Intramolecular versus intermolecular disulfide bonds in prion proteins

Prion protein (PrP) is the major component of the partially protease-resistant aggregate that accumulates in mammals with transmissible spongiform encephalopathies. The two cysteines of the scrapie form, PrP(Sc), were found to be in their oxidized (i.e. disulfide) form (Turk, E., Teplow, D. B., Hood, L. E., and Prusiner, S. B. (1988) Eur. J. Biochem. 176, 21-30); however, uncertainty remains as to whether the disulfide bonds are intra- or intermolecular. It is demonstrated here that the monomers of PrP(Sc) are not linked by intermolecular disulfide bonds. Furthermore, evidence is provided that PrP(Sc) can induce the conversion of the oxidized, disulfide-intact form of the monomeric cellular prion protein to its protease-resistant form without the temporary breakage and subsequent re-formation of the disulfide bonds in cell-free reactions.     

Proton translocation in hydrogen bonds with large proton polarizability formed between a Schiff base and phenols

OH…N ? O^?…H⁺N hydrogen bonds formed between N-all-transretinylidene butylamine (Schiff base) and phenols (1:1) are studied by IR spectroscopy. It is shown that both proton limiting structures of these hydrogen bonds have the same weight with Δ pK_a (50%) = (pK_a protonated Schiff base minus pK_a phenol) = 5.5. With the largely symmetrical systems, continua demonstrate that these hydrogen bonds show great proton polarizability. In the Schiff base + tyrosine system in a non-polar solvent the residence time of the proton at the tyrosine residue is much larger than that at the Schiff base. In CH₂CCl₂ these hydrogen bonds show, however, still proton polarizability, i.e., the position of the proton transfer equilibrium OH…N ? O^?…H⁺N is shifted to and fro as function of the nature of the environment of this hydrogen bond. Consequences regarding bacteriorhodopsin are discussed.     

Thermodynamics of proton transfer in carboxylic acid-retinal Schiff base hydrogen bonds with large proton polarizability

During the photocycle of bacteriorhodopsin (BR) the chromophore, a retinal Schiff base, is deprotonated. Simultaneously an asp residue is protonated. These results suggest that this deprotonation occurs via a Schiff base - asp hydrogen bond. Therefore, we studied carboxylic acid - retinal Schiff base model systems in CCl4 using IR spectroscopy. The IR spectra show that double minimum proton potentials are present in the OH ... N in equilibrium with O- ... HN+ H-bonds formed and that the proton can easily be shifted in these bonds by local electrical fields. The thermodynamic data of H-bond formation and proton transfer within these H-bonds are determined. On the basis of these data a hypothesis is developed with regard to the molecular mechanism of the deprotonation of the Schiff base of BR.     

Isotopic fractionation factors of intermolecular hydrogen bonds in water

Association constants for N---H⁺…⁻O hydrogen bond formation between substituted ammonium dications and phenolate ion were measured in water and deuterium oxide at 25°C and 2.0 ionic strength. In combination with isotopic fractionation factors for phenol and the conjugate diacid of 1,2-ethanediamine determined by ¹³C NMR spectroscopy, these yield isotopic fractionation factors for amine dication-phenolate ion hydrogen bonds in water: φ_AB = 0.69 for 1,2-propanediamine dication with a pK difference between donor and acceptor, ΔpK_a = −0.45, φ_AB = 0.88 for 1,2-ethanediamine dication (ΔpK_a = −2.1), and φ_AB = 1.1 for piperizine dication (ΔpK_a = −3.5). The hydrogen bond association constants follow Brønsted correlations α = 0.19 in water and α = 0.27 in deuterium oxide. The results are consistent with a double-minimum potential with a significant barrier for motion across the hydrogen bond.     

Intramolecular hydrogen bonds and conformation of the lincomycin molecule in organic solvents

IR spectra (1600-1800 and 3000-3650 cm-1) of lincomycin base solutions in inert (CCl4 and C2Cl4), proton acceptor (dioxane, dimethylsulfoxide and triethyl amine) and proton donor (CHCl3, CD3OD and D2O) solvents were studied. Analysis of the concentration and temperature changes in the spectra revealed that association in lincomycin in the inert solvents was due to intramolecular hydrogen linkage involving amide and hydroxyl groups. Disintegration of the associates after the solution dilution and temperature rise was accompanied by formation of intramolecular bonds stabilizing the stable conformation structure of the lincomycin molecule. The following hydrogen linkage in the conformation was realized: NH...N (band v NH...N at 3340 cm-1), OH...O involving the hydroxyl at C-7 and O atoms in the D-galactose ring (band v OH...O at 3548 cm-1), a chain of the hydrogen bonds OH...OH...OH in the lincomycin carbohydrate moiety (band v OH...O at 3593 cm-1 and v OH of the end hydroxyl group at 3625 cm-1). Bonds NH and C-O of the amide group were located in transconformation. Group C-O did not participate in the intramolecular hydrogen linkage.     

