Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions.

The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte-TMAO (trimethylamine N-oxide) and destabilizing osmolyte-urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.

Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent.

Infrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently, ab initio molecular dynamics (AIMD) simulations provide the solvation shell picture at an atomistic detail level and allow for a consistent decomposition of the theoretical IR spectrum in terms of distance-dependent contributions of the solvent molecules. Here, we show for the first time how the chemometric techniques designed with the analysis of experimental data in mind can be harnessed to extract corresponding information from the computed IR spectra for mutual benefit, but without any mutual input. The wide applicability of this two-track approach is demonstrated using lithium bromide solvation in γ-butyrolactone (GBL) as a showcase. GBL is a cyclic ester with extensive applications as a solvent in electrochemistry and we are particularly motivated by its usefulness in the rechargeable cell industry which justifies further studies of lithium cation solvation in GBL. The combination of experiment and simulations firmly asserts the strong solvent structuring character of Li+ and a comparatively weak influence exerted on the solvent by Br-.

Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme.

Osmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical denaturation of lysozyme in different solvent conditions to study the molecular mechanism by which two biologically relevant osmolytes, denaturing (urea) and stabilizing (betaine), affect the folding equilibrium. We found that urea interacts favorably with all types of residues via both hydrogen bonds and dispersion forces, and therefore accumulates in a diffuse solvation shell around the protein. This not only provides an enthalpic stabilization of the unfolded state, but also weakens the hydrophobic effect, as hydrophobic forces promote the association of urea with nonpolar residues, facilitating the unfolding. In contrast, we observed that betaine is excluded from the protein backbone and nonpolar side chains, but is accumulated near the basic residues, yielding a nonuniform distribution of betaine molecules at the protein surface. Spatially resolved solvent-protein interaction energies further suggested that betaine behaves in a ligand- rather than solvent-like manner and its exclusion from the protein surface arises mostly from the scarcity of favorable binding sites. Finally, we found that, in the presence of betaine, the reduced ability of water molecules to solvate the protein results in an additional enthalpic contribution to the betaine-induced stabilization.

Hydration of amino acids: FTIR spectra and molecular dynamics studies.

The hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results, molecular dynamics simulations of amino acids were performed. The structural-energetic characteristic of these solute-affected water molecules shows that, on average, water affected by amino acids forms stronger and shorter H-bonds than those in pure water. Differences in the influence of amino acids on water structure have been noticed. The effect of the hydrophobic side chain of an amino acid on the solvent interactions seems to be enhanced because of the specific cooperative coupling of water strong H-bond chain, connecting the carboxyl and amino groups, with the clathrate-like H-bond network surrounding the hydrocarbon side chain. The parameter derived from the spectral data, which corresponds to the contributions of the population of weak hydrogen bonds of water molecules which have been substituted by the stronger ones in the hydration sphere of amino acids, correlated well with the amino acid hydrophobicity indexes.

Weakly Hydrated Solute of Mixed Hydrophobic-Hydrophilic Nature.

Infrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane (MSM). In the hydration sphere of MSM, there are two types of populations of water molecules: a significant share of water molecules weakly bonded to the sulfone group and a smaller share of water molecules strongly bonded to each other around the methyl groups of MSM. The very weak hydrogen bond of water molecules with the hydrophilic group causes the extended network of water hydrogen bonds to be not "anchored" on the sulfone group, and consequently, the MSM hydration shell is labile.

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.

Application of the tetraphenylphosphonium tetraphenylborate (TPTB) assumption to the thermodynamic properties of solvated ions in dimethylsulfoxide.

The extra-thermodynamic tetraphenylphosphonium tetraphenylborate assumption has been tested for dimethylsulfoxide using ATR FTIR spectroscopy. Solute-affected DMSO spectra show that, contrary to the TPTB assumption, the charge density on BPh(4)(-) and Ph(4)P(+) ions is sufficiently high to influence the DMSO molecules orientation with respect to the cation and to the anion. Apparently, the Ph(4)P(+) cation does not affect the structure of DMSO whereas the BPh(4)(-) anion clearly breaks it up. Our results indicate that the TPTB extra-thermodynamic assumption is not a sound basis for splitting thermodynamic values obtained for DMSO solutions into ionic contributions.

Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation.

