Differential stability of the triple helix of (Pro-Pro-Gly)10 in H2O and D2O: thermodynamic and structural explanations

(Pro-Pro-Gly)10 [(PPG10)], a collagen-like polypeptide, forms a triple-helical, polyproline-II structure in aqueous solution at temperatures somewhat lower than physiological, with a melting temperature of 24.5 degrees C. In this article, we present circular dichroism spectra that demonstrate an increase of the melting temperature with the addition of increasing amounts of D2O to an H2O solution of (PPG)10, with the melting temperature reaching 40 degrees C in pure D2O. A thermodynamic analysis of the data demonstrates that this result is due to an increasing enthalpy of unfolding in D2O vs. H2O. To provide a theoretical explanation for this result, we have used a model for hydration of (PPG)10 that we developed previously, in which inter-chain water bridges are formed between sterically crowded waters and peptide bond carbonyls. Energy minimizations were performed upon this model using hydrogen bond parameters for water, and altered hydrogen bond parameters that reproduced the differences in carbonyl oxygen-water oxygen distances found in small-molecule crystal structures containing oxygen-oxygen hydrogen bonds between organic molecules and H2O or D2O. It was found that using hydrogen bond parameters that reproduced the distance typical of hydrogen bonds to D2O resulted in a significant lowering of the potential energy of hydrated (PPG)10. This lowering of the energy involved energetic terms that were only indirectly related to the altered hydrogen bond parameters, and were therefore not artifactual; the intra-(PPG10) energy, plus the water-(PPG10) van der Waals energy (not including hydrogen bond interactions), were lowered enough to qualitatively account for the lower enthalpy of the triple-helical conformation, relative to the unfolded state, in D2O vs. H2O. This result indicates that the geometry of the carbonyl-D2O hydrogen bonds allows formation of good hydrogen bonds without making as much of an energetic sacrifice from other factors as in the case of hydration by H2O.     

Thermal perturbation difference spectra and D2O vs H2O isothermal difference spectra of protein-model aromatic chromophores.

The thermal perturbation difference spectra of phenolic and indolic chromophores in water resemble the isothermal D₂O and H₂O spectra of these chromophores. For phenols approximately equal Δ? values are obtained in both types of spectra, but for their methyl ethers Δ? values of D₂O vs H₂O spectra are about half of those of the thermal perturbation spectra. Phenols and their methyl ethers were studied in deuterated ethylene glycol and glycerol vs the corresponding protiated solvent, and in nonprotic solvents containing 0.25–4% D₂O or H₂O. For phenols in D₂O vs H₂O, about one-third to one-half of the difference spectrum is attributed to solvent structure difference, and the remainder to the effects of replacing OH by OD and to differences in accepting hydrogen bonds from D₂O and H₂O. The refractive index difference between D₂O and H₂O was shown to be a minor contribution by means of experiments in which D₂O was at 5 dgC and H₂O at 47 dgC, conditions of equal refractive index (Na_D). D₂O vs H₂O and glycerol-d vs glycerol-h difference spectra of ribonuclease are about twice as large as expected from the known number of exposed tyrosyl side chains. Possible sources of error in D₂O vs H₂O spectra of proteins are discussed.     

Theoretical studies on the structures,intra- and inter-molecular hydrogen bonding interactions in HNF and HNF–H2O clusters in the gaseous,aqueous and solid phases

