Nuclear Overhauser Experiments Research Articles

Separation of terbutaline enantiomers in capillary electrophoresis with neutral cyclodextrin-type chiral selectors and investigation of the structure of selector-selectand complexes using nuclear magnetic resonance spectroscopy.

The major goal of this study was to determine the affinity pattern of the terbutaline (TB) enantiomers toward α-, β-, γ-, and heptakis(2,3-di-O-acetyl)-β-cyclodextrins and using NMR spectroscopy for the understanding of the fine mechanisms of interaction between the cyclodextrins (CD) and TB enantiomers. It was shown once again that CE in combination with NMR spectroscopy represents a sensitive tool to study the affinity patterns and structure of CD complexes with chiral guests. Opposite affinity patterns of TB enantiomers toward native α- and β-CDs were associated with significant differences between the structure of the related complexes in solution. In particular, the complex between TB enantiomers and α-CD was of the external type, whereas an inclusion complex was formed between TB enantiomers and β-CD. One of the possible structures of the complex between TB and heptakis(2,3-di-O-acetyl)-β-CD (HDA-β-CD) was quite similar to that of TB and β-CD, although the chiral recognition pattern and enantioselectivity of TB complexation with these two CDs were very different.

NMR solution geometry of saccharides containing the 6-O-(α-D-glucopyranosyl)-α/β-D-glucopyranose (isomaltose) or 6-O-(α-D-galactopyranosyl)-α/β-D-glucopyranose (melibiose) core

The solution geometries of D-Glcp, Me-D-Glcp, 6-O-Me-D-Glcp, Me-6-O-Me-D-Glcp, D-Glcp-(α-1,6)-D-Glcp (isomaltose), D-Glcp-(α-1,6)-D-Glcp-(α-1,6)-D-Glcp (isomaltotriose), D-Galp-(α-1,6)-D-Glcp (melibiose), D-Galp-(α-1,6)-D-Glcp-(α-1,2)-D-Fruf (raffinose), and D-Galp-(α-1,6)-D-Galp-(α-1,6)-D-Glcp-(α-1,2)-D-Fruf (stachyose) in water are described by NMR spectroscopy, molecular dynamic simulations and quantum mechanical calculations. Overall, a change in anomeric configuration at the reducing end and/or anomeric substitution (methylation) changed the conformational space of the terminal CH2OH group significantly. Conformational analysis of the free monosaccharides matched literature results very well. Dihedral angle histograms weighted against published Karplus equations yielded excellent matches of experimental J-values in some cases but significant deviations in other. The anomeric hemiacetal configuration appeared to have a significant remote influence on the conformational space of the α-1,6-glycosidic linkage. Rigid glycosidic φ-conformations (g+) combined with mostly st-conformations for glycosidic ψ-angles from computations matched experimental nuclear Overhauser enhancements in all cases. While the investigated Glcp-α-1,6-Glcp linkages were nearly identical in φ/ψ-conformation, differences were apparent in the Galp-α-1,6-Galp linkage of stachyose. Of twenty-one crystal structures, a total of fourteen had ligand conformations corresponding to the most abundant or second-most abundant solution geometry determined in this study.

Investigation of the complexation between cyclodextrins and medetomidine enantiomers by capillary electrophoresis, NMR spectroscopy and molecular modeling

The migration order of the enantiomers of medetomidine in the presence of cyclodextrins studied by capillary electrophoresis in phosphate buffer, pH 2.5, depended on the cavity size and the substitution pattern of the cyclodextrins. Opposite migration order was observed in the presence of β-cyclodextrin (β-CD) and γ-cyclodextrin (γ-CD) as well as randomly sulfated β-CD (S-β-CD) and heptakis(6-O-sulfo)-β-CD (HS-β-CD). This could be rationalized by the fact that dexmedetomidine formed more stable complexes with β-CD and S-β-CD, while levomedetomidine interacted stronger with γ-CD and HS-β-CD. The structure of the complexes was derived from rotating frame nuclear Overhauser (ROESY) experiments for β-CD, γ-CD and HS-β-CD. In the case of the native CDs, the phenyl ring of medetomidine entered the cavity through the wider secondary rim of the CDs, whereas the protonated imidazole ring was positioned inside the CD cavity interacting with the sulfate groups of HS-β-CD. Furthermore, molecular dynamics calculations also suggested opposite affinities of the medetomidine enantiomers toward β-CD and γ-CD.