In this paper, the hydration of a model protein--hen egg white lysozyme in aqueous solution has been presented. The leading method used was FTIR spectroscopy with an application of a technique of semi-heavy water (HDO) isotope dilution. Analysis of spectra of HDO isotopically diluted in water solution of lysozyme allowed us to isolate HDO spectra affected by lysozyme, and thus to characterise the energetic state of water molecules and their arrangement around protein molecules. The number of water molecules and the shape of the affected HDO spectrum were obtained using a classical and a chemometric method. This shape showed that the HDO spectrum affected by lysozyme may be presented as a superposition of two spectra corresponding to HDO affected by N-methylacetamide and the carboxylate anion (of the formic acid). Moreover, based on the difference in intermolecular distances distribution of water molecules (obtained from spectral data), we demonstrated that the lysozyme molecule causes a decrease in population of weak hydrogen bonds, and concurrently increases the probability of an occurrence of short hydrogen bonds in water affected by lysozyme. This conclusion was also confirmed by the molecular dynamics (MD) simulation.

Mechanism of Osmolyte Stabilization-Destabilization of Proteins: Experimental Evidence.

In this work, we investigated the influence of stabilizing (N,N,N-trimethylglycine) and destabilizing (urea) osmolytes on the hydration spheres of biomacromolecules in folded forms (trpzip-1 peptide and hen egg white lysozyme─hewl) and unfolded protein models (glycine─GLY and N-methylglycine─NMG) by means of infrared spectroscopy. GLY and NMG were clearly limited as minimal models for unfolded proteins and should be treated with caution. We isolated the spectral share of water changed simultaneously by the biomacromolecule/model molecule and the osmolyte, which allowed us to provide unambiguous experimental arguments for the mechanism of stabilization/destabilization of proteins by osmolytes. In the case of both types of osmolytes, the decisive factor determining the equilibrium folded/unfolded state of protein was the enthalpy effect exerted on the hydration spheres of proteins in both forms. In the case of stabilizing osmolytes, enthalpy was also favored by entropy, as the unfolded state of a protein was more entropically destabilized than the folded state.

Fourier transform infrared spectroscopic and theoretical study of water interactions with glycine and its N-methylated derivatives.

In this study we attempt to explain the molecular aspects of amino acids' hydration. Glycine and its N-methylated derivatives: N-methylglycine, N,N-dimethylglycine, and N,N,N-trimethylglycine were used as model solutes in aqueous solution, applying FT-IR spectroscopy as the experimental method. The quantitative version of the difference spectra method enabled us to obtain the solute-affected HDO spectra as probes of influenced water. The spectral results were confronted with density functional theory calculated structures of small hydration complexes of the solutes using the polarizable continuum model. It appears that the hydration of amino acids in the zwitterionic form can be understood allowing a synchronized fluctuation of hydrogen bonding between the solute and the water molecules. This effect is caused by a noncooperative interaction of water molecules with electrophilic groups of amino acid and by intramolecular hydrogen bond, allowing proton transfer from the carboxylic to the amine group, accomplishing by the chain of two to four water molecules. As a result, an instantaneous water-induced asymmetry of the carboxylate and the amino group of amino acid molecule is observed and recorded as HDO band splitting. Water molecules interacting with the carboxylate group give component bands at 2543 ± 11 and 2467 ± 15 cm(-1), whereas water molecules interacting with protons of the amine group give rise to the bands at 2611 ± 15 and 2413 ± 12 cm(-1). These hydration effects have not been recognized before and there are reasons to expect their validity for other amino 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.

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.

Systematic study of hydration patterns of phosphoric(V) acid and its mono-, di-, and tripotassium salts in aqueous solution.

Fourier transform infrared (FTIR) spectroscopy of the OD band of HDO molecules has been applied to perform a systematic study of various phosphate forms in the order of decreasing protonation: H3PO4, KH2PO4, K2HPO4, K3PO4. HDO isotopically diluted in H2O has been prepared by adding adequate amounts of D2O to aqueous solutions in ordinary water. The difference spectra procedure has been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. The position at maximum of the principal anion-affected HDO band for potassium phosphates moves in the order KH2PO4 (2478 cm(-1))>K2HPO4 (2363 cm(-1))>K3PO4 (2301 cm(-1)), that is, decreases with increasing solute basicity and charge. The number of moles of water affected by one mole of solute (N) equals 11.0, 13.8 and 16.2, respectively. Phosphoric acid affects statistically 13.9 water molecules and appears to be a "structure making" solute in water. The isotopic substitution with deuterium occurs also on the phosphate anions and phosphoric acid. The thus formed P-O-D groups interact with water molecules via strong hydrogen bonds and the relative strength of this interaction increases with increasing solute acidity. The plausible assignments of OD bands of HDO have been confirmed by calculating equilibrium structures of small aqueous clusters of the studied individual utilizing density functional theory. Further interpretation of the energetic and structural properties of hydrating water is enabled by calculating intermolecular interaction energy of water and probability distributions for interatomic oxygen-oxygen distance.

