Changes In Proton Chemical Shifts Research Articles

Coenzyme Q10-Loaded Fish Oil-Based Bigel System: Probing the Delivery Across Porcine Skin and Possible Interaction with Fish Oil Fatty Acids.

Coenzyme Q10 (CoQ10) is a vitamin-like oil-soluble molecule that has anti-oxidant and anti-ageing effects. To determine the most optimal CoQ10 delivery vehicle, CoQ10 was solubilised in both water and fish oil, and formulated into hydrogel, oleogel and bigel. Permeability of CoQ10 from each formulation across porcine ear skin was then evaluated. Furthermore, the effects of the omega-3 fatty eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids from fish oil on skin permeation were investigated by means of nuclear magnetic resonance (NMR) and computerised molecular modelling docking experiments. The highest drug permeation was achieved with the bigel formulation that proved to be the most effective vehicle in delivering CoQ10 across the skin membrane due to a combination of its adhesive, viscous and lipophilic properties. Furthermore, the interactions between CoQ10 and fatty acids revealed by NMR and molecular modelling experiments likely accounted for skin permeability of CoQ10. NMR data showed dose-dependent changes in proton chemical shifts in EPA and DHA. Molecular modelling revealed complex formation and large binding energies between fatty acids and CoQ10. This study advances the knowledge about bigels as drug delivery vehicles and highlights the use of NMR and molecular docking studies for the prediction of the influence of drug-excipient relationships at the molecular level.

EWGWS insert in Plasmodium falciparum ookinete surface enolase is involved in binding of PWWP containing peptides: Implications to mosquito midgut invasion by the parasite

There are multiple stages in the life cycle of Plasmodium that invade host cells. Molecular machinery involved is such host–pathogen interactions constitute excellent drug targets and/or vaccine candidates. A screen using a phage display library has previously demonstrated presence of enolase on the surface of the Plasmodium ookinete. Phage-displayed peptides that bound to the ookinete contained a conserved motif (PWWP) in their sequence. Here, direct binding of these peptides with recombinant Plasmodium falciparum enolase (rPfeno) was investigated. These peptides showed specific binding to rPfeno, but failed to bind to other enolases. Plasmodium spp enolases are distinct in having an insert of five amino acids (104EWGWS108) that is not found in host enolases. The possibility of this insert being the recognition motif for the PWWP containing peptides was examined, (i) by comparing the binding of the peptides with rPfeno and a deletion variant Δ-rPfeno lacking 104EWGWS108, (ii) by measuring the changes in proton chemical shifts of PWWP peptides on binding to different enolases and (iii) by inter-molecular docking experiment to locate the peptide binding site. Results from these studies showed that the pentapeptide insert of Pfeno indeed constitutes the binding site for the PWWP domain containing peptide ligands. Search for sequences homologous to phage displayed peptides among peritrophic matrix proteins resulted in identification of perlecan, laminin, peritrophin and spacran. The possibility of these PWWP domain-containing proteins in the peritrophic matrix of insect gut to interact with ookinete cell surface enolase and facilitate the invasion of mosquito midgut epithelium is discussed.

Probing Hydrogen Bonding in Cocrystals and Amorphous Dispersions Using 14N–1H HMQC Solid-State NMR

Cocrystals and amorphous solid dispersions have generated interest in the pharmaceutical industry as an alternative to more established solid delivery forms. The identification of intermolecular hydrogen bonding interactions in a nicotinamide palmitic acid cocrystal and a 50% w/w acetaminophen-polyvinylpyrrolidone solid dispersion are reported using advanced solid-state magic-angle spinning (MAS) NMR methods. The application of a novel (14)N-(1)H HMQC experiment, where coherence transfer is achieved via through-space couplings, is shown to identify specific hydrogen bonding motifs. Additionally, (1)H isotropic chemical shifts and (14)N electric field gradient (EFG) parameters, both accessible from (14)N-(1)H HMQC experiments, are shown to be sensitive to changes in hydrogen bonding geometry. Numerous indicators of molecular association are accessible from this experiment, including NH cross-peaks occurring from intermolecular hydrogen bonds and changes in proton chemical shifts or electric field gradient parameters. First-principles calculations using the GIPAW approach that yield accurate estimates of isotropic chemical shifts, and EFG parameters were used to assist in assignment. It is envisaged that (14)N-(1)H HMQC solid state NMR experiments could become a valuable screening technique of solid delivery forms in the pharmaceutical industry.

