Matjaž Bončina

Solubility of lysozyme in polyethylene glycol-electrolyte mixtures: the depletion interaction and ion-specific effects.

The solubility of aqueous solutions of lysozyme in the presence of polyethylene glycol and various alkaline salts was studied experimentally. The protein-electrolyte mixture was titrated with polyethylene glycol, and when precipitation of the protein occurred, a strong increase of the absorbance at 340 nm was observed. The solubility data were obtained as a function of experimental variables such as protein and electrolyte concentrations, electrolyte type, degree of polymerization of polyethylene glycol, and pH of the solution; the last defines the net charge of the lysozyme. The results indicate that the solubility of lysozyme decreases with the addition of polyethylene glycol; the solubility is lower for a polyethylene glycol with a higher degree of polymerization. Further, the logarithm of the protein solubility is a linear function of the polyethylene glycol concentration. The process is reversible and the protein remains in its native form. An increase of the electrolyte (NaCl) concentration decreases the solubility of lysozyme in the presence and absence of polyethylene glycol. The effect can be explained by the screening of the charged amino residues of the protein. The solubility experiments were performed at two different pH values (pH = 4.0 and 6.0), where the lysozyme net charge was +11 and +8, respectively. Ion-specific effects were systematically investigated. Anions such as Br(-), Cl(-), F(-), and H(2)PO(4)(-) (all in combination with Na(+)), when acting as counterions to a protein with positive net charge, exhibit a strong effect on the lysozyme solubility. The differences in protein solubility for chloride solutions with different cations Cs(+), K(+), and Na(+) (coions) were much smaller. The results at pH = 4.0 show that anions decrease the lysozyme solubility in the order F(-) < H(2)PO(4)(-) < Cl(-) < Br(-) (the inverse Hofmeister series), whereas cations follow the direct Hofmeister series (Cs(+) < K(+) < Na(+)) in this situation.

Thermodynamic fingerprints of ligand binding to human telomeric G-quadruplexes.

Thermodynamic studies of ligand binding to human telomere (ht) DNA quadruplexes, as a rule, neglect the involvement of various ht-DNA conformations in the binding process. Therefore, the thermodynamic driving forces and the mechanisms of ht-DNA G-quadruplex-ligand recognition remain poorly understood. In this work we characterize thermodynamically and structurally binding of netropsin (Net), dibenzotetraaza[14]annulene derivatives (DP77, DP78), cationic porphyrin (TMPyP4) and two bisquinolinium ligands (Phen-DC3, 360A-Br) to the ht-DNA fragment (Tel22) AGGG(TTAGGG)3 using isothermal titration calorimetry, CD and fluorescence spectroscopy, gel electrophoresis and molecular modeling. By global thermodynamic analysis of experimental data we show that the driving forces characterized by contributions of specific interactions, changes in solvation and conformation differ significantly for binding of ligands with low quadruplex selectivity over duplexes (Net, DP77, DP78, TMPyP4; KTel22 ≈ KdsDNA). These contributions are in accordance with the observed structural features (changes) and suggest that upon binding Net, DP77, DP78 and TMPyP4 select hybrid-1 and/or hybrid-2 conformation while Phen-DC3 and 360A-Br induce the transition of hybrid-1 and hybrid-2 to the structure with characteristics of antiparallel or hybrid-3 type conformation.

Thermodynamics of the lysozyme--salt interaction from calorimetric titrations.

It is well-known that the addition of salts influences the properties of proteins in solution. The essential nature of this phenomenon is far from being fully understood, partly due to the absence of the relevant thermodynamic information. To help fill this gap, in this work isothermal titration calorimetry (ITC) was employed to study the ion-lysozyme association in aqueous buffer solutions at pH = 4.0. ITC curves measured for NaCl, NaBr, NaI, NaNO3, NaSCN, KCl, CaCl2, and BaCl2 salts at three different temperatures were described by a model assuming two sets of independent binding sites on the lysozyme. The resulting thermodynamic parameters of binding of anions (counterions) to the first class of sites (N approximately 7) indicate that the binding constant (K approximately 102 M-1) increases in the order Cl- < Br- < I- < NO3- < SCN-. The anion-lysozyme association is entropy driven, accompanied by a small favorable enthalpy contribution and a positive change in heat capacity. It seems that the entropy and heat capacity increase is due to the water released upon binding, while the net exothermic effect originates from the anion-NH3+ pair formation. Moreover, the results reveal that the nature of the cation has little effect on the thermodynamics of the anion-lysozyme association under the given experimental conditions. Taken together, it seems that the observed thermodynamics of association is a result of a combination of both electrostatic and short-range interactions. The anion ordering reflects the strength of water mediated interactions between anions and lysozyme.

