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.

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

The addition of simple salt to a solution of conjugated polyelectrolyte can lead to substantial changes in its optical properties caused by the conformational change of the polymer chain. The effect of the addition of alkali metal and tetraalkylammonium chlorides to solutions of lithium salt of poly(thiophen-3-ylacetic acid) is investigated by NMR. The fractions of free alkali metal counterions are in agreement with predictions of the cylindrical Poisson-Boltzmann cell model. On the other hand, the fractions of free tetraalkylammonium counterions deviate from the prediction of this model and diminish with increasing size of these counterions. This trend is consistent with observed ultraviolet-visible absorption spectra and measured self-diffusion coefficients of the polyion in mixtures with tetraalkylammonium salts. A transition to more constricted conformation of the polyion chain becomes more pronounced with the lengthening of alkyl groups in the added tetraalkylammonium cation. Taking into account the obtained fractions of free counterions, existing thermodynamic data are reanalysed in order to determine thermodynamic parameters for binding of different counterions to the polyion. This analysis shows that standard enthalpies of binding of alkali metal counterions are distinctively different, which is most probably related to differences in hydration shells of counterions. On the other hand, such an analysis fails in the case of tetraalkylammonium chlorides where obviously more complex changes take place.

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

Why human telomere DNA fragments fold into different G-quadruplex structures with parallel, hybrid, and antiparallel strand orientations depending on the temperature and concentration of co-solutes remains poorly understood. Similarly, the formation of intermediate structures along the folding or interconversion pathways is not well understood. Herein, we address these questions by introducing a conceptual framework, based on the global thermodynamic analysis of DSC and CD spectroscopy data, which led to a detailed description of the topological phase space (phase diagram) of the stability of the human telomere fragment 5'-AGGG(TTAGGG)3 -3' (Tel22). This framework clarifies the driving forces of quadruplex folding and interconversion processes over a wide range of temperatures and ion (K(+) , Na(+) ) and polyethylene glycol (PEG) concentrations and demonstrates their linkage to the human telomere DNA structural features.

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.

Energetic basis of human telomeric DNA folding into G-quadruplex structures.

Recent theoretical studies performed on the folding/unfolding mechanism of the model telomeric human DNA, 5'-AGGGTTAGGGTTAGGGTTAGGG-3' (Tel22), have indicated that in the presence of K(+) ions Tel22 folds into two hybrid G-quadruplex structures characterized by one double and two reversal TTA loops arranged in a different way. They predicted a new unfolding pathway from the initial mixture of hybrid G-quadruplexes via the corresponding intermediate triplex structures into the final, fully unfolded state. Significantly, no experimental evidence supporting the suggested pathway has been reported. In the current work, we performed a comprehensive global thermodynamic analysis of calorimetric (DSC, ITC) and spectroscopic (CD) data obtained on monitoring the folding/unfolding of Tel22 induced by changes of temperature and K(+) concentration. We show that unfolding of Tel22 may be described as a monomolecular equilibrium three-state process that involves thermodynamically distinguishable folded (F), intermediate (I), and unfolded (U) state. Considering that calorimetric methods cannot distinguish between energetically similar G-quadruplex or triplex conformations predicted by the theoretical model one can conclude that our results represent the first experimental support of the suggested unfolding/folding mechanism of Tel22. This conclusion is confirmed by the fact that the estimated number of K(+) ions released upon each unfolding step in our thermodynamic model agrees well with the corresponding values predicted by the theoretical model and that the observed changes in enthalpy, entropy, and heat capacity accompanying the F → I and I → U transitions can be reasonably explained only if the intermediate state I is considered to be a triplex structural conformation.

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.

Specific counter-ion and co-ion effects revealed in mixing of aqueous solutions of 3,3 and 6,6-ionenes with solutions of low molecular weight salts.

Enthalpies of mixing of aliphatic 3,3 and 6,6-ionene fluorides with low molecular weight salts (sodium formate, acetate, nitrate, chlorate(v), and thiocyanate), all dissolved in water, were determined. In addition, to complement our previous study (Luksicet al., Phys. Chem. Chem. Phys., 2012, 14, 2024), new measurements were performed where aqueous solutions of 3,3 and 6,6-ionene bromides were mixed with solutions of sodium fluoride, chloride, bromide, and iodide. Electrostatic theory, based on Manning's limiting law or the Poisson-Boltzmann equation, predicted the enthalpy of mixing to be endothermic in all the cases, while experiments showed that this is not always true. When an aqueous solution of 3,3-ionene fluoride was mixed with a solution of sodium fluoride (or formate and acetate) in water, the effect was indeed endothermic. For all other salts, i.e. sodium chlorate, nitrate, and thiocyanate, heat was released upon mixing. The situation was similar for 6,6-ionene fluoride solutions with an exception of mixing with sodium chlorate, where the effect was endothermic. The enthalpy of mixing was strongly correlated with the enthalpy of hydration of the counterion of the low molecular weight salt. A lyotropic series, similar to that of Hofmeister, was obtained. To examine also the effect of co-ions, ionene bromides were titrated with tetramethyl-, tetraethyl-, or tetrapropylammonium bromides. The enthalpy was exothermic for all mixtures while, somewhat unexpectedly, the co-ion specific effect was quite strong.