PSEUDO-DEWETTING BEHAVIOR OF LOW MOLECULAR WEIGHT POLY(ETHYLENE OXIDE) MELTS ON MICA SURFACE

Micellization of a series of newly synthesized dialkyl benzene sulfonates was studied using proton chemical shift changes, spin-lattice, and spin-spin relaxation NMR spectroscopy, and two-dimensional nuclear Overhauser enhancement spectroscopy (2D NOESY). The o-substituted chains are normal alkyl chains with varying lengths, and the m-substituted ones are branched alkyl chains. The results showed that the longer the o-substituted normal alkyl chain, protons of more methylene groups participated in the formation of the rigid surface layer of the hydrophobic micellar core. Consequently, the larger was the area per molecule adsorbed on the interface between oil and water at saturation. The branched m-substituted alkyl chains of the dialkyl benzene sulfonates were less tightly packed than the o-substituted normal alkyl chains in the hydrophobic micellar cores. The shorter the m-substituted branched alkyl chains, the looser they were packed in the hydrophobic micellar core. The relative arrangement of the surfactant molecules in the micelles was elucidated.

Microstructures of 2,5-dialkyl benzene sulfonate micelles studied using 1H NMR

Micellization of a series of newly synthesized dialkyl benzene sulfonates was studied using proton chemical shift changes, spin-lattice and spin-spin relaxation NMR spectroscopy, and two-dimensional nuclear Overhauser enhancement spectroscopy (2D NOESY). The o-substituted chains are normal alkyl chains with varying lengths, and the m-substituted ones are branched alkyl chains. The results showed that the longer the o-substituted normal alkyl chain, the more the methylene groups participated in the formation of the rigid surface layers of the hydrophobic micellar cores. Consequently, the larger was the area per molecule adsorbed on the interface between oil and water at saturation. The branched m-substituted alkyl chains of the dialkyl benzene sulfonates were less tightly packed than the o-substituted normal alkyl chains in the hydrophobic micellar cores. The shorter the m-substituted branched alkyl chains, the looser they were packed in the hydrophobic micellar cores. The relative arrangement of the surfactant molecules in the micelles was elucidated.

Saturated Hydrocarbon−Benzene Complexes: Theoretical Study of Cooperative CH/π Interactions

High-level ab initio calculations at the CCSD(T)/aug-cc-pVTZ//MP2/aug(d,p)-6-311G(d,p) level were employed to investigate the cooperative CH/pi effects between the pi face of benzene and several modeled saturated hydrocarbons, propane, isobutane, cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclopentane, cyclooctane, and bicyclo[2.2.2]octane. In all cases, multiple C-H groups (2-4) are found to interact with the pi face of benzene, with one C-H group pointing close to the center of the benzene ring. The geometries of these complexes are governed predominantly by electrostatic interaction between the interacting systems. The calculated interaction energies (10-14 kJ mol(-1)) are 2-3 times larger than that of the prototypical methane-benzene complex. The trends of geometries, interaction energies, binding properties, as well as electron-density topological properties were analyzed. The calculated interaction energies correlate well with the polarizabilities of the hydrocarbons. AIM analysis confirms the hydrogen-bonded nature of the CH/pi interactions. Significant changes in proton chemical shift and stretching frequency (blue shift) are predicted for the ring C-H bond in these complexes.

