Characterizing Interactions Between Small Peptides and Dimethyl Sulfoxide Using Infrared Spectroscopy and Computational Methods.

This study provides a comprehensive analysis of the interactions between dimethyl sulfoxide (DMSO) and two small peptides, diglycine and -acetyl-glycine-methylamide (NAGMA), in aqueous solutions using FTIR spectroscopy and density functional theory (DFT) calculations. ATR-FTIR spectroscopy and DFT results revealed that DMSO does not form direct bonds with the peptides, suggesting that DMSO indirectly influences both peptides by modifying the surrounding water molecules. The analysis of HDO spectra allowed for the isolation of the contribution of water molecules that were simultaneously altered by the peptide and DMSO, and it also explained the changes in the hydration shells of the peptides in the presence of DMSO.

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).

Effect of ectoine on hydration spheres of peptides-spectroscopic studies.

In this paper, we use FTIR spectroscopy to characterize the hydration water of ectoine, its interactions with two peptides-diglycine and NAGMA, and the properties of water molecules in the hydration spheres of both peptides changed by the presence of the osmolyte. We found that the interaction of ectoine with the peptide hydration shells had no effect on its own hydration sphere. However, the enhanced hydration layer of the osmolyte influences the hydration shells of both peptides and does so in a different way for both peptides: (1) the interfacial interaction of the NAGMA peptide and ectoine hydration spheres strengthened the hydration shell of this peptide; (2) the inclusion of water molecules from the ectoine hydration sphere into the diglycine hydration sphere had only a marginally enhancing effect.

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.

Interactions in Ternary Aqueous Solutions of NMA and Osmolytes-PARAFAC Decomposition of FTIR Spectra Series.

Intermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel Factor Analysis (PARAFAC) decomposition of ternary solution spectra into parts that are easier to analyze.

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.

Preparation and characterization of dummy-template molecularly imprinted polymers as potential sorbents for the recognition of selected polybrominated diphenyl ethers.

The main aim of this work was to conduct the preliminary/basic research concerning the preparation process of a new dummy molecularly imprinted polymer (DMIP) materials. Developed DMIPs were proposed as a sorption material in solid-phase extraction (SPE) technique for recognition of selected low mass polybrominated diphenyl ethers (PBDEs) - PBDE-47 and PBDE-99. Four new DMIPs were synthesized employing bulky polymerization technique by application of structural analogue of low mass PBDEs - 4,4'-Dihydroxydiphenyl ether, as a dummy template.

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.

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.

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.

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.

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.

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.

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.