Estimation of the hydration of polar groups of α-amino acids by differential scanning calorimetry

The heat capacity of hydration of zwitterions derived from aliphatic amino acids depends linearly on the surface area of the amino acid side radicals accessible to water molecules with the slopeb = 2.35±0.11 J mol^–1 K^–1 Å^–2 at 298 K. The linear correlation between hydration heat capacities of zwitterions of aliphatic amino acids and the corresponding aliphatic alcohols with a coefficient of approximately unity confirms the assumption that hydrophobic hydration does not depend on the nature of the surrounding groups. Using the assumption that the hydration of hydrocarbon radicals is independent of the neighboring groups, theb value has been used to calculate the contributions of polar groups. The contributions of OH, COON, and CONH groups of the side radicals in polar amino acids in the zwitterion form are close to zero; in the case of organic nonionic molecules, these contributions are negative. The increments for polar groups obtained for the zwitterions can be used for the calculation of the heat capacities of proteins and polypeptides incorporating charged amino acid residues. The difference between hydrophilic and hydrophobic hydration mechanisms is manifested not only as different magnitudes and signs of heat capacities and temperature coefficients but also in the fact that the neighboring polar (charged) groups have an effect on hydrophilic hydration but have no effect on hydrophobic hydration.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 2237–2242, September, 1996.     

Ultrafast hydration dynamics in melittin folding and aggregation: helix formation and tetramer self-assembly

Melittin, an amphipathic peptide from honeybee venom, consists of 26 amino acid residues and adopts different conformations from a random coil, to an alpha-helix, and to a self-assembled tetramer under certain aqueous environments. We report here our systematic studies of the hydration dynamics in these conformations using single intrinsic tryptophan (W19) as a molecular probe. With femtosecond resolution, we observed the solvation dynamics occurring in 0.62 and 14.7 ps in a random-coiled primary structure. The former represents bulklike water motion, and the latter reflects surface-type hydration dynamics of proteins. As a comparison, a model tripeptide (KWK) was also studied. At a membrane-water interface, melittin folds into a secondary alpha-helical structure, and the interfacial water motion was found to take as long as 114 ps, indicating a well-ordered water structure along the membrane surface. In high-salt aqueous solution, the dielectric screening and ionic solvation promote the hydrophobic core collapse in melittin aggregation and facilitate the tetramer formation. This self-assembled tertiary structure is also stabilized by the strong hydrophilic interactions of charged C-terminal residues and associated ions with water molecules in the two assembled regions. The hydration dynamics was observed to occur in 87 ps, significantly slower than typical water relaxation at protein surfaces but similar to water motion at membrane interfaces. Thus, the observed time scale of approximately 100 ps probably implies appropriate water mobility for mediating the formation of high-order structures of melittin in an alpha-helix and a self-assembled tetramer. These results elucidate the critical role of hydration dynamics in peptide conformational transitions and protein structural stability and integrity.     

Volume properties of a ternary system: Water-urea-amino acid. Dilute and concentrated solutions

Partial molar volumes $ \bar V_U^0 $ \bar V_U^0 of amino acids in an aqueous urea solution are studied. For a saturated urea solution $ \bar V_U^0 $ \bar V_U^0 equals the molar volume of the amino acid, therefore, in the saturated solution, the amino acid dissolves without changing the system volume. Hydrophobic effects are manifested in the volumetric characteristics only in dilute (<1 mol/kg) urea solutions. Within a three-layer hydration model, the numbers of amino acid hydration are found. By the example of alanine and leucine, it is shown that their decrease with increasing urea concentration is determined by a zwitterionic moiety and does not depend on the size of the hydrocarbon radical of the amino acid.     

Oxygen permeability and the state of water in Nafion® membranes with alkali metal and amino sugar counterions

The mobility of hydration water and the dissolved oxygen permeability through different cation forms of the Nafion^® membranes were determined. Two alkali metals (Na and K) and two amino sugars (an equivalent molar mixture of d-glucopyranosyl-α(1′ → 6)-2-amino-2-deoxy-d-mannitol and its sorbitol (GPA)and d-glucosamine (GLU)) were used as counterions. Based on the two-state model, the content and mobility of hydration water were determined using DSC and ¹⁷O NMR. The dissolved oxygen permeability through the Nafion^® membrane containing GPA was the lowest value in this study because, for the membrane, the fraction of hydration water was the greatest and the mobility of hydration water was the lowest. The amount and location of the hydrophilic group contained in substances as well as the kind of hydrophilic group affected the fraction and mobility of hydration water and dissolved oxygen permeability through the membranes.     