Isothermal titration calorimetry and molecular dynamics study of ion-selectivity in mixtures of hydrophobic polyelectrolytes with sodium halides in water

Aliphatic x,y-ionenes are polyelectrolytes in which x and y denote the numbers of methylene groups separating quaternary ammonium ions. They represent useful model substances for studying hydrophobic and charge effects in aqueous solutions. We used isothermal titration calorimetry to measure the enthalpies of mixing, ΔH(mix), of 3,3- and 6,6-ionene fluorides and bromides with low molecular weight salts (NaF, NaCl, NaBr, and NaI) at 298 K in water. The signs and magnitudes of the measured enthalpies depend on the hydrophobicity of the ionene and on the nature of the added salt. For example, addition of sodium fluoride to solutions of 3,3- and 6,6-ionene fluorides produced endothermic effects, while addition of sodium bromide to 3,3-ionene bromide resulted in a strong exothermic effect. Interestingly, mixing of 6,6-ionene bromide and NaBr solutions in water gave a small exothermic heat effect. Polyelectrolyte theories, based on continuum-solvent models, predict enthalpies of mixing to be positive (endothermic) for all the solutions examined in this work. The ion-specific effect is more strongly expressed in ionene solutions with higher charge density (3,3-ionene). The most important result of this work is the finding that the enthalpy of mixing of 3,3- (and of 6,6-ionene) fluorides with sodium halides can be expressed as a linear function of the enthalpy of hydration of the halide counterions. The experimental results were complemented with an explicit water molecular dynamics simulation of solutions of oligoions modelling 3,3- and 6,6-ionenes. The computer simulation results for various nitrogen-counterion pair distribution functions were in most cases consistent with the enthalpy measurements.

Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations

Recently various pathways of human telomere (ht) DNA folding into G-quadruplexes and of ligand binding to these structures have been proposed. However, the key issue as to the nature of forces driving the folding and recognition processes remains unanswered. In this study, structural changes of 22-mer ht-DNA fragment (Tel22), induced by binding of ions (K(+), Na(+)) and specific bisquinolinium ligands, were monitored by calorimetric and spectroscopic methods and by gel electrophoresis. Using the global model analysis of a wide variety of experimental data, we were able to characterize the thermodynamic forces that govern the formation of stable Tel22 G-quadruplexes, folding intermediates, and ligand-quadruplex complexes, and then predict Tel22 behavior in aqueous solutions as a function of temperature, salt concentration, and ligand concentration. On the basis of the above, we believe that our work sets the framework for better understanding the heterogeneity of ht-DNA folding and binding pathways, and its structural polymorphism.

Thermodynamic analysis of the interaction of partially hydrophobic cationic polyelectrolytes with sodium halide salts in water

Isothermal titration calorimetry was used to determine the temperature and concentration dependence of the enthalpy of mixing of 3,3- and 6,6-ionene fluorides, bromides, and iodides with low molecular weight salts (NaF, NaCl, NaBr, and NaI) in water. The magnitudes of the enthalpies, measured in the temperature range from 273 to 318 K, depended on the number of methylene groups on the ionene polyion (hydrophobicity), and on the anion of the added salt (ion-specificity). All enthalpies of mixing of 3,3- and 6,6-ionene fluorides with low molecular weight salts (NaCl, NaBr, and NaI) were negative, which is in contrast to the predictions of standard theories of polyelectrolyte solutions. This fact was interpreted in the light of the ion–water short-range interactions that are not accounted for in those theories. In contrast, the enthalpies of mixing of 3,3- and 6,6-ionene bromides and iodides with NaF were positive, being in accord with theory. Using the calorimetric data, we performed a model thermodynamic analysis of the polyelectrolyte–salt mixing process to obtain changes in the apparent standard Gibbs free energy, enthalpy, entropy, and heat capacity relative to the pure ionene fluorides in water. The results prove that halide ions replace fluoride counterions with a strength increasing in the order chloride < bromide < iodide. The process is enthalpy governed, accompanied by a positive change in the heat capacity.

Salt-specific effects in lysozyme solutions

The effects of additions of low-molecular-mass salts on the properties of aqueous lysozyme solutions are examined by using the cloud-point temperature,

Influence of counterions on the conformation of conjugated polyelectrolytes: the case of poly(thiophen-3-ylacetic acid)

T_{cloud}

Energetic Basis of Human Telomeric DNA Folding into G-Quadruplex Structures

, measurements. Mixtures of protein, buffer, and simple salt in water are studied at pH=6.8 (phosphate buffer) and pH=4.6 (acetate buffer). We show that an addition of buffer in the amount above

Unraveling the Thermodynamics of the Folding and Interconversion of Human Telomere G-Quadruplexes

I_{buffer} = 0.6