The spatial structure of the axially bound methionine in solution conformations of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c 551 by 1H NMR

A generally applicable method for the determination of the spatial structure of the heme iron-bound methionine in c-type ferrocytochromes at atomic resolution is presented. It relies primarily on measurements of nuclear Overhauser effects between the individual hydrogen atoms of the axial methionine, and between individual hydrogens of the methionine and the heme group. Four different methionine conformers, corresponding to the four possible stereospecific assignments for the methionine methylene proton resonances, are generated by a structural interpretation of the nuclear Overhauser effects with the use of an interactive computer graphics technique. A unique structure and unique stereospecific resonance assignments are then obtained by discriminating between these four conformers on the basis of van der Waals' constraints and heme ring current effects on the chemical shifts. The use of the method is illustrated with studies of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c 551. Comparison with the crystal structures shows close coincidence between the methionine conformations in solution and in single crystals of these proteins.Abbreviations NMR nuclear magnetic resonance - NOE nuclear Overhauser effect - TOE truncated driven nuclear Overhauser effect     

Insight into the molecular recognition of spermine by DNA quadruplexes from an NMR study of the association of spermine with the thrombin‐binding aptamer

The preferred residence sites and the conformation of DNA‐bound polyamines are central to understanding the regulatory roles of polyamines. To this end, we have used a series of selective ¹³C‐edited and selective total correlation spectroscopy‐edited one‐dimensional (1D) nuclear Overhauser effect spectroscopy NMR experiments to determine a number of intramolecular ¹H nuclear Overhauser effect (NOE) connectivities in ¹³C‐labelled spermine bound to the thrombin‐binding aptamer. The results provide evidence that the aptamer‐bound spermine adopts a conformation that optimizes electrostatic and hydrogen bond contacts with the aptamer backbone. The distance between the nitrogen atoms of the central aminobutyl is reduced by an increase in the population of gauche conformers at the C6–C7 bonds, which results in either a curved or S‐shaped spermine conformation. Molecular modelling contributes insight toward the mode of spermine binding of these spermine structures within the narrow grooves of DNA quadruplexes. In each case, the N5 ammonium group makes hydrogen bonds with two nearby phosphates across the narrow groove. Our results have implications for the understanding of chromatin structure and the rational design of quadruplex‐binding drugs. Copyright © 2013 John Wiley & Sons, Ltd.     

Mobility of fluorescent probe molecules in lipid bilayer vesicles as studied by steady-state and time-dependent nuclear Overhauser effect measurements in 1H-nuclear magnetic resonance spectroscopy

In order to elucidate the mobilities of the fluorophores of fluorescent 2- and 16-(9-anthroyloxy)palmitic acids (16-AP and 2-AP, respectively) in lipid bilayer vesicles, the steady-state and time-dependent nuclear Overhauser effects in ¹H-NMR spectroscopy, but not the fluorescence depolarization in fluorescence spectroscopy, have been measured. The steady-state nuclear Overhauser effect measurements showed an appreciable magnitude of negative nuclear Overhauser effects between the resonances due to the fluorophores of the two fluorescent probes and lipids. These results definitely mean that in lipid bilayers, the fluorophores (anthroyloxy ring) of the fluorescent probes experience other types of motions with much longer correlation times than those detected by the fluorescence depolarization measurements, since at the correlation time showed by the fluorescent method (1–2 · 10⁻⁹ s or less), no such transfer of the negative nuclear Overhauser effects is expected to occur. The correlation times of the fluorophores, as calculated from the cross-relaxation rates of the anthroyl ring protons of 16-AP and 2-AP, were 3.8 · 10⁻⁸ and 1.1 · 10⁻⁷ s, respectively. These values, respectively, compare favorably with those of the terminal methyl of acyl chains and the choline methyl carbons which were estimated by ¹³C T₂ relaxation times. Thus, it is concluded that the fluorophores of both 16-AP and 2-AP have a slow form of motion which moves with a similar time scale to those of lipids in addition to the faster one that causes fluorescence depolarization.     

Conformation of cyclobradykinin by nmr and distance geometry calculations

The conformation of the head-to-tail cyclic analogue of bradykinin in DMSO was investigated by nmr. Three sets of resonances were detected and fully assigned. These were attributed to the presence of three stable conformers, two of which were exchanging on the nmr time scale. A fourth, incomplete set of resonances was detected but not assigned. The three major conformers differ in the conformation at the three X-Pro bonds present. From nuclear Overhauser effect spectroscopy (NOESY) spectra, three sets of interproton distances were derived and used in NOE-restrained distance geometry calculations. The resulting structures were refined by energy minimization to yield families of structures. Conformer I is characterized by the presence of two type VIb β-turns between Arg¹ and Gly⁴ and between Phe⁵ and Phe⁸. The first β-turn is present also in conformer II, while an inverse γ-turn bridging Pro³ is the most pronounced structural feature of conformer III. © 1995 John Wiley & Sons, Inc.     

