A pulsed field gradient NMR diffusion investigation of enkephalin peptide-sodium dodecyl sulfate micelle association

NMR Studies on the Interaction of Anticancer Drug Doxorubicin with Membrane Mimetic SDS

In the formulation of efficient drug delivery systems, it is essential to unravel the structural and dynamical aspects of the drug's interaction with biological membranes. This has been done for the anticancer drug-membrane system comprising doxorubicin hydrochloride (DOX), a water-soluble anticancer drug, and the micellar sodium dodecyl sulfate (SDS), the latter serving as a useful mimic for membrane proteins. Using a multimodal NMR approach involving ¹H, ²H, and ¹³C as probe nuclei and through the determination of chemical shifts, spin-relaxation, nuclear Overhauser enhancements (NOE), and translational self-diffusion (SD), the binding characteristics of the DOX with SDS have been determined. The perturbation to ¹³C chemical shifts of SDS indicate the penetration of DOX into the SDS micelle, which is further revealed by ¹H-¹H NOESY and SD measurements. ²H spin-relaxation measurements and their analysis using a two-step model show DOX induced SDS micellar volume changes, which determine the correlation times involved in the DOX-SDS mobility.

Exploring Conformational Preferences of Leu-enkephalin Using the Conformational Search and Double-Hybrid DFT Energy Calculations

The conformational preferences of Leu-enkephalin (Leu-Enk) were explored by the conformational search and density functional theory (DFT) calculations. By a combination of low-energy conformers of each residue, the initial structures of the neutral Leu-Enk were generated and optimized using the ECEPP3 force field in the gas phase. These structures were reoptimized at the HF/3-21G(d) and M06-2X levels of theory with 6-31G(d) and 6-31+G(d) basis functions. We finally located the 139 structures with the relative energy <10 kcal mol-1 in the gas phase, from which the structures of the corresponding zwitterionic Leu-Enk were generated and reoptimized at the M06-2X/6-31+G(d) level of theory using the implicit solvation model based on density (SMD) in water. The conformational preferences of Leu-Enk were analyzed using Gibbs free energies corrected by single-point energies calculated at the double-hybrid DSD-PBEP86-D3BJ/def2-TZVP level of theory in the gas phase and in water. The neutral Leu-Enk dominantly adopted a folded structure in the gas phase stabilized by three H-bonds with a βII'-bend-like motif at the Gly3-Phe4 sequence and a close contact between the side chains of Phe4 and Leu5. The zwitterionic Leu-Enk exhibited a folded structure in water stabilized by three H-bonds with double β-bends such as a βII' bend at the Gly2-Gly3 sequence and a βI bend at the Gly3-Phe4 sequence. The calculated ensemble-averaged distance between CGly2 α and CLeu5 α of the zwitterionic Leu-Enk in water is consistent with the value estimated from the simulated annealing using the distance constraints derived from nuclear Overhauser effect spectroscopy (NOESY) spectra in water. Interestingly, the preferred conformations of the neutral and zwitterionic Leu-Enk are new folded structures not predicted by earlier computational studies. According to the refined model of the zwitterionic Leu-Enk bound to δ-opioid receptor (δOR), there were favorable interactions of the terminal charged groups of Leu-Enk with the side chains of charged residues of δOR as well as a favorable CAryl···H interaction of the Phe4 residue of Leu-Enk with Trp284 of δOR. Hence, these favorable interactions would induce the folded structure of the zwitterionic Leu-Enk with double β-bends isolated in water into the "bioactive conformation" like an extended structure when binding to δOR.

Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation

The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between ¹H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).

Nuclear Magnetic Resonance Investigation of the Effect of pH on Micelle Formation by the Amino Acid-Based Surfactant Undecyl l-Phenylalaninate

Micelle formation by the anionic amino acid-based surfactant undecyl l-phenylalaninate (und-Phe) was investigated as a function of pH in solutions containing either Na⁺, l-arginine, l-lysine, or l-ornithine counterions. In each mixture, the surfactant's critical micelle concentration (CMC) was the lowest at low pH and increased as solutions became more basic. Below pH 9, surfactant solutions containing l-arginine and l-lysine had lower CMC than the corresponding solutions with Na⁺ counterions. Nuclear magnetic resonance (NMR) diffusometry and dynamic light scattering studies revealed that und-Phe micelles with Na⁺ counterions had hydrodynamic radii of approximately 15 Å throughout the investigated pH range. Furthermore, l-arginine, l-lysine, and l-ornithine were found to bind most strongly to the micelles below pH 9 when the counterions were cationic. Above pH 9, the counterions became zwitterionic and dissociated from the micelle surface. In und-Phe/l-arginine solution, counterion dissociation was accompanied by a decrease in the hydrodynamic radius of the micelle. However, in experiments with l-lysine and l-ornithine, micelle radii remained the same at low pH when counterions were bound and at high pH when they were not. This result suggested that l-arginine is attached perpendicular to the micelle surface through its guanidinium functional group with the remainder of the molecule extending into solution. Contrastingly, l-lysine and l-ornithine likely bind parallel to the micelle surface with their two amine functional groups interacting with different surfactant monomers. This model was consistent with the results from two-dimensional ROESY (rotating frame Overhauser enhancement spectroscopy) NMR experiments. Two-dimensional NMR also showed that in und-Phe micelles, the aromatic rings on the phenylalanine headgroups were rotated toward the hydrocarbon core of micelle.