Hydrazimium nitroformate ([N₂H₅]⁺[C(NO₂)₃]^? , HNF) is an ionic oxidiser used in solid propellants. Its properties are easily affected by H₂O because of its hygroscopicity. In this article, density functional theory (DFT) and molecular dynamics (MD) were employed to study the isolated HNF molecule and the HNF–H₂O cluster in gas phase and in the aqueous solution. Three stable conformations were obtained for HNF in the gas phase and in the aqueous solution, respectively, and each conformation can form several different HNF–H₂O clusters. Irrespective of whether it is in gas phase or in solution, intramolecular hydrogen bond interactions and other interactions (e.g. the binding energy, the dispersion energy, the second-order perturbation energy and the energy gap between frontier orbitals) of HNF are weaker in the clusters than in the isolated state. The initial decomposition energy of the cluster is lower than that of the isolated HNF molecule in both gaseous and aqueous phases, while the dissociation processes are the same. Molecular dynamic simulations showed that the clustered H₂O elongates and weakens the C–NO₂ bond in the solid HNF–H₂O cluster compared with that in the solid HNF. H₂O reduces and weakens intramolecular N–HΛO bonds too, and O–HΛN is the dominant intermolecular hydrogen bond between HNF and H₂O.     

Effect of deuterium oxide on the thermodynamic quantities associated with phase transitions of phosphatidylcholine bilayer membranes

The bilayer phase transitions of three kinds of phospholipids, dipalmitoylphosphatidylcholine (DPPC), distearoylphosphatidylcholine (DSPC) and dihexadecylphosphatidylcholine (DHPC), in deuterium oxide (D₂O) and hydrogen oxide (H₂O) were observed by differential scanning calorimetry (DSC) under ambient pressure and light-transmittance measurements under high pressure. The DSC measurements showed that the substitution of H₂O by D₂O affected the pretransition temperatures and the main-transition enthalpies of all PC bilayers. The temperature-pressure phase diagrams for these PC bilayer membranes in both solvents were constructed by use of the data of light-transmittance measurements. Regarding the main transition of all PC bilayer membranes, there was no appreciable difference between the transition temperatures in D₂O and H₂O under high pressure. On the other hand, the phase transitions among the gel phases including the pretransition were significantly affected by the solvent substitution. The thermodynamic quantities of phase transitions for the PC bilayer membranes were evaluated and the differences in thermodynamic properties by the water substitution were considered from the difference of interfacial-free energy per molecule in the bilayer in both solvents. It was proved that the substitution of H₂O by D₂O causes shrinkage of the molecular area of phospholipid at bilayer interface due to the difference in bond strength between deuterium and hydrogen bonds and produces the great influence on the bilayer phase with the smaller area. Further, the induction of bilayer interdigitation in D₂O turned out to need higher pressures than in H₂O.     

Calixarene building block bis(2-hydroxyphenyl)methane (2HDPM) and hydrogen-bonded 2HDPM-H2O complex in electronic excited state

Intramolecular and intermolecular hydrogen bonding in electronic excited states of calixarene building blocks bis(2-hydroxyphenyl)methane (2HDPM) monomer and hydrogen-bonded 2HDPM-H₂O complex were studied theoretically using the time-dependent density functional theory (TDDFT). Twenty-four stable conformations (12 pairs of enantiomers) of 2HDPM monomer have been found in the ground state. From the calculation results, the conformations 1a and 1b which both have an intramolecular hydrogen bond are the most stable ones. The infrared spectra of 2HDPM monomer and 2HDPM-H₂O complex in ground state and S₁ state were calculated. The stretching vibrational absorption band of O₂???H₃ group in the monomer and complex disappeared in the S₁ state. At the same time, a new strong absorption band appeared at the C=O stretching region. From the calculation of bond lengths, it indicates that the O₂???H₃ bond is significantly lengthened in the S₁ state. However, the C₁???O₂ bond is drastically shortened upon electronic excitation to the S₁ state and has the characteristics of C=O band. Furthermore, the intramolecular hydrogen bond O₂???H₃?·?·?·?O₄ of the 2HDPM monomer and the intermolecular hydrogen bonds O₂???H₃?·?·?·?O₇ and O₇???H₉?·?·?·?O₄ of 2HDPM-H₂O complex are all shortened and strengthened in the S₁ state.

