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).

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

In this work, we investigated the influence of stabilizing (,,-trimethylglycine) and destabilizing (urea) osmolytes on the hydration spheres of biomacromolecules in folded forms (-1 peptide and hen egg white lysozyme─) and unfolded protein models (glycine─GLY and -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.

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 -oxide) and destabilizing osmolyte-urea on hydration shells of two short peptides, NAGMA (-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations.

Taurine as a water structure breaker and protein stabilizer.

The enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as "structure breaking" solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between osmolytes and two proteins: lysozyme and ubiquitin.

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.

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.

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.

Correction: Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies.

Correction for 'Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies' by P. Bruździak et al., Phys.

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.

Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies.

Interactions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes -l-proline and trimethylamine-N-oxide (TMAO) - belong to a group of stabilizing osmolytes, and according to the preferential exclusion/hydration hypothesis, both should be excluded from the vicinity of the protein backbone and surface.

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.

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.

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.

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.

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.

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.

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.

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.

An effective method for studying intermolecular interactions in binary liquids with hydrogen bonds; FTIR spectra and ab initio calculations in the N-methylformamide-methanol system.

Molecular complexes in methanol (MeOH)-N-methylformamide (NMF) mixtures were studied based on their FTIR-ATR spectra, to which two methods of analysis were applied: factor analysis and a quantitative version of the difference-spectra method. The mean composition of a complex between NMF and MeOH molecules over the whole range of mixture compositions was determined. Absorbing species differentiated with regard to the interaction energies of the carbonyl oxygen with methanol molecules were recognized in both compositional regions with a marked excess of one component.

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.

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.

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.

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.

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.