Probing the nature of hydrogen bonds in DNA base pairs

Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler–London, polarization, electron-transfer and dispersion-energy terms, where the Heitler–London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson–Crick adenine–thymine (AT), guanine–cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (−25.4 kcal mol⁻¹ at the MP2/6-31G** level) twice that of the AT (−12.4 kcal mol⁻¹) and H-AT (−12.8 kcal mol⁻¹) pairs, compared with three conventional N-H···O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the π-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that π-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology “resonance-assisted hydrogen bonding (RHAB)” may be replaced with “resonance-assisted binding” which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds. Figure Electron density difference (EDD) maps for the GC pair: a shows the polarization effect (isodensity 1.2×10⁻³ a.u.); b shows the charge transfer effect (isodensity 2×10⁻⁴ a.u.) Dedicated to Professor Paul von Ragué Schleyer on the occasion of his 75th birthday     

A novel chromone Schiff base as Zn2+ turn-on fluorescent chemosensor in a mixed solution

In this study, a novel fluorescent chemosensor 1 based on chromone-3-carboxaldehyde Schiff base was synthesized and featured through nuclear magnetic resonance (NMR) and mass spectra. Spectroscopic investigation indicated that the fluorescent sensor showed high selectivity toward Zn²⁺ over other metal ions and that the detection limit of 1 could reach 10⁻⁷ M. These indicated that 1 acted as a highly selective and sensitive fluorescence chemosensor for Zn²⁺.     

Schiff base copper(II) chelate as a tool for intermolecular cross-linking and immobilization of protein

A new method for intermolecular cross-linking or bridging of protein has been proposed. The method is based on the spontaneous chelate formation process involving three components, salicylaldehyde, alpha-amino acid residue and copper(II). Reliability of the process as a tool for protein cross-linking was evaluated by chromatographic procedures. Behavior of salicylaldehyde in a column packed with Sepharose attached alpha-amino acid residue showed that salicylaldehyde was bound tightly to the gel in the presence of copper(II) ion and was eluted by the addition of EDTA. The association was shown strong enough to be applied for the purpose of cross-linking of proteins. It was also proved that BSA salicylaldehyde conjugate was immobilized specifically to the column, and the process was reversed by the addition of EDTA as well. The method is proposed to be useful not only for immobilization of enzyme but also for cross-linking of proteins since the method is free from unexpected random coupling products which are unavoidable with bifunctional cross-linking reagents.     

Vibrational fluctuations of hydrogen bonds in a DNA double helix with nonuniform base pairs.

The Green's function technique is applied to a study of breathing modes in a DNA double helix which contains a region of different base pairs from the rest of the double helix. The calculation is performed on a G-C helix in the B conformation with four consecutive base pairs replaced by A-T. The average stretch in hydrogen bonds is found amplified around the A-T base pair region compared with that of poly(dG)-poly(dC). This is likely related to the A-T regions lower stability against hydrogen bond melting. The A-T region may be considered to be the initiation site for melting in such a helix.     

Evidence for a bound water molecule next to the retinal Schiff base in bacteriorhodopsin and rhodopsin: a resonance Raman study of the Schiff base hydrogen/deuterium exchange.

The retinal chromophores of both rhodopsin and bacteriorhodopsin are bound to their apoproteins via a protonated Schiff base. We have employed continuous-flow resonance Raman experiments on both pigments to determine that the exchange of a deuteron on the Schiff base with a proton is very fast, with half-times of 6.9 +/- 0.9 and 1.3 +/- 0.3 ms for rhodopsin and bacteriorhodopsin, respectively. When these results are analyzed using standard hydrogen-deuteron exchange mechanisms, i.e., acid-, base-, or water-catalyzed schemes, it is found that none of these can explain the experimental results. Because the exchange rates are found to be independent of pH, the deuterium-hydrogen exchange can not be hydroxyl (or acid-)-catalyzed. Moreover, the deuterium-hydrogen exchange of the retinal Schiff base cannot be catalyzed by water acting as a base because in that case the estimated exchange rate is predicted to be orders of magnitude slower than that observed. The relatively slow calculated exchange rates are essentially due to the high pKa values of the Schiff base in both rhodopsin (pKa > 17) and bacteriorhodopsin (pKa approximately 13.5). We have also measured the deuterium-hydrogen exchange of a protonated Schiff base model compound in aqueous solution. Its exchange characteristics, in contrast to the Schiff bases of the pigments, is pH-dependent and consistent with the standard base-catalyzed schemes. Remarkably, the water-catalyzed exchange, which has a half-time of 16 +/- 2 ms and which dominates at pH 3.0 and below, is slower than the exchange rate of the Schiff base in rhodopsin and bacteriorhodopsin.(ABSTRACT TRUNCATED AT 250 WORDS)     

