Molecular insight into carboxylic acid-alkali metal cations interactions: reversed affinities and ion-pair formation revealed by non-linear optics and simulations.

Specific interactions between the carboxylic acid moiety and the monovalent salts CsCl, NaCl, and LiCl, have been investigated in Langmuir monolayers using vibrational sum frequency spectroscopy (VSFS) and complemented with coarse grained and all-atom molecular dynamics simulations. By exploiting VSFS's intrinsic surface specificity, an emphasis was made on targeting headgroup vibrations of both its charged and uncharged forms as well as water molecules in the interfacial layer. The degree of deprotonation of the monolayer as a function of cation concentration and pH was experimentally determined and theoretically rationalized. Starting from 100 mM, the surface charge was overestimated by the Gouy-Chapman model and varied depending on the identity of the cation, highlighting the appearance of ion specific effects. Agreement could be found using a modified Poisson-Boltzmann model that takes into account steric effects, with a fitted effective ion-size compatible with the hydrated ion diameters. The relative affinity of the cations to the carboxylic acid moiety was pH dependent: at pH 4.5 they arranged in the order Cs+ > Na+ > Li+, but fully reversed (Li+ > Na+ > Cs+) at pH 9. Simulations yielded microscopic insight into the origin of this behavior, with the cations showing contrasting interaction preferences for either the uncharged carboxylic acid or the charged carboxylate. Sum frequency spectra also provided evidence that all cations remained hydrated when interacting with the charged headgroup, forming solvent-separated or solvent-shared ion pairs. However, for the specific case of 1 M Li+ at pH 9, contact ion pairs were formed. Finally, the remarkable effect of trace metal multivalent cations in the interpretation of experiments is briefly discussed. The results provide exciting new insights into the complex interactions of alkali metal cations with the biophysically relevant carboxylic acid moiety.

Hydrodynamic trapping measures the interaction between membrane-associated molecules.

How membrane proteins distribute and behave on the surface of cells depends on the molecules' chemical potential. However, measuring this potential, and how it varies with protein-to-protein distance, has been challenging. Here, we present a method we call hydrodynamic trapping that can achieve this. Our method uses the focused liquid flow from a micropipette to locally accumulate molecules protruding above a lipid membrane. The chemical potential, as well as information about the dimensions of the studied molecule, are obtained by relating the degree of accumulation to the strength of the trap. We have used this method to study four representative proteins, with different height-to-width ratios and molecular properties; from globular streptavidin, to the rod-like immune cell proteins CD2, CD4 and CD45. The data we obtain illustrates how protein shape, glycosylation and flexibility influence the behaviour of membrane proteins, as well as underlining the general applicability of the method.

Binding of Divalent Cations to Insulin: Capillary Electrophoresis and Molecular Simulations.

In the present study, we characterize the binding of divalent cations to insulin in aqueous salt solutions by means of capillary electrophoresis and molecular dynamics simulations. The results show a strong pH dependence. At low pH, at which all the carboxylate groups are protonated and the protein has an overall positive charge, all the cations exhibit only weak and rather unspecific interactions with insulin. In contrast, at close to neutral pH, when all the carboxylate groups are deprotonated and negatively charged, the charge-neutralizing effect of magnesium, calcium, and zinc, in particular, on the electrophoretic mobility of insulin is significant. This is also reflected in the results of molecular dynamics simulations showing accumulation of cations at the protein surface, which becomes smaller in magnitude upon effective inclusion of electronic polarization via charge rescaling.

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.

Guanidinium can both Cause and Prevent the Hydrophobic Collapse of Biomacromolecules.

A combination of Fourier transform infrared and phase transition measurements as well as molecular computer simulations, and thermodynamic modeling were performed to probe the mechanisms by which guanidinium (Gnd+) salts influence the stability of the collapsed versus uncollapsed state of an elastin-like polypeptide (ELP), an uncharged thermoresponsive polymer. We found that the cation's action was highly dependent upon the counteranion with which it was paired. Specifically, Gnd+ was depleted from the ELP/water interface and was found to stabilize the collapsed state of the macromolecule when paired with well-hydrated anions such as SO42-. Stabilization in this case occurred via an excluded volume (or depletion) effect, whereby SO42- was strongly partitioned away from the ELP/water interface. Intriguingly, at low salt concentrations, Gnd+ was also found to stabilize the collapsed state of the ELP when paired with SCN-, which is a strong binder for the ELP. In this case, the anion and cation were both found to be enriched in the collapsed state of the polymer. The collapsed state was favored because the Gnd+ cross-linked the polymer chains together. Moreover, the anion helped partition Gnd+ to the polymer surface. At higher salt concentrations (>1.5 M), GndSCN switched to stabilizing the uncollapsed state because a sufficient amount of Gnd+ and SCN- partitioned to the polymer surface to prevent cross-linking from occurring. Finally, in a third case, it was found that salts which interacted in an intermediate fashion with the polymer (e.g., GndCl) favored the uncollapsed conformation at all salt concentrations. These results provide a detailed, molecular-level, mechanistic picture of how Gnd+ influences the stability of polypeptides in three distinct physical regimes by varying the anion. It also helps explain the circumstances under which guanidinium salts can act as powerful and versatile protein denaturants.

Lateral Protein-Protein Interactions at Hydrophobic and Charged Surfaces as a Function of pH and Salt Concentration.