19 F NMR matrix-assisted DOSY: a versatile tool for differentiating fluorinated species in mixtures

NMR is the most versatile tool for the analysis of organic compounds and, in combination with Diffusion-Ordered Spectroscopy ('DOSY'), can give information on compounds in complex mixtures without the need for physical separation. In mixtures where the components' diffusion coefficients are nearly identical, for example because of similar sizes, Matrix-Assisted DOSY ('MAD') can help separate the signals of different constituents, resolving their spectra. Unfortunately, DOSY (including MAD) typically fails where signals overlap, as is common in ¹ H NMR. Using ¹⁹ F NMR avoids such problems, because the great sensitivity of the ¹⁹ F chemical shift to local environment leads to very well-dispersed spectra. Another advantage is the absence of any ¹⁹ F background signals from the matrices typically used, avoiding interference with the analyte signals. In this study, differentiation among fluorophenol and fluoroaniline isomers was evaluated using normal and reverse micelles-of sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB) and dioctyl sodium sulfosuccinate (AOT)-as matrices. These surfactants provide useful diffusion separation in these difficult mixtures, with all the solutes interacting with the matrices to different extents, in some cases leading to differences in diffusion coefficient of more than 30%. The best matrices for separating the signals of both acid and basic species were shown to be AOT and CTAB, which are useful over a wide range of surfactant concentration. Copyright © 2016 John Wiley & Sons, Ltd.

Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials

Label-free methods to obtain hydrodynamic size from diffusion measurements are desirable in environments that contain multiple macromolecular species at a high total concentration: one example is the crowded cellular environment. In complex, multi-species macromolecular environments - in this article, we feature aqueous systems involving polymers, surfactants and proteins - the link between dynamics and size is harder to unpack due to macromolecular crowding and confinement. In this review, we demonstrate that the pulsed-field gradient NMR technique, with its spectral separation of different chemical components, is ideal for studying the dynamics of the entire system simultaneously and without labelling, in a wide range of systems. The simultaneous measurement of the dynamics of multiple components allows for internal consistency checks and enables quantitative statements about the link between macromolecular dynamics, size, complex formation and crowding in soft materials.

Silica sol assisted chromatographic NMR spectroscopy for resolution of trans- and cis-isomers

Chromatographic NMR spectroscopy can separate the mixtures of species with significantly different molecular size, but generally fails for isomeric species. Herein, we reported the resolution of trans- and cis-isomers and their structural analogue, which are different in molecular shapes, but similar in mass, were greatly enhanced in the presence of silica sol. The mixtures of maleic acid, fumaric acid and succinic acid, and the mixtures of trans- and cis-1,2-cyclohexanedicarboxylic acids, were distinguished by virtue of their different degrees of interaction with silica sol. Moreover, we found mixed solvents could improve the spectral resolution of DOSY spectra of mixtures.

Matrix-assisted diffusion-ordered spectroscopy

Matrix-assisted diffusion-ordered NMR spectroscopy has the potential to transform mixture analysis by DOSY NMR.

Polydimethylsiloxane: a general matrix for high-performance chromatographic NMR spectroscopy

The detection and structural characterization of the components of a mixture is a challenging task. Therefore, the development of a facile and general method that enables both the separation and the structural characterization of the components is desired. Diffusion-ordered NMR spectroscopy (DOSY) with the aid of a matrix is a promising tool for this purpose. However, because the currently existing matrices only separate limited components, the application of the DOSY technique is restricted. Herein we introduce a new versatile matrix, poly(dimethylsiloxane), which can fully separate many mixtures of different structural types by liquid-state NMR spectroscopy. With poly(dimethylsiloxane), liquid-state chromatographic NMR spectroscopy could become a general approach for the structural elucidation of mixtures of compounds.

