Janusz Stangret

Effects of Urea and Trimethylamine-N-oxide on the Properties of Water and the Secondary Structure of Hen Egg White Lysozyme

The influence of urea and trimethylamine-N-oxide (TMAO) on the structure of water and secondary structure of hen egg white lysozyme (HEWL) has been investigated. The hydration of these osmolytes was studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H(2)O. The difference spectra procedure was applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. The structural-energetic characteristic of these solute-affected water molecules shows that, on average, water affected by TMAO forms stronger H-bonds and is more ordered than pure water. In the case of urea, the H-bonds are very similar to those in pure water. To facilitate the interpretation of the obtained spectral results, calorimetric measurements, DFT calculations, and molecular dynamics (MD) simulations of aqueous osmolyte clusters were performed. All of these results confirmed that the interactions of TMAO with water molecules are much stronger than those of urea with water. Additional ATR FTIR measurements were performed to characterize the influence of the examined osmolytes on the secondary structure of HEW lysozyme. The type of interactions (direct or indirect) was determined, based on the second derivatives of ATR protein spectra record during an increase in the osmolyte concentration. The changes in the amide I band shape caused by urea or TMAO were found to correlate quite well with changes in the water structure around these osmolytes.

Hydration of simple amides. FTIR spectra of HDO and theoretical studies.

The hydration of formamide (F), N-methylformamide (NMF), N,N-dimethylformamide (DMF), acetamide (A), N-methylacetamide (NMA), and N,N-dimethylacetamide (DMA) has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure has been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To facilitate the interpretation of obtained spectral results, DFT calculations of aqueous amide clusters were performed. Molecular dynamics (MD) simulation for the cis and trans forms of NMA was also carried out for the SPC model of water. Infrared spectra reveal that only two to three water molecules from the surrounding of the amides are statistically affected, from among ca. 30 molecules present in the first hydration sphere. The structural-energetic characteristic of these solute-affected water molecules differs only slightly from that in the bulk and corresponds to the clathrate-like hydrogen-bonded cage typical for hydrophobic hydration, with the possible exception of F. MD simulations confirm such organization of water molecules in the first hydration sphere of NMA and indicate a practical lack of orientation and energetic effects beyond this sphere. The geometry of hydrogen-bonded water molecules in the first hydration sphere is very similar to that in the bulk phase, but MD simulations have affirmed subtle differences recognized by the spectral method and enabled their understanding. The spectral data and simulations results are highly compatible. In the case of F, NMF, and A, there is a visible spectral effect of water interactions with N-H groups, which have destabilizing influence on the amides hydration shell. There is no spectral sign of such interaction for NMA as the solute. The energetic stability of water H-bonds in the amide hydration sphere and in the bulk fulfills the order: NMA > DMA > A > NMF > bulk > DMF > F. Microscopic parameters of water organization around the amides obtained from the spectra, which have been used in the hydration model based on volumetric data, confirm the more hydrophobic character of the first three amides in this sequence. The increased stability of the hydration sphere of NMA relative to DMA and of NMF relative to DMF seems to have its origin in different geometries, and so the stability, of water cages containing the amides.

Hydration of Carboxylate Anions: Infrared Spectroscopy of Aqueous Solutions

Hydration of carboxylate ions was studied in aqueous solutions of sodium salts by means of FTIR spectroscopy using the HDO molecule as a probe. The quantitative version of the difference spectra method has been applied to determine the solute-affected water spectra. They display two-component bands of affected HDO at ca. 2550 and 2420 cm(-1). These bands are attributed to the -COO(-) group of the R-COO(-) ion (R = H, CH(3), C(2)H(5)), because water molecules surrounding the substituent R behave roughly as molecules in the bulk phase. For the studied carboxylates the net water structure making effect is observed, which increases with electron-donor ability of R, by means of changing the relative intensity of solute-affected HDO component bands. The observed splitting of the carboxylate-ion-affected HDO band is unique for these anions. The experimental results were confronted with DFT-calculated structures of small gas-phase and polarizable continuum model (PCM) solvated aqueous clusters to establish the structural and energetic states of carboxylate ions hydrates. This was achieved by comparison of the calculated optimal geometries with the interatomic distances derived from HDO band positions. Different possibilities have been considered to explain the peculiar spectral results. The plausible explanation assumes symmetry breaking of the carboxylate ion induced by interaction with water solvent: C-O bond lengths of RCOO(-) and electric charge localization become unequal. It is demonstrated by nonequivalent interaction of oxygen atoms of the RCOO(-) anion with water molecules. Taking into account only the energetic effect, the phenomenon is explained by the anticooperative H-bond formation of the carboxylate group with water molecules, which increases with the electron-donor ability of the substituent R. In this interaction two water molecules play an important part, as appears from the calculated clusters. They interact with oxygen atoms of the RCOO(-) ion, forming a cooperative system, within which solvent molecules are nonequivalent with respect to H-bond formation with both proton-accepting sites of the solute. This additionally enhances solvent-induced symmetry breaking of carboxylate anion. Strongly hydrogen-bonded solvent is more effective in inducing symmetry breaking; thus, increasing the temperature decreases the splitting of the carboxylate-ion-affected water, as experimentally observed.

Effect of tetraphenylphosphonium and tetraphenylborate ions on the water structure in aqueous solutions; FTIR studies of HDO spectra

FTIR spectroscopy has been used to study interactions of Ph4B- and Ph4P+ ions with water in aqueous solutions. The effect of Ph4BNa and Ph4PCl on the HDO vibration band in the fundamental region has been investigated. A new modification of the difference spectra method has been applied for the analysis of the spectral data. The results have revealed distinct differences in hydration of Ph4B- and Ph4P+ ions: Ph4B- ion strongly decreases the hydrogen-bond energy of surrounding water molecules, while Ph4P+ ion changes it slightly. The effect of Ph4B- is determined by anion–water interactions, while the effect of Ph4P+ is determined by water–water interactions around the cation. The changes in the energy of water hydrogen bonds upon the ions have been evaluated.

