a protonated histidine side chain group has a propensity for forming like-charged contact pairs with another protonated histidine or with arginine. This effect is of similar strength to that in previously observed arginine-arginine pairing. Even stronger contact pairs are formed in singly protonated or deprotonated dihistidine, where stacking of aromatic rings is not weakened by Coulomb repulsion between the side chains. Similar pairing behavior is also observed in a mixed solution of imidazole and imidazolium chloride.

Specificity of Ion−Protein Interactions: Complementary and Competitive Effects of Tetrapropylammonium, Guanidinium, Sulfate, and Chloride Ions

The interactions of ions with a model peptide (a single melittin alpha-helix) in solutions of tetrapropylammonium sulfate or guanidinium chloride were examined by molecular dynamics simulations. The tetrapropylammonium cation shares the geometrical property of essentially flat faces with the previously examined guanidinium cation, and it was found that that this geometry leads to a strong preference for tetrapropylammonium to interact in a similar stacking-type fashion with flat nonpolar groups such as the indole side chain of tryptophan. In contrast to guanidinium, however, tetrapropylammonium does not exhibit strong ion pairing or clustering with sulfate counterions in the solution. Sulfate was found to interact almost exclusively and strongly with the cationic groups of the peptide, such that, already in a 0.1 m solution of tetrapropylammonium sulfate, the 6+ charge of the peptide is effectively locally neutralized. In combination with previous simulations, neutron scattering studies, and experiments on the conformational stability of model peptides, the present results suggest that the Hofmeister series can be explained in higher detail by splitting ions according to the effect they have on hydrogen bonding, salt bridges, and hydrophobic interactions in the protein and how these effects are altered by the counterion.

Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions

Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting out/salting in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood. This situation could have been summarized as follows: Many chemists used the Hofmeister series as a mantra to put a label on ion-specific behavior in various environments, rather than to reach a molecular level understanding and, consequently, an ability to predict a particular effect of a given salt ion on proteins in solutions. In this Feature Article we show that the cationic and anionic Hofmeister series can now be rationalized primarily in terms of specific interactions of salt ions with the backbone and charged side chain groups at the protein surface in solution. At the same time, we demonstrate the limitations of separating Hofmeister effects into independent cationic and anionic contributions due to the electroneutrality condition, as well as specific ion pairing, leading to interactions of ions of opposite polarity. Finally, we outline the route beyond Hofmeister chemistry in the direction of understanding specific roles of ions in various biological functionalities, where generic Hofmeister-type interactions can be complemented or even overruled by particular steric arrangements in various ion binding sites.

Urea and guanidinium induced denaturation of a Trp-cage miniprotein.

Using a combination of experimental techniques (circular dichroism, differential scanning calorimetry, and NMR) and molecular dynamics simulations, we performed an extensive study of denaturation of the Trp-cage miniprotein by urea and guanidinium. The experiments, despite their different sensitivities to various aspects of the denaturation process, consistently point to simple, two-state unfolding process. Microsecond molecular dynamics simulations with a femtosecond time resolution allow us to unravel the detailed molecular mechanism of Trp-cage unfolding. The process starts with a destabilizing proline shift in the hydrophobic core of the miniprotein, followed by a gradual destruction of the hydrophobic loop and the α-helix. Despite differences in interactions of urea vs guanidinium with various peptide moieties, the overall destabilizing action of these two denaturants on Trp-cage is very similar.

Thermodynamic description of Hofmeister effects on the LCST of thermosensitive polymers.

Cosolvent effects on protein or polymer collapse transitions are typically discussed in terms of a two-state free energy change that is strictly linear in cosolute concentration. Here we investigate in detail the nonlinear thermodynamic changes of the collapse transition occurring at the lower critical solution temperature (LCST) of the role-model polymer poly(N-isopropylacrylamide) [PNIPAM] induced by Hofmeister salts. First, we establish an equation, based on the second-order expansion of the two-state free energy in concentration and temperature space, which excellently fits the experimental LCST curves and enables us to directly extract the corresponding thermodynamic parameters. Linear free energy changes, grounded on generic excluded-volume mechanisms, are indeed found for strongly hydrated kosmotropes. In contrast, for weakly hydrated chaotropes, we find significant nonlinear changes related to higher order thermodynamic derivatives of the preferential interaction parameter between salts and polymer. The observed non-monotonic behavior of the LCST can then be understood from a not yet recognized sign change of the preferential interaction parameter with salt concentration. Finally, we find that solute partitioning models can possibly predict the linear free energy changes for the kosmotropes, but fail for chaotropes. Our findings cast strong doubt on their general applicability to protein unfolding transitions induced by chaotropes.