NMR studies on self‐complementary oligonucleotides conjugated with methylene blue

A carboxyl-functionalized methylene blue (MB) derivative was synthesized and covalently coupled to three CG-rich self-complementary 2'-deoxyoligonucleotides at their 5'-end. Thermodynamic and structural details about the interactions between the dye and oligonucleotide duplexes were investigated employing ultraviolet (UV) melting and (1)H nuclear magnetic resonance (NMR) experiments. In contrast to previous findings on MB binding, no specific intercalation or binding in the minor or major groove of the double helix was found in a 100 mM NaCl buffer. Rather, proton chemical shift changes in the conjugates provide ample evidence for weak dye-DNA interactions largely through external MB stacking on the terminal base pairs.

Complexation-induced chemical shifts—ab initio parameterization of transferable bond anisotropies

Complexation-induced changes in proton chemical shifts provide a potent tool for conformational analysis, being highly dependent on intermolecular orientation. An important contribution to these shifts arises from the molecular magnetisability anisotropy, or more specifically from the anisotropy of certain groups, such as aromatic rings and unsaturated bonds. While the influence of aromatic rings has been well characterised via the ring current effect, unsaturated bonds have received much less attention and prediction of complexation shifts is hampered by the lack of accurate anisotropy parameters for these bonds. We have therefore used ab initio calculations at the HF/aug-cc-pVDZ level to obtain bond anisotropies for C–H, N–H, CO, CC, CN, NN, CC, and CN. Fitting the anisotropies to bond magnetic dipoles (the McConnell equation) gives non-transferable values for C–H and N–H bonds. We have therefore expanded in terms of bond magnetic dipoles, quadrupoles, and octopoles for double and triple bonds only, obtaining highly accurate shielding surfaces in all cases. The transferable nature of the anisotropies is confirmed by comparing with shifts obtained in larger molecules containing unsaturated bonds.

Multiple structures for the 2-aminopurine-cytosine mispair.

The base pair formed between 2-aminopurine (2AP) and cytosine (C) is an intermediate in transition mutations generated by 2AP. To date, several structures have been proposed for the 2AP-C mispair, including those involving a rare tautomer, a protonated base pair, and a neutral wobble structure. In this paper, we describe a series of UV, fluorescence, and NMR studies which demonstrate that an equilibrium exists between the neutral wobble and the protonated Watson-Crick structures. The apparent pK value for the transition between the structures is 5.9-6.0. Formation of a Watson-Crick base pair is accomplished predominantly by protonation of the 2AP residue as indicated by UV spectral changes, fluorescence quenching, and changes in proton chemical shifts. Rapid transfer of the shared proton between the 2AP and cytosine residues is indicated by the rapid exchange of the cytosine amino protons of the protonated Watson-Crick configuration. The relative contribution of the neutral wobble and protonated Watson-Crick configurations to 2AP-induced transition mutations is discussed.

CD, 1H NMR and molecular modeling studies of the interaction of Ca2+ with substance P and Ala7-substance P in a non-polar solvent.

The biologically relevant conformation of substance P is likely to be dictated by the lipid milieu wherein the hormone would interact with its receptor. Assuming that specific constraints to the hormone structure may be imparted by its interaction with Ca2+ ions in the low dielectric lipid medium, the interaction of substance P and its inactive analog, Ala7-substance P, has been characterized in a lipid-mimetic solvent. Circular dichroism (CD) and NMR spectral methods were employed to study the conformation of the free and Ca2+-bound forms of the peptides and the conformational changes that occur on Ca2+ binding. The results show that both peptides assume a helical structure in the non-polar solvent used, a mixture of acetonitrile and trifluoroethanol. The N-terminal region is, however, less ordered in the analog peptide compared with the native hormone. Ca2+ addition causes significant conformational changes in both the peptides. However, while substance P binds two Ca2+ ions in a cooperative manner, Ala7-substance P binds only one Ca2+ ion with a relatively weaker affinity. Computations of the minimum-energy conformations of the free and Ca2+-bound peptides were performed using interproton distances derived from nuclear Overhauser enhancement spectra of the two peptides, as well as the information provided by changes in proton chemical shifts caused by Ca2+ addition. Taken together, the results of this study suggest that differences in the interaction of substance P and Ala7-substance P with Ca2+ in the non-polar milieu, which in turn leads to differences in their Ca2+-bound conformations, may be the basis for the differences in their biological potencies.