Cooperativity of intermolecular hydrogen bonds in microsolvated DMSO and DMF clusters: a DFT,AIM, and NCI analysis

Density functional theory (DFT) calculations are performed to study the hydrogen-bonding in the DMSO-water and DMF-water complexes. Quantitative molecular electrostatic potential (MESP) and atoms-in-molecules (AIM) analysis are applied to quantify the relative complexation of DMSO and DMF with water molecules. The interaction energy of DMSO with water molecules was higher than in DMF-water complexes. The existence of cooperativity effect helps in the strong complex formation. A linear dependence was observed between the hydrogen bond energies E_HB, and the total electron densities in the BCP’s of microsolvated complexes which supports the existence of cooperativity effect for the complexation process. Due to the stronger DMSO/DMF and water interaction, the water molecules in the formed complexes have a different structure than the isolated water clusters. NCI analysis shows that the steric area is more pronounced in DMF-water complex than the DMSO-water complex which accounts for the low stability of DMF-water complexes compared to the DMSO-water complex.

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Graphical abstract NCI analysis shows that the steric area is more pronounced in DMF-water complex than the DMSO-water complex which accounts for the low stability of DMF-water complexes compared to the DMSO-water complex.

     

Similarities between intra- and intermolecular hydrogen bonds in RNA kissing complexes found by means of cross-correlated relaxation

The bond lengths and dynamics of intra- and intermolecular hydrogen bonds in an RNA kissing complex have been characterized by determining the NMR relaxation rates of various double- and triple-quantum coherences that involve an imino proton and two neighboring nitrogen-15 nuclei belonging to opposite bases. New experiments allow one to determine the chemical shift anisotropy of the imino protons. The bond lengths derived from dipolar relaxation and the lack of modulations of the nitrogen chemical shifts indicate that the intermolecular hydrogen bonds which hold the kissing complex together are very similar to the intramolecular hydrogen bonds in the double-stranded stem of the RNA.     

Role of the retinal hydrogen bond network in rhodopsin Schiff base stability and hydrolysis

Little is known about the molecular mechanism of Schiff base hydrolysis in rhodopsin. We report here our investigation into this process focusing on the role of amino acids involved in a hydrogen bond network around the retinal Schiff base. We find conservative mutations in this network (T94I, E113Q, S186A, E181Q, Y192F, and Y268F) increase the activation energy (E(a)) and abolish the concave Arrhenius plot normally seen for Schiff base hydrolysis in dark state rhodopsin. Interestingly, two mutants (T94I and E113Q) show dramatically faster rates of Schiff base hydrolysis in dark state rhodopsin, yet slower hydrolysis rates in the active MII form. We find deuterium affects the hydrolysis process in wild-type rhodopsin, exhibiting a specific isotope effect of approximately 2.5, and proton inventory studies indicate that multiple proton transfer events occur during the process of Schiff base hydrolysis for both dark state and MII forms. Taken together, our study demonstrates the importance of the retinal hydrogen bond network both in maintaining Schiff base integrity in dark state rhodopsin, as well as in catalyzing the hydrolysis and release of retinal from the MII form. Finally, we note that the dramatic alteration of Schiff base stability caused by mutation T94I may play a causative role in congenital night blindness as has been suggested by the Oprian and Garriga laboratories.     

Probing the role of hydrogen bonds in the stability of base pairs in double-helical DNA

Aromatic stacking and hydrogen bonding between nucleobases are two of the key interactions responsible for stabilization of DNA double-helical structures. The present work aims at defining the specific contributions of these interactions to the stability of individual base pairs in DNA. The two DNA double helices investigated are formed, respectively, by the palindromic base sequences 5'-dCCAACGTTGG-3' and 5'-dCGCAGATCTGCG-3'. The strength of the N==H...N inter-base hydrogen bond in each base pair is characterized from the measurement of the protium-deuterium fractionation factor of the corresponding imino proton using NMR spectroscopy. The structural stability of each base pair is evaluated from the exchange rate of the imino proton, measured by NMR. The results reveal that the fractionation factors of the imino protons in the two DNA double helices investigated fall within a narrow range of values, between 0.92 and 1.0. In contrast, the free energies of structural stabilization for individual base pairs span 3.5 kcal/mol, from 5.2 to 8.7 kcal/mol (at 15 degrees C). These findings indicate that, in the two DNA double helices investigated, the strength of N==H...N inter-base hydrogen bonds does not change significantly depending on the nature or the sequence context of the base pair. Hence, the variations in structural stability detected by proton exchange do not involve changes in the strength of inter-base hydrogen bonds. Instead, the results suggest that the energetic identity of a base pair is determined by the number of inter-base hydrogen bonds, and by the stacking interactions with neighboring base pairs.     