Investigations into the nature of halogen- and hydrogen-bonding interactions of some heteroaromatic rings with dichlorine monoxide

We have studied the structures, properties, and nature of halogen- and hydrogen-bonding interactions between some heteroaromatic rings (C₅H₅N, C₄H₄O, and C₄H₄S) with Cl₂O at the MP2/aug-cc-pVTZ level. We also considered the solvent effect on the halogen bonds and hydrogen bonds in the C₅H₅N-Cl₂O complexes and found that the solvent has a weakening effect on the π-type halogen bond and hydrogen bond but a prominent enhancing effect on σ-type halogen bond. The complexes have also been analyzed with symmetry adapted perturbation theory method (SAPT).     

A Study of the Interaction of Cr(III) Complexes and Their Selective Binding with B-DNA: A Molecular Modeling Approach

Abstract

Molecular modeling and energy minimisation calculations have been used to investigate the interaction of chromium(III) complexes in different ligand environments with various sequences of B-DNA. The complexes are [Cr(salen)(H₂O)₂]⁺; salen denotes 1, 2 bis-salicylideneaminoethane, [Cr(salprn)(H₂O)₂]⁺; salprn denotes 1, 3 bis- salicylideneamino-propane, [Cr(phen)₃]³⁺; phen denotes 1, 10 phenanthroline and [Cr(en)₃]³⁺; en denotes eth- ylenediamine. All the chromium(III) complexes are interacted with the minor groove and major groove of d(AT)₁₂, d(CGCGAATTCGCG)₂ and d(GC)₁₂ sequences of DNA. The binding energy and hydrogen bond parameters of DNA-Cr complex adduct in both the groove have been determined using molecular mechanics approach. The binding energy and formation of hydrogen bonds between chromium(III) complex and DNA has shown that all complexes of chromium(III) prefer minor groove interaction as the favourable binding mode.     

Proton relaxation studies in H 2 O-D 2 O mixtures. The binding of manganese (II) to bovine serum albumin

We have used the direct method for determining longitudinal relaxation times of water protons in H₂OD₂O mixtures. The relaxation time of pure water (2.7 sec) increases to 9.0 sec in 10% H₂O-90% D₂O mixture. This larger relaxation time enables us to use the direct method to accurately determine relaxation rate enhancements due to paramagnetic metal ions. The binding parameters for the interaction of manganese(II) to bovine serum albumin determined by this method are in excellent agreement with those determined earlier using pulsed methods.     

Effect of Na+ and K+ Ions on the Initial Crystallization Process of Lysozyme in the Presence of D2O and H2O

In the initial stage of the crystallization of egg-white lysozyme, monomeric lysozyme aggregated rapidly to form a nucleus in the presence of high salt concentrations. In the present studies, we examined the initial aggregation process of lysozyme (initial crystallization process of lysozyme) in D₂O/H₂O with sodium ions or potassium ions, and investigated the relationship between the surface hydrophobicity and the aggregation rate of lysozyme. The effect of sodium ions or potassium ions on the initial aggregation process of lysozyme in D₂O was clearly different from H₂O. The initial aggregation rate of lysozyme in H₂O was slower than in D₂O. In the case of H₂O, the initial aggregation rate was about the same in both ions. But in the case of D₂O, the initial aggregation rate was affected by the ion species and the value was lower in potassium ions than in sodium ions. These results suggest that the interaction between lysozyme molecules is stronger in D₂O than in H₂O. Furthermore, sodium ions have a stronger effect on the interaction than potassium ions in the case of D₂O. There was a good correlation among the initial aggregation rate, surface hydrophobicity, and ζ-potential of lysozyme. The hydrophobic interaction may be an important active force in the initial aggregation process of lysozyme.     