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.     

Hydration numbers of glycine in aqueous sodium chloride and urea solutions

The hydration number of the glycine amino acid in aqueous sodium chloride solution is less than in aqueous urea solution; the difference increases significantly with increasing concentration of the nonaqueous component. Given the same partial volume of water, the hydration numbers of glycine in the two systems are close together (δ ≈ 5%).     

L-alanine in a droplet of water: a density-functional molecular dynamics study

We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid in neutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treated quantum mechanically. We found that the hydrophobic side chain (R = CH3) defines the trajectory path of the molecule. Initially fully hydrated in an isolated droplet of water, the amino acid moves to the droplet's surface, exposing its hydrophobic methyl group and alpha-hydrogen out of the water. The structure of an L-alanine with the methyl group exposed to the water surface was found to be energetically favorable compared to a fully hydrated molecule. The dynamic behavior of the system suggests that the first hydration shell of the amino acid is localized around carboxylate (CO2-) and ammonium (NH3+) functional groups; it is highly ordered and quite rigid. In contrast, the hydration shell around the side chain is much less structured, suggesting a modest influence of the methyl group on the structure of water. The number of water molecules in the first hydration shell of an alanine molecule is constantly changing; the average number was found to equal 7. The molecular dynamics results show that L-alanine in water does not have a preferred conformation, as all three of the molecule's functional sites (i.e., CH3, NH3+, CO2-) perform rotational movements around the C(alpha)-site bond.     

Water hydrogen bond analysis on hydrophilic and hydrophobic biomolecule sites

Elastic and quasielastic neutron scattering experiments have been used to investigate the hydrogen bonding network dynamics of hydration water on hydrophilic and hydrophobic sites. To this end the evolution of hydration water dynamics of a prototypical hydrophobic amino acid with polar backbone, N-acetyl-leucine-methylamide (NALMA), and hydrophilic amino acid, N-acetyl-glycine-methylamide (NAGMA), has been investigated as a function of the molecular ratio water : peptide. The results suggest that the dynamical contribution of the intrinsic and low hydration molecules of water is characteristic of pure librational/rotational movement. The water molecule remains attached to the hydrophilic site with only the possibility of hindered rotations that eventually break the bond with the peptide and reform it immediately after. A gradual evolution from librational motions to hindered rotations is observed as a function of temperature. When the hydration increases, we observe (together with the hindered rotations of hydrogen bonds) a slow diffusion of water molecules on the surface of the peptides.     

Hydration, charge, size, and shape characteristics of peptides from their CZE analyses

A CZE model is presented for peptide characterization on the basis of well-established physicochemical equations. The effective mobility is used as basic data in the model to estimate relevant peptide properties such as, for instance, hydration, net and total electrical charge numbers, hydrodynamic size and shape, particle average orientation, and pH-microenvironment from the charge regulation phenomenon. Therefore 102 experimental effective mobilities of different peptides are studied and discussed in relation to previous work. An equation for the estimation of peptide hydration as a function of ionizing, polar, and non-polar amino acid residues is included in the model. It is also shown that the shape-orientation factor of peptides may be either lower or higher than one, and its value depends on a complex interplay among total charge number, molar mass, hydration, and amino acid sequence.     

Studies of protein hydration in aqueous solution by high-resolution nuclear magnetic resonance spectroscopy

Individual hydration water molecules in aqueous protein solutions have been observed using experimental schemes for homonuclear two-dimensional and heteronuclear three-dimensional NMR experiments in H₂O solution, which do not require suppression of the solvent line by presaturation. In these experiments, the location of the hydration waters is determined from their nuclear Overhauser effects (NOE s) with individual hydrogen atoms of distinct amino acid residues. In the basic pancreatic trypsin inhibitor (BPTI ), four internal water molecules that had been reported in three different crystal forms were also found to be in the same locations in the solution structure, with lifetimes with respect to exchange of the water protons in excess of 0.3 ns. Additional NOE s with polypeptide protons located on the protein surface may involve either hydration water molecules or hydroxyl protons of amino acid side chains. Their total number is small compared to the number of NOE s expected from the hydration water molecules identified in the crystal structures of BPTI .     