Surface adsorption of Thermomyces lanuginosus lipase (TLL)-a widely used industrial biocatalyst-is studied experimentally and theoretically at different pH and salt concentrations. The maximum achievable surface coverage on a hydrophobic surface occurs around the protein isoelectric point and adsorption is reduced when either increasing or decreasing pH, indicating that electrostatic protein-protein interactions in the adsorbed layer play an important role. Using Metropolis Monte Carlo (MC) simulations, where proteins are coarse grained to the amino acid level, we estimate the protein isoelectric point in the vicinity of charged surfaces as well as the lateral osmotic pressure in the adsorbed monolayer. Good agreement with available experimental data is achieved and we further make predictions of the protein orientation at hydrophobic and charged surfaces. Finally, we present a perturbation theory for predicting shifts in the protein isoelectric point due to close proximity to charged surfaces. Although this approximate model requires only single protein properties (mean charge and its variance), excellent agreement is found with MC simulations.

Hydration of hydroxyl and amino groups examined by molecular dynamics and neutron scattering.

Neutron diffraction with isotopic substitution was performed on aqueous solutions of isopropyl alcohol and isopropylamine. The difference between these two measurements primarily contains information about the different hydration of the alcohol and amino group. This data is used as a test of the accuracy of molecular dynamic simulations of the same systems. Having established the level of accuracy of the modeling, it is employed as an interpretive tool for the experimental data. Even though the alcohol and the amine possess comparable hydrogen bonding capabilities, consisting respectively of either two hydrogen bond acceptors and one donor, or two hydrogen bond donors and one acceptor, we find significant differences in the hydration of the hydroxyl and amino groups.

Specific potassium ion interactions facilitate homocysteine binding to betaine-homocysteine S-methyltransferase.

Betaine-homocysteine S-methyltransferase (BHMT) is a zinc-dependent methyltransferase that uses betaine as the methyl donor for the remethylation of homocysteine to form methionine. This reaction supports S-adenosylmethionine biosynthesis, which is required for hundreds of methylation reactions in humans. Herein we report that BHMT is activated by potassium ions with an apparent K(M) for K⁺ of about 100 µM. The presence of potassium ions lowers the apparent K(M) of the enzyme for homocysteine, but it does not affect the apparent K(M) for betaine or the apparent k(cat) for either substrate. We employed molecular dynamics (MD) simulations to theoretically predict and protein crystallography to experimentally localize the binding site(s) for potassium ion(s). Simulations predicted that K⁺ ion would interact with residues Asp26 and/or Glu159. Our crystal structure of BHMT bound to homocysteine confirms these sites of interaction and reveals further contacts between K⁺ ion and BHMT residues Gly27, Gln72, Gln247, and Gly298. The potassium binding residues in BHMT partially overlap with the previously identified DGG (Asp26-Gly27-Gly28) fingerprint in the Pfam 02574 group of methyltransferases. Subsequent biochemical characterization of several site-specific BHMT mutants confirmed the results obtained by the MD simulations and crystallographic data. Together, the data herein indicate that the role of potassium ions in BHMT is structural and that potassium ion facilitates the specific binding of homocysteine to the active site of the enzyme.

Electrophoretic mobilities of neutral analytes and electroosmotic flow markers in aqueous solutions of Hofmeister salts.

Small neutral organic compounds have traditionally the role of EOF markers in electrophoresis, as they are expected to have zero electrophoretic mobility in external electric fields. The BGE contains, however, ions that have unequal affinities to the neutral molecules, which in turn results in their mobilization. In this study we focused on two EOF markers-thiourea and DMSO, as well as on N-methyl acetamide (NMA) as a model of the peptide bond. By means of CE and all atom molecular dynamics simulations we explored mobilization of these neutral compounds in large set of Hofmeister salts. Employing a statistical mechanics approach, we were able to reproduce by simulations the experimental electrophoretic mobility coefficients. We also established the role of the chemical composition of marker and the BGE on the measured electrophoretic mobility coefficient. For NMA, we interpreted the results in terms of the relative affinities of cations versus anions to the peptide bond.

Release of halide ions from the buried active site of the haloalkane dehalogenase LinB revealed by stopped-flow fluorescence analysis and free energy calculations.

Release of halide ions is an essential step of the catalytic cycle of haloalkane dehalogenases. Here we describe experimentally and computationally the process of release of a halide anion from the buried active site of the haloalkane dehalogenase LinB. Using stopped-flow fluorescence analysis and umbrella sampling free energy calculations, we show that the anion binding is ion-specific and follows the ordering I(-) > Br(-) > Cl(-). We also address the issue of the protonation state of the catalytic His272 residue and its effect on the process of halide release. While deprotonation of His272 increases binding of anions in the access tunnel, we show that the anionic ordering does not change with the switch of the protonation state. We also demonstrate that a sodium cation could relatively easily enter the active site, provided the His272 residue is singly protonated, and replace thus the missing proton. In contrast, Na(+) is strongly repelled from the active site containing the doubly protonated His272 residue. Our study contributes toward understanding of the reaction mechanism of haloalkane dehalogenase enzyme family. Determination of the protonation state of the catalytic histidine throughout the catalytic cycle remains a challenge for future studies.

Effects of End Group Termination on Salting-Out Constants for Triglycine.

Salting out constants for triglycine were calculated for a series of Hofmeister salts using molecular dynamics simulations. Three variants of the peptide were considered with both termini capped, just the N-terminus capped, and without capping. The simulations were supported by NMR and FTIR measurements. The data provide strong evidence that earlier experimental values of salting out constants assigned to the fully capped peptide (as previously assumed) should have been assigned to the half-capped peptide instead. Therefore, these values cannot be used to directly establish Hofmeister ordering of ions at the peptide backbone, since they are strongly influenced by interactions of the ions with the negatively charged C-terminus.