Heteronuclear relaxation study of the PH domain of β-spectrin: restriction of loop motions upon binding inositol trisphosphate

The structural dynamics of protein ligand binding sites is one factor determining the specificity towards related ligands. In this context, the spectrin PH domain, which binds to a number of phosphatidylinositol lipid head groups, was investigated with respect to the dynamics of the binding loops. The latter were found to be of intermediate flexibility on a picosecond to nanosecond time-scale in the free protein and become more rigid upon ligand binding. Significant 15N and proton chemical shift changes occur in the binding loops. The internal correlation time, determined from 15N heteronuclear relaxation data using the standard model-free approach, decreases upon ligand binding. For several residues a concomitant rise in the generalized order parameter is observed. This is interpreted as a dampening effect of the ligand on a slow loop motion, while a fast component is not affected. Molecular dynamics simulations were performed to further investigate this situation. In fact, two time-scales of loop motions in the free state are observed in a 9 ns molecular dynamics trajectory. Agreement with generalized order parameters obtained from the experiment improves when a subtrajectory is analyzed that excludes rare dihedral transitions.

Investigation of Hydrophobic Interactions in Colloidal and Biological Systems by Molecular Dynamics Simulations and NMR Spectroscopy

Interactions of hydrophobic molecular domains determine many of the functional properties of food proteins and colloidal food aggregates, such as emulsification, gelation, and foaming ability. A molecular basis for macromolecular interactions and conformational stability is established through investigation of simple model systems. Molecular modeling and dynamics simulations have been used to study the role of hydrophobic interaction forces in driving the formation of model amphiphile aggregate systems. An approximation to hydrophobic attraction between hydrocarbon tails was required to achieve stable, dynamic aggregate models for Aerosol-OT (AOT)/water/oil microemulsions, micelles of AOT in water, and a stacked AOT/para-chlorophenol gel in either CCl4 or benzene. One- and two-dimensional NMR spectroscopic methods have been used to characterize the pH and temperature dependent conformational changes in the model polypeptide poly(l-lysine). Changes in proton chemical shifts and line widths indicate that the backbone mobility of poly(l-lysine) is not greatly diminished by the coil−helix transition. ROESY and transverse-ROESY couplings, as well as T1 and T2 relaxation measurements, suggest that lysyl side chain mobility remains largely unrestricted upon formation of periodic secondary structure. Molecular dynamics simulations of poly(l-lysine) conformers substantiate the importance of hydrophobic side chain domains in stabilizing secondary structural features in aqueous solution.

Effect of methylation on the pyrimidine-pyrimidine stacking interaction studied by 1H NMR chemical shift

Mutually induced proton chemical shift changes were measured for the mixed solutions of pyrimidine and its methylated forms in deuterium oxide at 35°C. The chemical shift vs. concentration profiles were analyzed using a three-state decomposition model based on competitive self- and hetero-association dimer equilibria. The equilibrium constants show an increasing association tendency within the series pyrimidine-5-methyl-pyrimidine (0.23 ± 0.02 M −1) < pyrimidine-4,6-dimethyl-pyrimidine (0.32 ± 0.04 M −1) < 5-methyl-pyrimidine-4,6-dimethyl-pyrimidine (0.51 ± 0.04 M −1). The upfield dimer shifts suggest an offset stacked geometry for the structure of associations between the parent molecule of the pyrimidine nucleobases and its methylated derivatives in aqueous solution.

Helix formation in model peptides based on nucleolin TPAKK motifs

The structures formed by peptide models of the N-terminal domain of the nucleolar protein nucleolin were studied by CD and nmr. The sequences of the peptides are based on the putative nucleic acid binding sequence motif TPAKK. The peptides TP1 and TP2 have the sequence acetyl-G(ATPAKKAA)nG-amide, with n = 1 and 2, respectively. CD measurements indicate structural changes in both peptides when the lysine side chains are uncharged by increasing the pH or acetylation of the side-chain amines. When trifluoroethanol (TFE) is added, more extensive structural changes are observed, resembling helical structure based on nmr nuclear Overhauser effect (NOE) and C alpha proton chemical shift changes, and CD spectra. The structure formed in 0.5M NaClO4 as observed by nmr is similar to that when the lysine side chains are acetylated, due presumably to interactions of perchlorate ion with side-chain charges on lysines. The helical structure observed in TPAKK motifs may be stabilized via N-capping interactions involving threonine. The structures observed in TFE suggest that the Thr-Pro sequence initiates short helical segments in TPAKK motifs, and these helical structures might interact with nucleic acids, presumably via interactions between lysines and threonines of nucleolin.