Intramolecular acyl migration and enzymatic hydrolysis of a novel monoacylated ascorbic acid derivative, 6-O-dodecanoyl-2-O-α-d-glucopyranosyl-l-ascorbic acid

A stable ascorbic acid derivative, 2-O-α-d-glucopyranosyl-l-ascorbic acid (AA-2G), exhibits vitamin C activity in vitro and in vivo after enzymatic hydrolysis to ascorbic acid. AA-2G has been approved by the Japanese Government as a quasi-drug principal ingredient in skin care and as a food additive. In order to achieve efficient action as an ascorbic acid source, a pro-vitamin C agent, on a variety of cells or tissues, we have synthesized a series of monoacyl AA-2G derivatives. Our previous studies indicate that a series of the derivatives is a readily available source of AA activity in vitro and in vivo, and suggested that intramolecular acyl migration of the derivatives might have occurred in a neutral aqueous solution. In this study, intramolecular acyl migration and enzymatic hydrolysis of a monoacyl AA-2G derivative, 6-O-dodecanoyl-2-O-α-d-glucopyranosyl-l-ascorbic acid (6-sDode-AA-2G), were investigated. 6-sDode-AA-2G underwent an intramolecular acyl migration to yield ca. 10% of an isomer in neutral aqueous solutions, and the acyl-migrated isomer was isolated and characterized as 5-O-dodecanoyl-2-O-α-d-glucopyranosyl-l-ascorbic acid (5-sDode-AA-2G). In some tissue homogenates from guinea pigs as well as in neutral aqueous solutions, 6-sDode-AA-2G underwent partial acyl migration to give 5-sDode-AA-2G. 6-sDode-AA-2G and the resulting 5-sDode-AA-2G were predominantly hydrolyzed with esterase to AA-2G and then with α-glucosidase to ascorbic acid in the tissue homogenates. The results will provide a further basis for its use as an ingredient in skin care, as an effective pharmacological agent and as a promising food additive.     

Synthesis, antiproliferative activity and genotoxicity of novel anthracene-containing aminophosphonates and a new anthracene-derived Schiff base

A new Schiff base, 9-anthrylidene-furfurylamine and three novel anthracene-containing α-aminophosphonates, [N-methyl(dimethoxyphosphonyl)-1-(9-anthryl)]-p-toluidine, [N-methyl(diethoxyphosphonyl)-1-(9-anthryl)]-p-toluidine and [N-methyl(diethoxyphosphonyl)-1-(9-anthryl)]furfurylamine were synthesized. The compounds have been characterized by elemental analysis, TLC, IR, NMR and fluorescent spectra. The aminophosphonates and their synthetic precursors were tested for in vitro antitumor activity on a panel of seven human epithelial cancer cell lines. Safety testing was performed both in vitro (3T3 NRU test) and in vivo on ICR mice for genotoxicity and antiproliferative activity. 9-Anthrylidene-furfurylamine and [N-methyl(diethoxyphosphonyl)-1-(9-anthryl)]furfurylamine were most potent cytotoxic agents towards colon carcinoma cell line HT-29. The latter compound exhibited also antiproliferative activity to HBL-100, MDA-MB-231 and 647-V cells. The aminophosphonate [N-methyl(dimethoxyphosphonyl)-1-(9-anthryl)]-p-toluidine and its synthetic precursor 9-anthrylidene-p-toluidine were found to be cytotoxic to HBL-100 and HT-29 tumor cell lines, respectively. Moderate genotoxic and antiproliferative activity in vivo and low toxicity to Balb/c 3T3 (clone 31) mouse embryo cells were observed for all tested compounds. The subcellular distribution of two tested compounds in a tumor cell culture system was also studied.     

Unusual dinuclear copper(II) and nickel(II) complexes of a novel Schiff base deriving from 2-aminoethanol

It is generally accepted that copper(II) complexes involving 2-aminoethanol or a Schiff base deriving from this aminoalcohol display a tetranuclear structure with a Cu₄O₄ ‘cubane’ core. Using a Schiff base obtained by reacting 2′-aminoacetophenone with 2-aminoethanol, we have prepared copper(II) and nickel(II) complexes whose properties are fully consistent with a dinuclear structure. The copper complex is characterized by a low antiferromagnetic interaction.