DFT studies of the adsorption and dissociation of H2O on the Al13 cluster: origins of this reactivity and the mechanism for H2 release

A theoretical study of the chemisorption and dissociation pathways of water on the Al₁₃ cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculations revealed that the H₂O molecule is easily adsorbed onto the Al₁₃ surface, forming adlayers. The dissociation of the first H₂O molecule from the bimolecular H₂O structure via the Grotthuss mechanism is the most kinetically favorable among the five potential pathways for O–H bond breaking. The elimination of H₂ in the reaction of an H₂O molecule with a hydrogen atom on the Al cluster via the Eley–Rideal mechanism has a lower activation barrier than the elimination of H₂ in the reaction of two adsorbed H atoms or the reaction of OH and H. Following the adsorption and dissociation of H₂O, the structure of Al₁₃ is distorted to varying degrees.

A vibrational spectroscopic study of the ice-melting-induced transition of 1,2-dibehenoyl-sn-glycero-3-phosphocholine

The phase transition of bilayers of 1,2-dibehenoyl-sn-glycero-3-phosphocholine (DBPC) induced by ice (H₂O and D₂O) melting has been investigated by infrared and Raman spectroscopy. Spectral changes observed at this transition are smaller at lower water content. These spectral changes are interpreted in terms of increased molecular mobility. Slightly different temperature dependencies are observed for various spectral parameters between samples dispersed in H₂O and D₂O.     

Kinetic Studies on the Initial Crystallization Process of Lysozyme in the Presence of D2O and H2O

In the initial stages of the crystallization of egg-white lysozyme, monomeric lysozyme aggregates rapidly and forms a nucleus in the presence of high salt concentrations. The formation process of the aggregates was examined to make clear the difference between the situations in heavy water and in water at the same sodium ion concentration. The aggregation in both cases was observed at unsaturated and/or saturated lysozyme concentrations. The turbidity at 350 nm of lysozyme increased remarkably within 60 min under each experimental condition and showed no appreciable changes over 60 min. The increase of turbidity in H₂O was much slower than in D₂O at the same salt concentration (3%). Lysozyme showed a critical concentration for nucleus formation whose value in H₂O was lower than in D₂O at 3% salt concentration. There are two different aggregation models, depending on the concentration of lysozyme. However, similar results were not obtained at 3% sodium ions in H₂O. The initial aggregation rate was also dependent on the concentrations of both lysozyme and NaCI. Therefore, the effect of lysozyme concentration on the aggregation process in H₂O may be smaller than in D₂O.     

DFT study of CO<Subscript>2</Subscript> and H<Subscript>2</Subscript>O co-adsorption on carbon models of coal surface

The moisture content of coal affects the adsorption capacity of CO₂ on the coal surface. Since the hydrogen bonds are formed between H₂O and oxygen functional group, the H₂O cluster more easily adsorbs on the coal micropore than CO₂ molecule. The coal micropores are occupied by H₂O molecules that cannot provide extra space for CO₂ adsorption, which may leads to the reduction of CO₂ adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO₂ and adsorbed H₂O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H₂O to CO₂ adsorption. This study reports some typical coal-H₂O···CO₂ complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H₂O molecule can more stably adsorb on the aromatic ring surface than CO₂ molecule, and the absolute values of local ESP maximum and minimum of H₂O cluster are greater than CO₂. AIM analysis shows a detailed interaction path and strength between atoms in CO₂ and H₂O, and RDG analysis shows that the interactions among CO₂, H₂O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO₂ and H₂O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H₂O can promote CO₂ adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO₂ adsorption capacity, the attractive interaction of adsorbed H₂O to CO₂ makes little contribution.     

Sites of action of D2O in intact and skinned crayfish muscle fibers

Summary The effect on tension development of replacing 90% of the H₂O of the bathing saline with D₂O was studied on intact single fibers, and on skinned fibers before and after the latter were treated so as to eliminate Ca-accumulation by the sarcoplasmic reticulum (SR). Excitation-contraction coupling (ECC) of intact fibers is not abolished, but is depressed by D₂O so that higher depolarizations are required to elicit a given tension. The reduction in tension at a given level of depolarization is not due to inhibition of the contractile system. The latter showed an enhanced Ca sensitivity; that is, skinned fibers respond to Ca concentrations that are 1–2 orders of magnitude smaller in D₂O than in H₂O saline. When bathed in D₂O saline, intact fibers or skinned fibers with functional SR can still accumulate and release Ca in sufficient quantities to allow repeated induction of maximum tensions. Relaxation is slowed in all three types of preparation, perhaps because of an increased affinity of troponin to Ca in D₂O salines.     