Separation of enilconazole enantiomers in capillary electrophoresis with cyclodextrin-type chiral selectors and investigation of structure of selector-selectand complexes by using nuclear magnetic resonance spectroscopy.

In the present study, the enantiomer migration order (EMO) of enilconazole in the presence of various cyclodextrins (CDs) was investigated by capillary electrophoresis (CE). Opposite EMO of enilconazole were observed when β-CD or the sulfated heptakis(2-O-methyl-3,6-di-O-sulfo)-β-CD (HMDS-β-CD) was used as the chiral selectors. Nuclear magnetic resonance (NMR) spectroscopy was used to study the mechanism of chiral recognition between enilconazole enantiomers and those two cyclodextrins. On the basis of rotating frame nuclear Overhauser (ROESY) experiments, the structure of an inclusion complex between enilconazole and β-CD was derived, in which (+)-enilconazole seemed to form a tighter complex than the (-)-enantiomer. This correlates well with the migration order of enilconazole enantiomers observed in CE. No evidence of complexation between enilconazole and HMDS-β-CD could be gathered due to lack of intermolecular nuclear Overhauser effect (NOE). Most likely the interaction between enilconazole and HMDS-β-CD leads to formation of a shallow external complex that is sufficient for separation of enantiomers in CE but cannot be evidenced based on ROESY experiment. Thus, in this particular case CE documents the presence of intermolecular interactions which are at least very difficult to be evidenced by other instrumental techniques.

Chiral Propargylic Cations as Intermediates in SN1-Type Reactions: Substitution Pattern, Nuclear Magnetic Resonance Studies, and Origin of the Diastereoselectivity

Nine propargylic acetates, bearing a stereogenic center (-C*HXR(2)) adjacent to the electrophilic carbon atom, were prepared and subjected to SN1-type substitution reactions with various silyl nucleophiles employing bismuth trifluoromethanesulfonate [Bi(OTf)3] as the Lewis acid. The diastereoselectivity of the reactions was high when the alkyl group R(2) was tertiary (tert-butyl), irrespective of the substituent X. Products were formed consistently with a diastereomeric ratio larger than 95:5 in favor of the anti-diastereoisomer. If the alkyl substitutent R(2) was secondary, the diastereoselectivity decreased to 80:20. The reaction was shown to proceed stereoconvergently, and the relative product configuration was elucidated. The reaction outcome is explained by invoking a chiral propargylic cation as an intermediate, which is preferentially attacked by the nucleophile from one of its two diastereotopic faces. Density functional theory (DFT) calculations suggest a preferred conformation in which the group R(2) is almost perpendicular to the plane defined by the three substituents at the cationic center, with the nucleophile approaching the electrophilic center opposite to R(2). Transition states calculated for the reaction of allyltrimethylsilane with two representative cations support this hypothesis. Tertiary propargylic cations with a stereogenic center (-C*HXR(2)) in the α position were generated by ionization of the respective alcohol precursors with FSO3H in SO2ClF at -80 °C. Nuclear magnetic resonance (NMR) spectra were obtained for five cations, and the chemical shifts could be unambiguously assigned. The preferred conformation of the cations as extracted from nuclear Overhauser experiments is in line with the preferred conformation responsible for the reaction of the secondary propargylic cations.

Separation of enantiomers of norephedrine by capillary electrophoresis using cyclodextrins as chiral selectors: Comparative CE and NMR studies

In this study, the enantiomer migration order (EMO) of norephedrine (NEP) in the presence of various CDs was investigated by CE. NMR and CE techniques were used to analyze the mechanism of the chiral recognition between NEP enantiomers and four CDs, i.e., native α-CD, β-CD, heptakis(2,3-di-O-acetyl-6-O-sulfo)-β-CD (HDAS-β-CD), and heptakis(2,3-di-O-methyl-6-O-sulfo)-β-CD (HDMS-β-CD). EMO was reversed in the presence of α-CD and β-CD, although only minor differences in the structures of the complexes formed between NEP and these CDs could be derived from rotating frame nuclear Overhauser experiments (ROESY). The complexes between the enantiomers of NEP and the sulfated CDs, HDMS-β-CD, and HDAS-β-CD, were substantially different. However, EMO of NEP was identical in the presence of these CDs. HDAS-β-CD proved to be the most suitable chiral selector for the CE enantioseparation of NEP.