Conformational studies of nikkomycin X in aqueous solution

Nikkomycin X is a peptidyl-nucleoside antibiotic that inhibits chitin synthesis in fungi. Information on its conformation in aqueous solution was obtained from pH titration studies in which the nmr shifts of exchangeable and nonexchangeable protons were monitored. These studies and nuclear Overhauser effects support an unfolded or conformationally flexible structure for the antibiotic, and the syn and anti conformations of the nucleoside moiety were found to coexist. The conformation of the ribose ring was determined using a two-state model; a slight shift from type N to type S conformers occurred as the pH was raised from 1 to 6.     

Solution conformation of sialosylcerebroside (GM4) and its NeuAc(alpha 2----3)Gal beta sugar component

The solution conformations of GM4 ganglioside [NeuAc(alpha 2----3)Gal (beta 1----1)Cer] in (2H3C)2SO and its component disaccharide in 2H2O were investigated with the aid of 1H-nuclear magnetic resonance spectroscopy (nuclear Overhauser effect, analysis of coupling constants) and by energy-minimum calculations. The existence of three low-energy conformers obtained by theoretical calculations was supported by experimental findings in the case of GM4, whereas the disaccharide appears to exist as a mixture of two conformers.     

Ligand discovery using the inter-ligand Overhauser effect: horse liver alcohol dehydrogenase

Two dimensional nuclear Overhauser effect spectroscopy (NOESY) studies on horse liver alcohol dehydrogenase (LADH) in the presence of several ligands revealed unanticipated cross peaks arising from inter-ligand Overhasuer effects (ILOEs) connecting resonances of an inhibitor, m-methylbenzamide, and the reducing agent, cyanoborohydride, initially present to maintain NADH in the reduced state. The presence of NADH was not required to observe of these inter-ligand Overhauser effects. A model for the ternary complex was developed in which the methylbenzamide inhibitors bind to the hydrophobic pocket of the active site involved in benzyl alcohol binding, while the cyanoborohydride coordinates directly with Zn²⁺ at the active site. The observation of these effects supports the use of inter-ligand Overhauser effects for the identification of unanticipated ternary complexes that are of potential utility for the development of novel enzyme inhibitors.     

Nuclear magnetic resonance studies on oligo-deoxyribonucleotides containing thedam methylation site GATC. Adenine methylation of d(GGATCC) does not change the helix geometry

We have studied the conformation of two hexanucleotides d(GGATCC) and d(GGm⁶ATCC) using proton nuclear magnetic resonance. Nuclear Overhauser effect measurements show that d(GGATCC) assumes a normal right handed B helix. The single and double strand resonances are in fast exchange on a proton nuclear magnetic resonance time scale. For d(GGm⁶ATCC), up to the Tm separate resonances are observed for each state, indicating slow exchange, though above the Tm it becomes more rapid. The orientation of the adenosine methyl-amino group, preferentiallycis to N¹, hinders base pair formation.The connectivities of the resonances of the two states were established by saturation transfer experiments. At 0°C irradiation of the m⁶ A-T imino proton gives an nuclear Overhauser effect to AH² showing that base pairing is Watson-Crick. Intra and interresidue nuclear Overhauser effects starting from the 3′ terminus show that the helix is right handed and in the B-form.The results on the two oligomers demonstrate that adenosine methylation induces little or no change in the conformation of the helix, but reduces the Tm from 45° to 32°C and slows the opening and closing of the m₆A.T base pair by a factor of about 100.     

1H and 13c nmr analysis of lycorine and α-dihydrolycorine

-The ¹H and ¹³C NMR spectra of lycorine and its α-dihydro derivative have been studied. The employment of nuclear magnetic double resonance, nuclear Overhauser effect and acetylated derivatives, allows the assignment of all proton resonances. The assignments of the carbon shifts have been obtained by means of proton noise decoupled, single frequency off-resonance decoupled, single frequency selective decoupling, time dependence nuclear Overhauser effect and by comparison with reference compounds.     

A folded structure for the lac-repressor headpiece

A combination of selective ¹H nuclear Overhauser effects and other evidence indicates that the headpiece of the lac-repressor protein folds back on itself “head-to-tail” with residues in the N-terminal and C-terminal portions near to each other.     

The solution conformation of nicotinamide mononucleotide: a quantitative application of the nuclear Overhauser effect.

Torsion about the glycosidic linkage in nicotinamide mononucleotide has been investigated by quantitative application of the nuclear Overhauser effect. These measurements show that the syn (chi congruent to 20 degrees) and anti (chi congruent to 200 degrees) conformers of the title compound are isoenergetic, or nearly so, and interconverting rapidly. The syn/anti partition is not measurably affected by either changes in pH or temperature.     