Evaluation of the separation performance of polyvinylpyrrolidone as a virtual stationary phase for chromatographic NMR

Polyvinylpyrrolidone (PVP) was used as a virtual stationary phase to separate p-xylene, benzyl alcohol, and p-methylphenol by the chromatographic NMR technique. The effects of concentration and weight-average molecular weight (Mw) of PVP, solvent viscosity, solvent polarity, and sample temperature on the resolution of these components were investigated. It was found that both higher PVP concentration and higher PVP Mw caused the increase of diffusion resolution for the three components. Moreover, the diffusion resolution did not change at viscosity-higher solvents. Moreover, the three components showed different resolution at different solvents. As temperature increased, the diffusion resolution between p-xylene and benzyl alcohol gradually increased, and the one between p-xylene and p-methylphenol slightly increased from 278 to 298 K and then decreased above 298 K. It was also found that the polarity of the analytes played an important role for the separation by affecting the diffusion coefficient.

Matrix-assisted diffusion-ordered spectroscopy: application of surfactant solutions to the resolution of isomer spectra

The component spectra of a mixture of isomers with nearly identical diffusion coefficients cannot normally be distinguished in a standard diffusion-ordered spectroscopy (DOSY) experiment but can often be easily resolved using matrix-assisted DOSY, in which diffusion behaviour is manipulated by the addition of a co-solute such as a surfactant. Relatively little is currently known about the conditions required for such a separation, for example, how the choice between normal and reverse micelles affects separation or how the isomer structures themselves affect the resolution. The aim of this study was to explore the application of sodium dodecyl sulfate (SDS) normal micelles in aqueous solution and sodium 1,4-bis(2-ethylhexyl)sulfosuccinate (AOT) aggregates in chloroform, at a range of concentrations, to the diffusion resolution of some simple model sets of isomers such as monomethoxyphenols and short chain alcohols. It is shown that SDS micelles offer better resolution where these isomers differ in the position of a hydroxyl group, whereas AOT aggregates are more effective for isomers differing in the position of a methyl group. For both the normal SDS micelles and the less well-defined AOT aggregates, differences in the resolution of the isomers can in part be rationalised in terms of differing degrees of hydrophobicity, amphiphilicity and steric effects.

Kinetics of binding and diffusivity of leucine-enkephalin in large unilamellar vesicle by pulsed-field-gradient 1H NMR in situ

The kinetics of binding, the diffusivity, and the binding amount of a neuropeptide, leucine-enkephalin (L-Enk) to lipid bilayer membranes are quantified by pulsed-field-gradient (PFG) ¹H NMR in situ. The peptide signal is analyzed by the solution of the Bloch equation with exchange terms in the presence of large unilamellar vesicles (LUVs) as confined, but fluid model cell membranes. Even in the case that the membrane-bound and the free states of L-Enk cannot be distinguished in the one-dimensional NMR spectrum, the PFG technique unveils the bound component of L-Enk after the preferential decay of the free component at the high field gradient. In 100-nm diameter LUVs consisting of egg phosphatidylcholine, the rate constants of the peptide binding and dissociation are 0.040 and 0.40 s⁻¹ at 303 K. This means that the lifetime of the peptide binding is of the order from second to ten-second. The diffusivity of the bound L-Enk is 5×10⁻¹²m²/s, almost 60 times as restricted as the movement of free L-Enk at 303K. One-tenth of 5mM L-Enk is bound to 40mM LUV. The binding free energy is calculated to be −2.9 kJ/mol, the magnitude close to the thermal fluctuation, 2.5 kJ/mol. The result demonstrates the potential of PFG ¹H NMR to quantify molecular dynamics of the peptide binding to membranes.

Matrix-assisted diffusion-ordered spectroscopy: mixture resolution by NMR using SDS micelles

Diffusion-ordered spectroscopy (DOSY) is a powerful technique for mixture analysis, but in its basic form it cannot separate the component spectra for species with very similar diffusion coefficients. It has been recently demonstrated that the component spectra of a mixture of isomers with nearly identical diffusion coefficients (the three dihydroxybenzenes) can be resolved using matrix-assisted DOSY (MAD), in which diffusion is perturbed by the addition of a co-solute such as a surfactant [R. Evans, S. Haiber, M. Nilsson, G. A. Morris, Anal. Chem. 2009, 81, 4548-4550]. However, little is known about the conditions required for such a separation, for example, the concentrations and concentration ratios of surfactant and solutes. The aim of this study was to explore the concentration range over which matrix-assisted DOSY using the surfactant SDS can achieve diffusion resolution of a simple model set of isomers, the monomethoxyphenols. The results show that the separation is remarkably robust with respect to both the concentrations and the concentration ratios of surfactant and solutes, supporting the idea that MAD may become a valuable tool for mixture analysis.