Structure of Peptides on Metal Oxide Surfaces Probed by NMR

Peptides that bind inorganic surfaces and template the formation of nanometer-sized inorganic particles are of great interest for the self- or directed assembly of nanomaterials for sensors and diagnostic applications. These surface-recognizing peptides can be identified from combinatorial phage-display peptide libraries, but little experimental information is available for understanding the relationship between the peptide sequence, structure at the nanoparticle surface, and function. We have developed NMR methods to determine the structures of peptides bound to inorganic nanoparticles and report on the structure of three peptides bound to silica and titania surfaces. Samples were prepared under conditions leading to rapid peptide exchange at the surface such that solution-based nuclear Overhauser experiments can be used to determine the three-dimensional structure of the bound peptide. The binding motif is defined by a compact "C"-shaped structure for the first six amino acids in the 12-mer. The orientation of the peptide on the nanoparticle surface was determined by magnetization transfer from the nanoparticle surface to the nearby peptide protons. These methods can be applied to a wide variety of abiotic interfaces to provide an insight into the relationship between the primary sequence of peptides and their functionality at the interface.

Restriction Endonuclease Inhibitor IPI* of Bacteriophage T4: A Novel Structure for a Dedicated Target

Phage T4 protects its DNA from the two-gene-encoded gmrS/gmrD ( glucose- modified hydroxymethylcytosine restriction endonuclease) CT of pathogenic Escherichia coli, CT596, by injecting several hundred copies of the 76-amino-acid-residue nuclease inhibitor, IPI*, into the infected host. Here, the three-dimensional solution structure of mature IPI* is reported as determined by nuclear magnetic resonance techniques using 1290 experimental nuclear Overhauser effect and dipolar coupling constraints (∼ 17 constraints per residue). Close examination of this oblate-shaped protein structure reveals a novel fold consisting of two small β-sheets (β1: B1 and B2; β2: B3–B5) flanked at the N- and C-termini by α-helices (H1 and H2). Such a fold is very compact in shape and allows ejection of IPI* through the narrow 30-Å portal and tail tube apertures of the virion without unfolding. Structural and dynamic measurements identify an exposed hydrophobic knob that is a putative gmrS/gmrD-binding site. A single gene from the uropathogenic E. coli UT189, which codes for a gmrS/gmrD-like UT fusion enzyme (with ∼ 90% identity to the heterodimeric CT enzyme), has evolved IPI* inhibitor immunity. Analysis of the gmrS/gmrD restriction endonuclease enzyme family and its IPI* family phage antagonists reveals an evolutionary pathway that has elaborated a surprisingly diverse and specifically fitted set of coevolving attack and defense structures.

Triumphalone, a diketone from the volatile oil of the leaves of Melaleuca triumphalis, and its spontaneous conversion into isotriumphalone

The major component (35–65%) of the volatile oil obtained by steam distillation of the leaves of Melaleuca triumphalis has been identified as ( rel)-1β-pentyl-1α,6α-dihydroxy-3,3,5,5-tetramethylcyclohexa-2,4-dione (trivial name triumphalone). Relative stereochemistry was established by nuclear Overhauser experiments and X-ray studies on the 2-(3,5-dinitrobenzoic acid) derivative. The remainder of the oil was composed of mono- and sesquiterpene hydrocarbons and alcohols. On prolonged standing the presence of a rearrangement product of triumphalone was observed which was characterized as ( rel)-1β-pentyl-1α,3α-dihydroxy-4,4,6,6-tetramethylcyclohexa-2,5-dione (trivial name isotriumphalone), presumably arising from an acid catalyzed shift of the pentyl group from C-1 to C-2.