Separation of bonito extract by composite UF membranes of sulfonated polysulfone coated on ceramics

Separation of ingredients in bonito extract was studied by a composite UF membrane of ceramic/sulfonated polysulfone (SPS). The bonito extract mainly contained inosine-5′-monophosphate (IMP), glutamic acid as a tasty ingredient and hypoxanthine, histidine as a putrefaction ingredient. The composite membrane showed a high rejection against negatively charged IMP, but permeated non-charged hypoxanthine. This is because of the negatively charged repulsion between the membrane and the solute. The permeation of amino acid could be controlled using the difference in isoelectric points of amino acids themselves. When the amino acid solution was filtrated by the composite membrane at pH 7, glutamic acid was rejected and no histidine was rejected. The charges of composite membrane were found to have an effect on the separation of ingredients in bonito extract.The composite membrane was stable within a wide pH range from 3 to 9, and had a thermal durability under 353 K.     

Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models

We present an extensive study on hydration thermodynamic properties of analogues of 13 amino acid side chains at 298 K and 1 atm. The hydration free energies DeltaG, entropies DeltaS, enthalpies DeltaH, and heat capacities Deltac(P)() were determined for 10 combinations of force fields and water models. The statistical sampling was extended such that precisions of 0.3, 0.8, 0.8 kJ/mol and 25 J/(mol K) were reached for DeltaG, TDeltaS, DeltaH, and Deltac(P)(), respectively. The three force fields used in this study are AMBER99, GROMOS 53A6, and OPLS-AA; the five water models are SPC, SPC/E, TIP3P, TIP4P, and TIP4P-Ew. We found that the choice of water model strongly influences the accuracy of the calculated hydration entropies, enthalpies, and heat capacities, while differences in accuracy between the force fields are small. On the basis of an analysis of the hydrophobic analogues of the amino acid side chains, we discuss what properties of the water models are responsible for the observed discrepancies between computed and experimental values. The SPC/E water model performs best with all three biomolecular force fields.     

Molecular Modelling of Disease-Causing Single-Nucleotide Polymorphisms in Collagen

Abstract

The purpose of the work was to investigate at the molecular structural and energy levels the consequence of amino acid substitutions in collagen that cause systemic diseases. The data have been systematized on defects in human collagen III, and the patterns of single-nucleotide polymorphisms collected. Then molecular mechanics calculations were performed for native and mutant collagen molecule fragments. The observed energy components and structural alterations that accompany particular amino acid substitutions were used to propose an interpretation of negative consequences in terms of stability and hydration of the macromolecule.     

Influence of various salts on the reversed-phase retention of some dansylated amino acids in TLC

Summary The retention of 14 dansylated amino acid derivatives was determined using aqueous LiCl, NaCl, KCl, RbCl and CsCl solutions as eluents in reversed-phase thinlayer chromatography. The salts exerted typical salting-out effects, the retention of each dansylated amino acid increased with increasing concentration of salt in the eluent. This effect has been tentatively explained by the suppression of the dissociation of the polar groups in the solute molecules resulting in increased apparent lipophilicity. The correlation between the increased retention of dansyl amino acids and the salt concentration was found to be linear. The hydrated radii and energy of hydration of cations as well as the hydrophobicity of free amino acids and the pK value of the -amino groups simultaneously influenced the retention.     

Hydration of the H<Superscript>+</Superscript>, Li<Superscript>+</Superscript>, Na<Superscript>+</Superscript>, and Cs<Superscript>+</Superscript> ions in MF-4SK perfluorinated sulfonic acid cation-exchange membranes modified with inorganic dopants

The hydration, state, and mobility of protons and Li⁺, Na⁺, and Cs⁺ ions in MF-4SK perfluorinated sulfonic acid cation-exchange membranes doped with silicon dioxide and phosphotungstic acid have been investigated by NMR and impedance spectroscopy. The dopants increase the moisture content of the membrane and change the system of pores and channels in which ion transport takes place. At low humidities, the dopant particles are involved in ion transport. The greatest effect is observed for the membranes doped with both SiO₂ and phosphotungstic acid. The water molecules sorbed by dopant particles as a material participate in the hydration of alkali metal cations in the membrane.     