Effects of D2O on permeation and gating in the Ca2+-activated potassium channel fromChara

We studied the effects of H₂O/D₂O substitution on the permeation and gating of the large conductance Ca²⁺-activated K⁺ channels inChara gymnophylla droplet membrane using the patchclamp technique. The selectivity sequence of the channel was: K⁺>Rb⁺≫Li⁺, Na⁺, Cs⁺ and Cl⁻. The conductance of this channel in symmetric 100mm KCl was found to be 130 pS. The single channel conductance was decreased by 15% in D₂O as compared to H₂O. The blockade of channel conductance by cytosolic Ca²⁺ weakened in D₂O as a result of a decrease in zero voltage Ca²⁺ binding affinity by a factor of 1.4. Voltage-dependent channel gating was affected by D₂O primarily due to the change in Ca²⁺ binding to the channel during the activation step. The Hill coefficient for Ca²⁺ binding was 3 in D₂O and around 1 in H₂O. The values of the Ca²⁺ binding constant in the open channel conformation were 0.6 and 6 μm in H₂O and D₂O, respectively, while the binding in the closed conformation was much less affected by D₂O. The H₂O/D₂O substitution did not produce a significant change in the slope of channel voltage dependence but caused a shift as large as 60 mV with 1mm internal Ca²⁺.     

Conformational change of the triple-helical structure. III. Stabilizing forces in the triple helix

The analysis of thermal melting curves of (PPG)_n (n = 10, 12, 14, and 15) and (PPG)_n(APG)_m (PPG)_n (2n + m = 15; m = 1, 3, and 5) revealed that the enthalpy and entropy changes accompanying the transition from the random coil to the triple helix are ?2500 cal and ?6.3 e.u. per one mole of the tripeptide of the form of Pro-Pro-Gly, and ?3100 cal and ?11.2 e.u. per one mole of the tripeptide of the form of Ala-Pro-Gly. The thermal instability of the triple helix composed of Ala-Pro-Gly sequences, compared to the helix of Pro-Pro-Gly sequences, is due to the larger entropy change of Ala-Pro-Gly (?11.2 e.u.) compared to that of Pro-Pro-Gly (?6.3 e.u.), not from the difference in the enthalpy change. The difference in the enthalpy change between Pro-Pro-Gly and Ala-Pro-Gly arises from the hydrophobic bond between two pyrrolidine rings of proline residues formed in the triple helix. Since the enthalpy change for the formation of hydrophobic bonds is positive, it is also concluded that only one hydrogen bond is formed in a tripeptide unit, regardless of the amino acid sequence. The enthalpy change for the formation of this hydrogen bond is ?3100 cal/mol, and that of the hydrophobic bond between two pyrrolidine rings is +600 cal/mol.     

Ortho/para spin-isomers of H2O molecules as a factor responsible for formation of two structural motifs in water

According to the latest results obtained by small-angle X-ray scattering and X-ray spectroscopy, it was suggested that water on a nanometer scale represents a fluctuating mixture of clusters with tetrahedral structure and a subphase with partially broken hydrogen bonds, whereas the nuclear configuration of the H₂O molecule corresponds to single tetrahedral coordination. The basic reason of such structural partition is not clear until now. Here we show that it can be associated with existence of two nuclear H₂O spin isomers that have different probability to be in one or the other subphase. The para molecule can transfer an excess of its rotational energy to the environment, up to complete stopping of rotation because its rotational quantum number J = 0 in the basic state. This property is favorable for formation of clusters with closed H-bonds. Ortho molecules with odd-numbered J states lack this property and thus should be predominantly present in the locations with impaired bonds.     

