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.

Peptide-Based Rapid and Selective Detection of Mercury in Aqueous Samples with Micro-Volume Glass Capillary Fluorometer.

Mercury, a toxic heavy metal produced through both natural and anthropogenic processes, is found in all of Earth's major systems. Mercury's bioaccumulation characteristics in the human body have a significant impact on the liver, kidneys, brain, and muscles. In order to detect Hg ions, a highly sensitive and specific fluorescent biosensor has been developed using a novel, modified seven amino acid peptide, FY7.

Gold(III) complexes with chloride and cyanopyridines: Facilitated hydrolysis of nitrile ligand to amide and antibacterial activity.

A range of novel simple gold(III) compounds has been synthesized in their monocrystalline form, including two previously unknown chloro-complexes of Au with 2-cyanopyridine or 3-cyanopyridine, respectively. Our investigations have revealed the intricate nature of the reaction between 2-cyanopyridine and tetrachloroauric acid, yielding at least three distinct products. The main product, obtained in high yield, is a salt featuring a tetrachloroauric anion and a pyridinium cation stabilized by a hydrogen bond to a further 2-cyanopyridine molecule.

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.

Solvent influence on the crystal structures of new cadmium tri-tert-butoxysilanethiolate complexes with 1,4-bis(3-aminopropyl)piperazine: luminescence and antifungal activity.

Monocrystals of dinuclear μ-1,4-bis(3-aminopropyl)piperazine-κN,N:N,N-bis[bis(tri-tert-butoxysilanethiolato-κS)cadmium(II)], [Cd(CHOSSi)(CHN)] or [Cd{SSi(OtBu)}(μ-BAPP)], 1, and polynuclear catena-poly[[bis(tri-tert-butoxysilanethiolato-κS)cadmium(II)]-μ-1,4-bis(3-aminopropyl)piperazine-κN:N], [Cd(CHOSSi)(CHN)] or [Cd{SSi(OtBu)}(μ-BAPP)], 2, with 1,4-bis(3-aminopropyl)piperazine (BAPP) and tri-tert-butoxysilanethiolate ligands, were obtained from the same ratio of reactants, but with different solvents used for the crystallization processes. The structures and properties of both complexes were characterized using elemental analysis, X-ray diffraction and FT-IR, H NMR and luminescence spectroscopy. Applied density functional theory (DFT) computational methods and noncovalent interaction (NCI) analysis were used for geometry optimization and visualization of the interactions between the metallic centres and their surroundings.

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.

Influence of Urea and Dimethyl Sulfoxide on K-Peptide Fibrillation.

Protein fibrillation leads to formation of amyloids-linear aggregates that are hallmarks of many serious diseases, including Alzheimer's and Parkinson's diseases. In this work, we investigate the fibrillation of a short peptide (K-peptide) from the amyloidogenic core of hen egg white lysozyme in the presence of dimethyl sulfoxide or urea. During the studies, a variety of spectroscopic methods were used: fluorescence spectroscopy and the Thioflavin T assay, circular dichroism, Fourier-transform infrared spectroscopy, optical density measurements, dynamic light scattering and intrinsic fluorescence.

DMSO and TMAO-Differences in Interactions in Aqueous Solutions of the K-Peptide.

Interactions between a solvent and their co-solute molecules in solutions of peptides are crucial for their stability and structure. The K-peptide is a synthetic fragment of a larger hen egg white lysozyme protein that is believed to be able to aggregate into amyloid structures. In this study, a complex experimental and theoretical approach is applied to study systems comprising the peptide, water, and two co-solutes: trimethylamide -oxide (TMAO) or dimethyl sulfoxide (DMSO).

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.

A shear stress micromodel of urinary tract infection by the Escherichia coli producing Dr adhesin.

In this study, we established a dynamic micromodel of urinary tract infection to analyze the impact of UT-segment-specific urinary outflow on the persistence of E. coli colonization. We found that the adherence of Dr+ E.

Vapor correction of FTIR spectra - A simple automatic least squares approach.

FTIR spectroscopy is one of the best techniques to study intermolecular interactions. However, such an application requires high quality spectra with as little noise as possible, which are often difficult to obtain. One of the main sources of unwanted interference is water vapor.

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.

Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic .

Dr fimbriae are homopolymeric adhesive organelles of uropathogenic composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond that joins their A and B strands.

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.

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.

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.

Biochemical characteristic of biofilm of uropathogenic Escherichia coli Dr(+) strains.

Urinary tract infections caused by Escherichia coli are very common health problem in the developed countries. The virulence of the uropathogenic E. coli Dr(+) IH11128 is determined by Dr fimbriae, which are homopolymeric structures composed of DraE subunits with the DraD protein capping the fiber.

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.

Analysis of the unique structural and physicochemical properties of the DraD/AfaD invasin in the context of its belonging to the family of chaperone/usher type fimbrial subunits.

Background: DraD invasin encoded by the dra operon possesses a classical structure characteristic to fimbrial subunits of the chaperone/usher type. The Ig-fold of the DraD possesses two major characteristics distinguishing it from the family of fimbrial subunits: 1) a distortion of the β-barrel structure in the region of the acceptor cleft, demonstrated by a disturbance of the main-chain hydrogen bonds network, and 2) an unusually located disulfide bond connecting B and F strands - the localization exclusively observed in the subfamily of DraD/AfaD-type subunits.

Results: To evaluate the influence of the DraD-sc specific structural features on its stability and mechanism of thermal denaturation, a series of DSC and FT-IR denaturation experiments were performed giving following conclusions.

The noncanonical disulfide bond as the important stabilizing element of the immunoglobulin fold of the Dr fimbrial DraE subunit.

Fimbrial adhesins of pathogenic bacteria are linear protein associates responsible for binding to the specific host cell receptors. They are assembled via the chaperone/usher pathway conserved in Gram-negative bacteria. These adhesive organelles are characterized by the high resistance to dissociation and unfolding caused by temperature or chemical denaturants.