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.

Solvation of cobalt(II) and trifluoromethanesulfonate ions in N,N-dimethylformamide-methanol mixed solvent studied by means of FT-IR spectroscopy.

FT-IR spectra of Co(CF(3)SO(3))(2)-N,N-dimethylformamide (DMF)-methanol (MeOH) solutions have been measured over the whole range of solvent composition. The data together with the obtained previously spectra of DMF-MeOH mixtures have been analyzed using the difference spectra method in the region of CO and OH stretching bands. The number of DMF and MeOH molecules in the first solvation sphere of Co(II) ion versus solvent composition has been determined. The second solvation sphere has been revealed and characterized quantitatively. Solvation of trifluoromethanesulfonate (triflate) ion as well as ion association in DMF solution have been also studied.

Protein thermal stabilization in aqueous solutions of osmolytes.

Proteins' thermal stabilization is a significant problem in various biomedical, biotechnological, and technological applications. We investigated thermal stability of hen egg white lysozyme in aqueous solutions of the following stabilizing osmolytes: Glycine (GLY), N-methylglycine (NMG), N,N-dimethylglycine (DMG), N,N,N-trimethylglycine (TMG), and trimethyl-N-oxide (TMAO). Results of CD-UV spectroscopic investigation were compared with FTIR hydration studies' results. Selected osmolytes increased lysozyme's thermal stability in the following order: Gly>NMG>TMAO≈DMG>TMG. Theoretical calculations (DFT) showed clearly that osmolytes' amino group protons and water molecules interacting with them played a distinctive role in protein thermal stabilization. The results brought us a step closer to the exact mechanism of protein stabilization by osmolytes.

General Mechanism of Osmolytes' Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent.

The stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called "structurally different water". The addition of such osmolytes causes "dissolution" of the specific protein hydration sphere and destabilizes its folded form. No relationship is seen between the stabilizing/destabilizing properties of osmolytes and their structure-making/-breaking influence on water. Furthermore, their accumulation at the protein surface or their exclusion does not determine the osmolytes' effect on protein stability. An explanation to the osmolytes' stabilizing/destabilizing influence originates in the similarity of water properties in osmolytes and protein solutions. The spectral infrared characteristic of water in an osmolyte solution allowed us to develop practical criteria for classifying solutes as stabilizing or destabilizing agents.

Analysis of spectral data by complementary methods. Inspection of the molecular complex in N,N-dimethylformamide-methanol mixtures.

FT-IR spectra of N,N-dimethylformamide (DMF)-methanol (MeOH) mixtures have been measured in the range of 4000-950 cm(-1). The data have been analyzed using the difference spectra method and factor analysis. The usefulness of the methods for recognizing the hydrogen bonds in the mixtures has been critically examined. It has been shown that 1:1 intermolecular complex existing in the whole range of the mixture composition is modified by interactions with environment. The structure of different forms of the complex depending on the solvent composition has been shown. Weak CH...O hydrogen bonds have been postulated for explanation of the spectra.

Influence of osmolytes on protein and water structure: a step to understanding the mechanism of protein stabilization.

Results concerning the thermostability of hen egg white lysozyme in aqueous solutions with stabilizing osmolytes, trimethylamine-N-oxide (TMAO), glycine (Gly), and its N-methyl derivatives, N-methylglycine (NMG), N,N-dimethylglycine (DMG), and N,N,N-trimethylglycine (betaine, TMG), have been presented. The combination of spectroscopic (IR) and calorimetric (DSC) data allowed us to establish a link between osmolytes' influence on water structure and their ability to thermally stabilize protein molecule. Structural and energetic characteristics of stabilizing osmolytes' and lysozyme's hydration water appear to be very similar. The osmolytes increase lysozyme stabilization in the order bulk water < TMAO < TMG < Gly < DMG < NMG, which is consistent with the order corresponding to the value of the most probable oxygen-oxygen distance of water molecules affected by osmolytes in their surrounding. Obtained results verified the hypothesis concerning the role of water molecules in protein stabilization, explained the osmophobic effect, and finally helped to bring us nearer to the exact mechanism of protein stabilization by osmolytes.