Decreased interstrand H2-H1' distance in the GC-rich part of the duplex d(CCTCAAACTCC).d(GGAGTTTGAGG) in solution at low temperature: proton nuclear magnetic resonance investigation.

The non-self-complementary undecadeoxyribonucleotide duplex d(CCTCAAACTCC).d(GGAGTTTGAGG) was studied by one- and two-dimensional NMR methods in solution at low and room temperatures. The width of the minor groove of the duplex was determined on the basis of the NOE's between adenine's H2 protons and H1' protons from the complementary strand. In agreement with the previous reports, we found that the A3.T3 block forms a structure with a narrow minor groove at 5 degrees C, with the H2-H1' interstrand distance decreasing in the 5'-to-3' direction along the strand of adenines. Surprisingly, this distance is still short in the GC-rich part of the duplex downstream from the A-tract. This finding is interpreted in terms of pronounced buckle angles in the oligo(purine).oligo(pyrimidine) blocks, which diminish the H2-H1' interstrand distances. Both CA(n)- and AnC- junctions have distinct patterns of the proton chemical shifts, which suggests that both junctions may have some specific conformations in solution. Also, we report the temperature-driven changes in proton chemical shifts, which are significant in all parts of the duplex, except the 5'-ends of both strands. The structural interpretation for these changes is proposed, on the basis of the following notion: at low temperature the narrow minor groove is formed between the central A3.T3 trimer and the 3'-ends of both DNA strands, while the 5'-ends remain relatively exposed to the solvent.

Comparative 1H NMR chemical shift study on the stacking interaction of pyrimidine with purine and 6-methylpurine

The pyrimidine-purine and pyrimidine-6-methylpurine cross-interactions were compared by measuring the mutually induced concentration-dependent changes in proton chemical shifts in deuterium oxide at 35°C. The chemical shift vs. concentration profiles were analysed using a competitive dimer model. The equilibrium constants (0.41 ± 0.06 and 0.74 ± 0.05 l mol −1 for the pyrimidine-purine and pyrimidine-6-methylpurine hetero-associations, respectively) and the dimer shifts imply that the methylation of purine significantly influences the stacking interaction between the parent molecules of nucleic acid bases and thus their plane-to-plane association structure.

1H NMR chemical shift study on the stacking interaction between purine and 6‐methylpurine

AbstractMutually induced proton chemical shift changes were measured for purine‐6‐methylpurine solutions in deuterium oxide at 35° C. The chemical shift vs. concentration profiles were analysed using a three‐state decomposition model based on simultaneous, competitive dimer equilibria. The association parameters for purine‐6‐methylpurine hetero‐association provide some additional information about the effect of methylation on the stacking interaction between nucleic acid bases. The equilibrium constant (2.54 ± 0.17 and 2.57 ± 0.29 I mol−1, calculated from the experimental data on purine and 6‐methylpurine, respectively) suggests the dominant role of the methylated counterpart in the association. The upfield dimer shifts indicate that the methyl group perturbs the plane‐to‐plane or stacking‐like arrangement in the associated state.