Global thermodynamic analysis of conductivity data.

Conductivity can serve as a tool to study ion properties in different solvents. In the current study, principles of the global modelling of the conductivity data measured at different concentrations and temperatures are demonstrated. Global model was developed on the basis of two modern conductivity theories; the low concentration chemical model and the Quint-Viallard model. It was tested on three different systems; NaCl in water, NaCl in water-1,4 dioxane mixture and MgSO4 in water. It turned out, that such approach successfully describes all the measured experimental data simultaneously. The applied global analysis of the experimental data allows determination of the thermodynamic profile of ion pairing process and the transport properties of ions at the same time.

Aggregation Time Machine: A Platform for the Prediction and Optimization of Long-Term Antibody Stability Using Short-Term Kinetic Analysis.

Monoclonal antibodies are the fastest growing class of therapeutics. However, aggregation limits their shelf life and can lead to adverse immune responses. Assessment and optimization of the long-term antibody stability are therefore key challenges in the biologic drug development. Here, we present a platform based on the analysis of temperature-dependent aggregation data that can dramatically shorten the assessment of the long-term aggregation stability and thus accelerate the optimization of antibody formulations. For a set of antibodies used in the therapeutic areas from oncology to rheumatology and osteoporosis, we obtain an accurate prediction of aggregate fractions for up to three years using the data obtained on a much shorter time scale. Significantly, the strategy combining kinetic and thermodynamic analysis not only contributes to a better understanding of the molecular mechanisms of antibody aggregation but has already proven to be very effective in the development and production of biological therapeutics.

Long-term stability predictions of therapeutic monoclonal antibodies in solution using Arrhenius-based kinetics.

Long-term stability of monoclonal antibodies to be used as biologics is a key aspect in their development. Therefore, its possible early prediction from accelerated stability studies is of major interest, despite currently being regarded as not sufficiently robust. In this work, using a combination of accelerated stability studies (up to 6 months) and first order degradation kinetic model, we are able to predict the long-term stability (up to 3 years) of multiple monoclonal antibody formulations. More specifically, we can robustly predict the long-term stability behaviour of a protein at the intended storage condition (5 °C), based on up to six months of data obtained for multiple quality attributes from different temperatures, usually from intended (5 °C), accelerated (25 °C) and stress conditions (40 °C). We have performed stability studies and evaluated the stability data of several mAbs including IgG1, IgG2, and fusion proteins, and validated our model by overlaying the 95% prediction interval and experimental stability data from up to 36 months. We demonstrated improved robustness, speed and accuracy of kinetic long-term stability prediction as compared to classical linear extrapolation used today, which justifies long-term stability prediction and shelf-life extrapolation for some biologics such as monoclonal antibodies. This work aims to contribute towards further development and refinement of the regulatory landscape that could steer toward allowing extrapolation for biologics during the developmental phase, clinical phase, and also in marketing authorisation applications, as already established today for small molecules.

G-Quadruplex Stability from DSC Measurements.

Guanine-rich DNA oligonucleotides can adopt G-quadruplex (G4) structures in the presence of specific cations. Folding and unfolding of G4 can be characterized thermodynamically, providing the information on the stability of various G4 conformations. We show how the relevant thermodynamic and sometimes kinetic parameters are obtained by employing differential scanning calorimetry (DSC) and global fitting of an appropriate model to the DSC data. We demonstrate that best-fit values of the thermodynamic parameters can be interpreted in terms of the driving forces accompanying the G4 folding/interconversion and how they are translated into the phase diagrams, which provide an elegant description of the G4 phase space over a wide range of solution conditions.

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.

Electrical conductances of dilute aqueous solutions of sodium penicillin G, potassium penicillin G, and potassium penicillin V in the 278.15-313.15 K temperature range.

Systematic determinations of electrical conductivities of sodium penicillin G, potassium penicillin G, and potassium penicillin V in the 278.15-313.15 K temperature range are reported. These conductivities are examined by applying the Quint-Viallard conductivity equations and the Debye-Hückel equations for activity coefficients. Determined dissociation constants and the limiting conductances of penicillin anions are based on the assumption that in dilute aqueous solutions, penicillin salts behave as acidic salts of dibasic acids, which are the final products of degradation reactions in acidic media.

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.