The Conformation of a Signal Peptide Bound by Escherichia coli Preprotein Translocase SecA

To understand the structural nature of signal sequence recognition by the preprotein translocase SecA, we have characterized the interactions of a signal peptide corresponding to a LamB signal sequence (modified to enhance aqueous solubility) with SecA by NMR methods. One-dimensional NMR studies showed that the signal peptide binds SecA with a moderately fast exchange rate (Kd approximately 10(-5) m). The line-broadening effects observed from one-dimensional and two-dimensional NMR spectra indicated that the binding mode does not equally immobilize all segments of this peptide. The positively charged arginine residues of the n-region and the hydrophobic residues of the h-region had less mobility than the polar residues of the c-region in the SecA-bound state, suggesting that this peptide has both electrostatic and hydrophobic interactions with the binding pocket of SecA. Transferred nuclear Overhauser experiments revealed that the h-region and part of the c-region of the signal peptide form an alpha-helical conformation upon binding to SecA. One side of the hydrophobic core of the helical h-region appeared to be more strongly bound in the binding pocket, whereas the extreme C terminus of the peptide was not intimately involved. These results argue that the positive charges at the n-region and the hydrophobic helical h-region are the selective features for recognition of signal sequences by SecA and that the signal peptide-binding site on SecA is not fully buried within its structure.

Backbone dynamics of human parathyroid hormone (1–34): Flexibility of the central region under different environmental conditions

The presence of a stable tertiary structure in the bioactive N-terminal portion of parathyroid hormone (PTH), a major hormone in the maintenance of extracellular calcium homeostasis, is still debated. In this work, 15N relaxation parameters of the 33 backbone amides of human PTH(1-34) were determined in phosphate-buffered saline solution (PBS) and in the presence of dodecylphosphocholine (DPC) micelles. The relaxation parameters were analyzed using both the model-free formalism (G. Lipari and A. Szabo, Journal of the American Chemical Society, 1982, Vol. 104, pp. 4546-4549) and the reduced spectral density functions approach (J.-F. Lefevre, K. T. Dayie, J. W. Peng, and G. Wagner, Biochemistry, 1996, Vol. 35, pp. 2674-2686). In PBS, the region around Gly12 possesses a high degree of flexibility and the C-terminal helix is less flexible than the N-terminal one. In the presence of DPC micelles, the mobility of the entire molecule is reduced, but the stability of the N-terminal helix increases relative to the C-terminal one. A point of relatively higher mobility at residue Gly12 is still present and a new site of local mobility at residues 16-17 is generated. These results justify the lack of experimental nuclear Overhauser effect (NOE) restraints with lack of tertiary structure and support the hypothesis that, in the absence of the receptor, the relative spatial orientation of the two N- and C-terminal helices is undefined. The flexibility in the midregion of PTH(1-34), maintained in the presence of the membrane-mimetic environment, may enable the correct relative disposition of the two helices, favoring a productive interaction with the receptor.

Mode of binding of camptothecins to double helix oligonucleotides.

We report an NMR study on the interaction of topotecan (Tpt) and other camptothecins (Cpts) with several double helix and single strand oligonucleotides. The results obtained by (31)P NMR spectroscopy, nuclear Overhauser experiments (NOE) and molecular dynamics (MD) simulations show that Cpt drugs do not intercalate into the double helix, as suggested by many authors. Phosphorus NMR spectra indicated that no deformation occurs at any level of the phosphodiester backbone, while 2D NOESY experiments allowed the detection of several contacts between the aromatic protons of Cpts and those of the double helix. Models of the drug/oligonucleotide complexes, built on the basis of NOE data, show that the drug is located at the end of the double helix, by stacking the A and B rings with the guanine or cytidine of the terminal CG base pairs, with a preference for the 3[prime or minute]-terminal end sites. Cpts interact with double strand, as well as with single strand oligomers, as can be seen from the NMR shift variation observed on the drug protons; but this shielding effect cannot be an evidence of intercalation, as it is largely due to external non-specific interactions of the positively charged drug with the negatively charged ionic surface of the oligonucleotide. The molecular weight of one of the complexes was obtained from the correlation time value. The conformational behaviour of the DNA fragment d(CGTACG)(2) was studied by MD simulations on a ns time scale in the presence of water molecules and Na(+) ions. Different models were examined and the deformations induced on the phosphodiester backbone by molecules that are known to intercalate, were monitored by MD simulations.

Nitration and Bromination of N-(Dimethylphenyl)Methane-Sulfonamides

The orientation of the products of nitrosation: nitration and bromination of the methanesulfonamides of the six isomeric dimethylanilines have been established by 1H NMR nuclear Overhauser experiments.