NMR studies of the interaction of chromomycin A3 with small DNA duplexes. Binding to GC-containing sequences

The interaction of chromomycin A3 with the oligodeoxyribonucleotides 1, d(ATGCAT), 2, d(ATCGAT), 3, d(TATGCATA), and 4, d(ATAGCTAT), has been investigated by 1H and 31P NMR. In the presence of Mg2+, chromomycin binds strongly to the three GC-containing oligomers 1, 3, and 4 but not to the CG-containing oligomer 2. The proton chemical shift changes for 1 and 3 are similar, and these DNA duplexes appear to bind with a stoichiometry of 2 drugs:1 Mg2+:1 duplex. The same stoichiometry of 2 drugs:1 duplex is confirmed with 4; however, proton chemical shift changes differ. An overall C2 symmetry is exhibited by the drug complex with 1, 3, and 4. At a molar ratio of 2.0 (drugs:duplex), no free DNA proton NMR signals remain. Two-dimensional nuclear Overhauser exchange spectroscopy (NOESY) of the saturated chromomycin complex with 1 and 3 positions both chromomycinone hydroxyls and the E carbohydrates in the minor groove and provides evidence suggesting that the B carbohydrates lie on the major-groove side. This is supported by several dipolar coupling cross-peaks between the drug and the DNA duplex. Drug-induced conformational changes in duplex 1 are evaluated over a range of NOESY mixing times and found to possess some characteristics of both B-DNA and A-DNA, where the minor groove is wider and shallower. A widening of the minor groove is essential for the DNA duplex to accommodate two drug molecules. This current minor-groove model is a substantial revision of our earlier major-groove model [Keniry, M.A., Brown, S.C., Berman, E., & Shafer, R.H. (1987) Biochemistry 26, 1058-1067] and is in agreement with the model recently proposed by Gao and Patel [Gao, X., & Patel, D. J. (1989a) Biochemistry 28, 751-762].

Study of the self‐association of methylated pyrimidines in aqueous solutions by 1H NMR chemical shifts

AbstractThe self‐association of pyrimidine and its methylated derivatives was studied by measuring the concentration‐dependent changes in proton chemical shifts in deuterium oxide at 35°C. The data were analysed by a dimer model with two parameters. The equilibrium constants give an increasing tendency for self‐association within the series pyrimidine (0.091 ° 0.006 l mol−1) &lt; 5‐methylpyrimidine (0.165 ° 0.006 l mol−1) ≈ 4‐methylpyrimidine (0.183 ± 0.005 l mol−1) &lt; 4,6‐dimethylpyrimidine (0.410 ± 0.011 l mol−1), and the values of the dimer shifts suggest a stacking‐like arrangement for the associated molecules.

Binding of actinomycin D to [d(ATCGAT)]2: NMR evidence of multiple complexes

Actinomycin D (actD) binds to the oligonucleotide [d(ATCGAT)]2 with a hypochromatic and red-shifted visible absorbance band compared to free drug and a CD spectrum with double negative bands at 460 and 385 nm. These spectral features are similar to those of the actD-[d(ATGCAT)]2 complex, while actD-[d(AT)5]2 gives spectra similar to those of free drug. Upon dilution or raising the temperature, the spectral characteristics accompanying complex formation disappear in the actD-[(ATCGAT)]2 sample but remain in the actD-[d(ATGCAT)]2 complex under the same experimental conditions. These results suggest that (a) sequence-specific binding of actD occurs with [d(ATCGAT)]2 but not with [d(AT)5]2, (b) the binding is not as strong as with [d(ATGCAT)]2, and (c) actD binds [d(ATCGAT)]2 with the same mechanism as it binds [d(ATGCAT)]2, i.e., by intercalation. From NMR spectra of the actD-[d(ATCGAT)]2 complex, three types of signals can be detected below 20 degrees C, one major and two minor ones. At higher temperatures, exchange between the two minor ones becomes fast enough that only one type of minor signal was seen. Partial resonance assignments were made by using 2D nuclear Overhauser effect (NOE) and 2D homonuclear Hartmann-Hahn (HOHAHA) experiments. Proton chemical shift changes of the major complex are consistent with actD chromophore ring intercalation between hexamer base pairs. Data from NOE-detected dipolar interactions between actD and [d(ATCGAT)]2 protons were interpreted in terms of a major complex with the actD chromophore ring system intercalated at the CG position and minor complexes with the drug intercalated off center at the GA positions.(ABSTRACT TRUNCATED AT 250 WORDS)