Studies on the catalytic mechanism of H2-forming methylenetetrahydromethanopterin dehydrogenase: para-ortho H2 conversion rates in H2O and D2O

H₂–forming N ⁵,N ¹⁰ –methylenetetrahydromethanopterin dehydrogenase is a novel type of hydrogenase that contains neither nickel nor iron-sulfur clusters. Evidence has been presented that the reaction mechanism catalyzed by the enzyme is very similar to that of the formation of carbocations and H₂ from alkanes under superacidic conditions. We present here further results in support of this mechanism. It was found that the purified enzyme per se did not catalyze the conversion of para H₂ to ortho H₂, a reaction catalyzed by all other hydrogenases known to date. However, it catalyzed the conversion in the presence of the substrate N ⁵,N ¹⁰ –methenyltetrahydromethanopterin (CH≡H₄MPT⁺), indicating that for heterolytic cleavage of H₂ the enzyme-CH≡H₄MPT⁺ complex is required. In D₂O, the formation of HD and D₂ from H₂ rather than a para–ortho H₂ conversion was observed, indicating that after heterolytic cleavage of H₂ the dissociation of the proton from the enzyme-substrate complex is fast relative to the re-formation of free H₂.     

Stabilization of hydrolytically labile iron(II)–cysteine peptide thiolate complexes in aqueous triton X-100 micelle solution: Spectroscopic properties mimicking of reduced rubredoxin

The absorption, CD, and ¹H- and ¹⁹F-nmr spectroscopic features of Fe(II) complexes with a series of cysteine-containing oligopeptides were investigated in aqueous (H₂O or D₂O) 10% Triton X-100 micelle solution. The complexes with distal aromatic rings, [Fe(Z-cys-Pro-Leu-cys-Gly-X)₂]²⁻ (Z = benzyloxycarbonyl; X = NH-C₆H₄-p-F, NH-CH₂-CH₂-C₆H₄-p-F, and Phe-OMe), were found to be quite stable in such aqueous micelle solution. The coordination of cysteine–peptide ligands to the Fe(II) ion is revealed by isotropically shifted ¹H-nmr signals due to the Cys C_βH₂ protons occurring at 120 ∼ 250 ppm in a D₂O Triton X-100 micelle solution (10%) at 60°C that are very similar to those reported for native reduced rubredoxin. The high stability of these cysteine peptide–Fe(II) complexes in aqueous micellar system was explained by the combined contributions from NH—S hydrogen bonds and the effect of the proximity of aromatic groups. The existence of such NH—S hydrogen bonds and interactions between aromatic ring and sulfur atom was confirmed by ¹⁹F-nmr spectral and ¹⁹F spin–lattice relaxation times (T₁) measurements. © 1998 John Wiley & Sons, Inc. Biopoly 46: 1–10, 1998     

Chalcogen- and halogen-bonds involving SX<Subscript>2</Subscript> (X = F,Cl, and Br) with formaldehyde

The capacity of SX₂ (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl₂ (SBr₂) has two σ-holes upon extension of Cl (Br)?S bonds, and two σ-holes upon extension of S?Cl (Br) bonds. SF₂ contains only two σ-holes upon extension of the F?S bond. Consequently, SCl₂ and SBr₂ form chalcogen and halogen bonds with the electron donor H₂CO while SF₂ forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF₂:H₂CO complex. The S···O chalcogen bond between SF₂ and H₂CO is the strongest, while the strongest halogen bond is Br···O between SBr₂ and H₂CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X₂S···H₂CO···SX′₂ (X = F, Cl, Br, and X′ = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds.

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Graphical Abstract Molecular electrostatic potential and contour map of the Laplacian of the electron density in Cl₂S···H₂CO···SCl₂ complex