How does the solvent guide the hydration process?

The hydration numbers are investigated of the glycine amino acid in solutions of substances with different effects on the structure of water: urea, monomethylurea, and 1,3-dimethylurea. Glycine loses a half of its hydration water in a 20m urea solution and only a quarter of it in a 20m dimethylurea solution. The constancy of the hydration number of glycine in concentrated dimethylurea solutions is due to the compensatory effect of the interactions in the ternary and binary systems.     

Evolving the Promiscuity of Elizabethkingia meningoseptica Oleate Hydratase for the Regio‐ and Stereoselective Hydration of Oleic Acid Derivatives

The addition of water to non‐activated carbon–carbon double bonds catalyzed by fatty acid hydratases (FAHYs) allows for highly regio‐ and stereoselective oxyfunctionalization of renewable oil feedstock. So far, the applicability of FAHYs has been limited to free fatty acids, mainly owing to the requirement of a carboxylate function for substrate recognition and binding. Herein, we describe for the first time the hydration of oleic acid (OA) derivatives lacking this free carboxylate by the oleate hydratase from Elizabethkingia meningoseptica (OhyA). Molecular docking of OA to the OhyA 3D‐structure and a sequence alignment uncovered conserved amino acid residues at the entrance of the substrate channel as target positions for enzyme engineering. Exchange of selected amino acids gave rise to OhyA variants which showed up to an 18‐fold improved conversion of OA derivatives, while retaining the excellent regio‐ and stereoselectivity in the olefin hydration reaction.     

Diastereoselective synthesis of the 5-hydroxy-pyrrolidinone amino acid of the microsclerodermins and model studies for an end-game strategy for microsclerodermin B

The first diastereoselective synthesis of the 5-hydroxy-pyrrolidinone amino acid common to eight members of the microsclerodermin family is presented. Our strategy involves formal hydration of an unsaturated precursor via the use of a two-step hydroxybromination-debromination protocol; this procedure provides exclusively the requisite 4,5-cis-pyrrolidinone. Furthermore model studies are presented that indicated the potential viability of this hydration strategy in the context of a synthesis of microsclerodermin B.     

Investigation of hydration of α-amino acids by means of absorption millimeter spectroscopy

The hydration indexes for 19 protein -amino acids are measured by means of absorption millimeter spectroscopy (AMS) at 31.42 GHz. The plot of the hydration indexes on the area of surface of aliphatic amino acid molecules accessible for water is a straight line located above the points corresponding to aromatic or polar amino acids. The contribution of nonpolar groups in the hydration index is greater than that of polar groups provided that their accessible surface areas are equal. The contribution to hydration of -OH and-CONH₂ groups in Ser. Gin, and Asn coincides in sign with that of pure hydrophobic hydration but the value of the contribution is significantly smaller. The change in mobility of water molecules, which is the basis of the AMS method, may serve as the physicochemical foundation for the construction of a new hydrophobicity scale for amino acids comparable with the already existing scales.Deceased September 2, 1995.Translated fromIzvestiya Akodemii Nauk. Seriya Khimicheskaya, No. 3, pp. 618–622, March, 1996.     

Specific anion effects on the optical rotation of alpha-amino acids

Changes in optical rotation of some alpha-amino acids are induced by electrolytes. Such effects on l- and d-enantiomers of a range of amino acids are explored for sodium salts with varying anion. The amino acids studied were alanine, aspartic acid, glutamic acid, glutamine, proline, threonine, and tryptophan. The anion's polarizability in solution accounts for the change in [alpha] only for the halides. Self-association of amino acids in solution and pH changes due to the presence of the electrolytes do not account for the observed variations in optical activity. Specific interactions of anions with the chiral amino acids (Hofmeister effects) and salt-induced perturbations of the amino acid hydration shell appear to be responsible for the effects, and conformational changes in the chiral solutes due to the presence of ionic species are discussed.