Control of disaccharide conformation by π-stacking

The conformations of a series of derivatives of the disaccharide α-L-fucopyranosyl-(1[Formula: see text]3)-2-acetamido-2-deoxy-D-glucopyranoside, part of the Lex determinant, were studied by molecular modelling using the MM3* forcefield and by 1H NMR spectroscopy. Unusually shielded O-benzyl protons were observed in the 1H NMR spectrum of phenyl 2,3,4-tri-O-benzyl-α-L-fucopyranosyl-(1[Formula: see text]3)-2-deoxy-2-phthalimido-1-thio-α-D-glucopyranoside and assigned to the 2-O-benzyl group. This observation was explained by a shift in the population of the conformational mixture present about the glycosidic linkage from the positive Ψ region in the unsubstituted disaccharide to the negative Ψ region induced by π-stacking between the phthalimide and the 2-O-benzyl phenyl ring. The experimental nuclear Overhauser enhancements confirm the accuracy of the calculations.Key words: disaccharide, conformation, π-stacking, Lex determinant, NOE measurements, MM3 calculations.

CLOUDS, a protocol for deriving a molecular proton density via NMR.

We demonstrate the feasibility of computing realistic spatial proton distributions for proteins in solution from experimental NMR nuclear Overhauser effect data only and with minimal assignments. The method, CLOUDS, relies on precise and abundant interproton distance restraints calculated via a relaxation matrix analysis of sets of experimental nuclear Overhauser effect spectroscopy crosspeaks. The MIDGE protocol was adapted for this purpose. A gas of unassigned, unconnected H atoms is condensed into a structured proton distribution (cloud) via a molecular dynamics simulated-annealing scheme in which the internuclear distances and van der Waals repulsive terms are the only active restraints. Proton densities are generated by combining a large number of such clouds, each computed from a different trajectory. After filtering by reference to the cloud closest to the mean, a minimal dispersion proton density (foc) is identified. The latter affords a quasi-continuous hydrogen-only probability distribution that conveys immediate information on the protein surface topology (grooves, protrusions, potential binding site cavities, etc.), directly related to the molecular structure. Feasibility of the method was tested on NMR data measured on two globular protein domains of low regular secondary structure content, the col 2 domain of human matrix metalloproteinase-2 and the kringle 2 domain of human plasminogen, of 60 and 83 amino acid residues, respectively.

Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water

Two molecular dynamics simulations of 5 ns each have been carried out for rat intestinal fatty acid binding protein, in apo-form and with bound palmitate. The fatty acid and a number of water molecules are encapsulated in a large interior cavity of the barrel-shaped protein. The simulations are compared to experimental data and analyzed in terms of root mean square deviations, atomic B-factors, secondary structure elements, hydrogen bond patterns, and distance constraints derived from nuclear Overhauser experiments. Excellent agreement is found between simulated and experimental solution structures of holo-FABP, but a number of differences are observed for the apo-form. The ligand in holo-FABP shows considerable displacement after about 1.5 ns and displays significant configurational entropy. A novel computational approach has been employed to identify internal water and to capture exchange pathways. Orifices in the portal and gap regions of the protein, discussed in the experimental literature, have been confirmed as major openings for solvent exchange between the internal cavity and bulk water. A third opening on the opposite side of the barrel experiences significant exchange but it does not provide a pathway for further passage to the central cavity. Internal water is characterized in terms of density distributions, interaction energies, mobility, protein contact times, and water molecule coordination. A number of differences are observed between the apo and holo-forms and related to differences in the protein structure. Solvent inside apo-FABP, for example, shows characteristics of a water droplet, while solvent in holo-FABP benefits from interactions with the ligand headgroup and slightly stronger interactions with protein residues.