Vibrational spectroscopy of semiheavy water (HDO) as a probe of solute hydration

Vibrational spectroscopy is an ideally suited tool for the study of solute hydration. Nevertheless, water is commonly considered by spectroscopists a difficult solvent to work with. However, by using the isotopic dilution technique, in which a small amount of D2O is introduced into H2O or vice versa with formation of semiheavy water (HDO), many technical and interpretative problems connected with measurement of infrared spectra of water may be circumvented. Particularly, the isotopic decoupling of stretching vibrational modes greatly simplifies interpretation of the spectra. Systematic studies conducted in several laboratories since the 1980s up to the present day have provided a vast amount of data, concerning mainly ionic hydration. Many of these experiments have been performed in our laboratory. The analysis method we applied is based on the quantitative version of the difference spectra technique and allows separation of the spectrum of solute-affected HDO from the bulk solvent. This review illustrates the development of vibrational spectroscopy of HDO and spectral analysis methods over the years, as well as summarizes the results obtained for ionic and nonionic solutes, including some general hydration models formulated on their basis.

Intramolecular interactions in crystals of tris(2,6-diisopropylphenoxy)silanethiol and its sodium salts.

Hydrolytically stable silanethiol tris(2,6-diisopropylphenoxy)silanethiol (TDST) has been synthesized and reacted with sodium metal. In solid state TDST exhibits π-interactions between the S-H unit and the π-system of the arene, replaced by cation-π interactions in its sodium salts. The interactions are documented by crystal structures and FT-IR spectroscopy.

Donor properties of water in organic solvents derived from infrared spectra of HDO

The co-operativity of water hydrogen bonds has been discussed, as a key to the appropriate interpretation of water infrared spectra. In that respect, interaction energy values have been ascribed to some structural arrangements of water. A scale for water electron donor properties in aprotic solvents has been proposed, basing on Gutmanns donor numbers.

Hydration of simple carboxylic acids from infrared spectra of HDO and theoretical calculations.

The hydration of carboxylic acids in dilute aqueous solutions is important for our understanding of their functioning in the biochemical context. Here we apply vibrational spectra of HDO isotopically diluted in H(2)O to study this phenomenon, using the difference spectra method for analysis and interpretation of the results. The spectra of HDO affected by formic, acetic, and propionic acid display characteristic component bands, significantly red-shifted from the bulk HDO band position. The appearance of these component bands is linked with isotopic substitution on the carboxylic acid molecule, which forms a short and strong hydrogen bond with a water molecule. Additionally, a charge separation due to the proton transfer in the neutral form of the complex leading to a contact ion pair formation may be inferred from the affected HDO spectra. Apart from the contraction of the principal acid-water hydrogen bond, it results in other major structural changes in the hydration shell, as revealed by density functional theory (DFT) calculations of optimal geometries of aqueous clusters of the studied acids.

Preclusion of Irreversible Destruction of Dr Adhesin Structures by a High Activation Barrier for the Unfolding Stage of the Fimbrial DraE Subunit

Dr fimbriae of uropathogenic Eschericha coli strains are an example of surface-located adhesive structures assembled via the chaperone-usher pathway. These structures are crucial for specific attachment of bacteria to host receptors. Dr fimbriae are linear associates of DraE proteins, the structure of which is determined by a donor strand complementation between the consecutive subunits. The biogenesis of these structures is dependent on a function of the specific periplasmic chaperone and outer membrane usher proteins. In a consequence of these structural and assembly properties the potential unfolding of a single subunit in a linear associate would cause a destruction of fimbrial adhesion function. This correlates with the observed high resistance of fimbrial structures for denaturation. In this paper we show that the mechanism of thermal denaturation of DraE-sc protein is well described by an irreversible two-state model which is the reduced form of a Lumry-Eyring protein denaturation model. In theory of this model the observed stability of DraE-sc protein is determined by the high activation barrier for the unfolding stage N-->U. The microcalorimetry experiments permit to determine kinetic parameters of the DraE-sc unfolding process: energy of activation of 463.5 +/- 20.8 kJ.mol(-1) and rate constant of order 10(-17) s(-1). This corresponds to the dissociation/unfolding half-life of Dr fimbriae of 10(8) years at 25 degrees C. The FT-IR experiments show that the high stability of DraE is determined by the cooperative rigid protein core. The presented mechanism of kinetic stability of Dr fimbriae is probably universal to adhesive structures of the chaperone-usher type.

Chemometric method of spectra analysis leading to isolation of lysozyme and CtDNA spectra affected by osmolytes.

In this paper we present a chemometric method of analysis leading to isolation of Fourier transform infrared (FT-IR) spectra of biomacromolecules (HEW lysozyme, ctDNA) affected by osmolytes (trimethylamine-N-oxide and N,N,N-trimethylglycine, respectively) in aqueous solutions. The method is based on the difference spectra method primarily used to characterize the structure of solvent affected by solute. The cyclical usage of factor analysis allows precise information to be obtained on the shape of “affected spectra” of analyzed biomacromolecules. “Affected spectra” of selected biomacromolecules give valuable information on their structure in the presence of the osmolytes in solution, as well as on the level of perturbation in dependence of osmolyte concentration. The method also gives a possibility of insight into the mechanism of interaction in presented types of systems. It can be easily adapted to various chemical and biochemical problems where vibrational or ultraviolet-visible (UV-Vis) spectroscopy is used.