Structural basis for the association of the redox-sensitive target of rapamycin FATC domain with membrane-mimetic micelles

The target of rapamycin (TOR) is a conserved eukaryotic Ser/Thr kinase that regulates cellular growth in response to the nutrient and energy state. TOR signaling plays an important role in the development of diseases such as cancer, obesity, and diabetes and in different redox-sensitive processes (hypoxia, apoptosis, and aging). Because TOR has been detected at different cellular membranes and in the nucleus, its localization may influence the specific signaling readout. To better understand how TOR can associate with different membranes, the lipid-binding properties of the redox-sensitive yeast TOR1 FATC domain (y1fatc) have been characterized by solution NMR spectroscopy. Binding studies with different lipids indicate that y1fatc interacts specifically with a membrane-mimetic environment but appears not to recognize a specific lipid headgroup. In both, the structures of oxidized and reduced micelle-bound y1fatc, residues Ile-2456 to Trp-2470 of the lipid-binding motif form a hydrophobic bulb that has a rim of charged residues. The diffusion constants for both micelle-bound states are consistent with the rotational correlation times from the analysis of the (15)N relaxation data. Based on the K(d) values, the oxidized form (K(d) approximately 0.31 mm) binds dodecyl phosphocholine micelles slightly tighter than the reduced form (K(d) approximately 1.86 mM). Binding studies with y1fatc in which one or both tryptophans (Trp-2466 and Trp-2470) were replaced by alanine suggest that these residues are important for the exact positioning in the membrane and that the other aromatic (His-2462, Tyr-2463, and Phe-2469) and aliphatic residues (Ile-2456, Leu-2459, Ile-2464, and Pro-2468) in the lipid-binding motif contribute significantly to the affinity.

NMR characterization of 1,1'-binaphthyl-2,2'-diyl hydrogen phosphate binding to chiral molecular micelles

NMR spectroscopy was used to characterize the binding of the chiral compound 1,1'-binaphthyl-2,2'-diyl hydrogen phosphate (BNP) to five molecular micelles with chiral dipeptide headgroups. Molecular micelles have covalent linkages between the surfactant monomers and are used as chiral mobile phase modifiers in electrokinetic chromatography. Nuclear overhauser enhancement spectroscopy (NOESY) analyses of (S)-BNP:molecular micelle mixtures showed that in each solution the (S)-BNP interacted predominately with the N-terminal amino acid of the molecular micelle's dipeptide headgroup. NOESY spectra were also used to generate group binding maps for (S)-BNP:molecular micelle mixtures. In these maps, percentages are assigned to the (S)-BNP protons to represent the relative strengths of their interactions with a specified molecular micelle proton. All maps showed that (S)-BNP inserted into a previously reported chiral groove formed between the molecular micelle's dipeptide headgroup and hydrocarbon chain. In the resulting intermolecular complexes, the (S)-BNP protons nearest to the analyte phosphate group were found to point toward the N-terminal Halpha proton of the molecular micelle headgroup. Finally, pulsed field gradient NMR diffusion experiments were used to measure association constants for (R) and (S)-BNP binding to each molecular micelle. These K values were then used to calculate the differences in the enantiomers' free energies of binding, Delta(DeltaG). The NMR-derived Delta(DeltaG) values were found to scale linearly with electrokinetic chromatography (EKC) chiral selectivities from the literature.

Interaction of a tripeptide with cesium perfluorooctanoate micelles

The interaction of alanyl-phenylalanyl-alanine (Ala-Phe-Ala) with the micelles formed by cesium perfluorooctanoate (CsPFO) in water was studied in the isotropic phase by means of 1H NMR and by molecular dynamics (MD) simulations. Information on the location of the peptide was experimentally obtained from selective variations in Ala-Phe-Ala chemical shifts and from differential line broadening in the presence of the paramagnetic ion Mn2+. The peptide-micelle association constant was estimated analyzing the chemical shift variations of the most sensitive Ala-Phe-Ala resonances with the peptide concentration. MD simulations of Ala-Phe-Ala in the micellar environment confirmed the experimental observations, identifying the hydrogen bonding interactions of the different peptide moieties with the micelle, yielding a binding constant close to the experimental one. NOESY experiments suggest that the peptide in the micellar environment does not adopt a preferred conformation but is mainly unstructured. Details on the conformational behavior of the peptide in the micellar solution observed through MD were consistent with a different conformational equilibrium in the proximity of the micelle. Information on Ala-Phe-Ala dynamics was obtained from 1H T1 data and compared to MD simulation results on the overall tumbling motion.