Studies on the reactivity of some N‐aryl‐ and N‐heteroaryl‐N'‐alkylthioureas towards electrophilic reagents. Synthesis of new N‐pyridylthioureas and thiazolines maría

AbstractHere in we describe our findings about the behaviour of some N‐aryl‐ and N‐heteroaryl‐N'‐alkylthioureas towards electrophilic reagents. In acid medium, the treatment of thioureas bearing aryl groups with 4‐chloropyridine in 2‐propanol yielded N‐aryl‐N‐(4‐pyridyl)‐N'‐alk;ylthioureas and N‐aryl‐N'‐alkylureas, whereas the heteroarylthioureas tested under similar reaction conditions afforded N‐heteroaryl‐N'‐alkyl‐O‐(2‐propyl)isoureas. The reaction of N‐(5,6,7,8‐tetrahydronaphth‐1‐yl)‐ and N‐(2‐benzimidazolyl)‐N'‐butyl‐thiourea with propargyl bromide in acid medium led to the formation of 2‐butylimino‐3‐arylthiazolines, in a regioselective way. However, when this reaction was carried out in basic conditions the regioselectivity failed and a mixture of isomeric thiazolines was obtained. The Z‐ or E‐configuration of the imino group of the synthesized thiazolines was studied by molecular modelling and by selective nuclear Overhauser experiments in nuclear magnetic resonance.

Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations.

To evaluate the ability of molecular dynamics (MD) simulations using atomic force-fields to correctly predict stable folded conformations of a peptide in solution, we show results from MD simulations of the reversible folding of an octapeptide rich in alpha-aminoisobutyric acid (2-amino-2-methyl-propanoic acid, Aib) solvated in di-methyl-sulfoxide (DMSO). This solvent generally prevents the formation of secondary structure, whereas Aib-rich peptides show a high propensity to form secondary structural elements, in particular 3(10)- and alpha-helical structures. Aib is, moreover, achiral, so that Aib-rich peptides can form left- or right-handed helices depending on the overall composition of the peptide, the temperature, and the solvation conditions. This makes the system an interesting case to study the ensembles of peptide conformations as a function of temperature by MD simulation. Simulations involving the folding and unfolding of the peptide were performed starting from two initial structures, a right-handed alpha-helical structure and an extended structure, at three temperatures, 298 K, 340 K, and 380 K, and the results are compared with experimental nuclear magnetic resonance (NMR) data measured at 298 K and 340 K. The simulations generally reproduce the available experimental nuclear Overhauser effect (NOE) data, even when a wide range of conformations is sampled at each temperature. The importance of adequate statistical sampling in order to reliably interpret the experimental data is discussed.

Comparison between Roesy and 13C NMR Complexation Shifts in Deriving the Geometry of Inclusion Compounds: A Study on the Interaction between Hyodeoxycholic Acid and 2-Hydroxypropyl-β-Cyclodextrin

The formation and geometry of the hyodeoxycholic acid (HDCA)/2-hydroxypropyl-β-cyclodextrin (HPβCD) complex in methanol-d4 solution was determined through a rotating frame nuclear Overhauser (ROESY) experiment. The reported results confirmed those independently and previously obtained though the use of 13C complexation shifts in the same solvent. The 13C approach, which needs shorter experimental times and is currently used in the study of HPβCD/bile acid systems, was then substantiated.

A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G.

The structural and dynamical behavior of the 41-56 beta-hairpin from the protein G B1 domain (GB1) has been studied at different temperatures using molecular dynamics (MD) simulations in an aqueous environment. The purpose of these simulations is to establish the stability of this hairpin in view of its possible role as a nucleation site for protein folding. The conformation of the peptide in the crystallographic structure of the protein GB1 (native conformation) was lost in all simulations. The new equilibrium conformations are stable for several nanoseconds at 300K (>10 ns), 350 K (>6.5 ns), and even at 450 K (up to 2.5 ns). The new structures have very similar hairpin-like conformations with properties in agreement with available experimental nuclear Overhauser effect (NOE) data. The stability of the structure in the hydrophobic core region during the simulations is consistent with the experimental data and provides further evidence for the role played by hydrophobic interactions in hairpin structures. Essential dynamics analysis shows that the dynamics of the peptide at different temperatures spans basically the same essential subspace. The main equilibrium motions in this subspace involve large fluctuations of the residues in the turn and ends regions. Of the six interchain hydrogen bonds, the inner four remain stable during the simulations. The space spanned by the first two eigenvectors, as sampled at 450 K, includes almost all of the 47 different hairpin structures found in the database. Finally, analysis of the hydration of the 300 K average conformations shows that the hydration sites observed in the native conformation are still well hydrated in the equilibrium MD ensemble.