13 C NMR Chemical shifts and carbon-proton coupling constants of some furocoumarins and furochromones

The ¹³C NMR spectra of a variety of furocoumarins, dihydrofurocoumarins and furochromones are reported. The signals were assigned using carbon-proton coupling constants, ring annullation shifts, nuclear Overhauser effect considerations and shift effects caused by monothioester formation. Substituent effects on ¹³C chemical shifts and carbon-proton coupling constants are discussed. Methoxyl induced shifts of 5- and 8-substituted furocoumarins are additive, but their effects cannot be transferred to the furochromone system.     

Structural and Conformational Studies on Deoxyguanosyl-3′,5′-Deoxyadenosine Monophosphate and Its Ethyl Phosphotriester Analogs - Left-Handed Dimers

Abstract

The mode of base-base stacking, the handedness and the sugar(dGpA)phosphate backbone conformation of deoxyguanosyl 3′-5′ deoxyadenosine and its diastereomeric ethyl phosphotriester analogs were studied by ¹H NMR, UV and CD spectroscopy. The results indicate the three dimers are left-handed, while the sugar phosphate backbone is comprised predominantly of C_2′-endo, gg (C_4′-C_5′) and g′g′ (C_5′-O) conformers. The two bases are extensively stacked and interact about 90° along the dyad axes. The extent of base overlap in dGpA is slightly greater than in either ethyl phosphotriester analog. The absolute configurations of the two ethyl phosphotriester diastereoisomers of dGpA can be assigned by one-dimensional and two-dimensional ¹H NMR nuclear Overhauser enhancement experiments.     

Assignment of the 1H-NMR resonances of the four rotamers of beta-casomorphin-5 in DMSO.

We report the complete assignment of the 1H-nmr spectrum of beta-casomorphin-5 in DMSO-d6 solution. With a combination of one-dimensional, double quantum filtered correlated spectroscopy, homonuclear Hartmann-Hahn, and rotating frame nuclear Overhauser enhancement spectroscopy (ROESY) spectra, we were able to differentiate the four conformers originating from two Xxx-Pro bonds present in the sequence. Exchange peaks in the ROESY spectra confirmed the presence of four interchanging conformational isomers. Based on integrations, the relative populations of the four species were estimated, while characteristic sequential nuclear Overhauser enhancements (NOEs) were used to determine the orientation of the Xxx-Pro bonds. This orientation was also shown to correlate with the chemical shift changes for the alpha protons of both the Xxx and Pro residues. Finally, interresidue NOEs indicate conformational preferences for the aromatic side chains, especially in the all-trans conformer.     

Aminoglycoside antibiotics bound to aminoglycoside-detoxifying enzymes and RNA adopt similar conformations

Conformations of ribostamycin and isepamicin, aminoglycoside antibiotics, bound to an aminoglycoside antibiotic, 3′-phosphotransferase, were determined by transferred nuclear Overhauser effect spectroscopy and molecular modeling. Two major conformers of enzyme-bound ribostamycin, a neomycin-group aminoglyeoside were observed. The 3′- and 5″-OH groups (reactive hydroxyl groups) in the conformers are placed in approximate locations. One of the conformers is similar to the structure of paromomycin bound to a 27-nucleotide piece of ribosomal RNA that represents the A-site of the small ribosomal subunit, where rings A and C are in an orthogonal arrangement. Isepamicin, a kanamycin-group aminoglycoside antibiotic, also showed two major enzyme-bound conformations. Both conformations were similar to those observed for bound isepamicin in the active site of an aminoglycoside(6′)-acetyl transferase-Ii. Conformations of other RNA-bound kanamycin-group aminoglycosides were also similar to the enzyme-bound conformations of isepamicin. These observations suggest that aminoglycosides may adopt similar conformations when bound to RNA and protein targets. This may have significant implications in the design of enzyme inhibitors and/or antibiotics.     

Structural and mode of action studies on bio-active molecules

The technique of nuclear Overhauser effect difference spectroscopy allows the determination, from¹H nuclear magnetic resonance spectra, of those protons in a structure which are near in space to a selected, irradiated proton. The experiment is extremely powerful in the determination of structure in solution, and is sufficiently precise often to give stereochemical detail. The method was used in determination of the structures of the antibiotics of the teicoplanin complex (members of the vancomycin group), and the principles are briefly illustrated. Additionally, nuclear magnetic resonance pulse sequences can be used to edit¹³C spectra (separate the spectrum into four spectra, containing C, CH, CH₂, and CH₃ carbons), and this technique also aided the structure elucidation of the teicoplanin complex. Finally, it is emphasised that nuclear Overhauser effect difference spectroscopy can be used to determine the molecular details of drug binding sites, and an example is given.     

Individual assignments of amide proton resonances in the proton NMR spectrum of the basic pancreatic trypsin inhibitor.

Studies of proton-proton nuclear Overhauser effects were used to obtain individual assignments of 17 amide proton resonances in the 360 MHz proton nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor. First, optimizing the conditions for obtaining selective nuclear Overhauser effects in the presence of spin diffusion in macromolecules is discussed. Truncated driven nuclear Overhauser experiments were used to assing the amide proton resonances of the beta-sheet in the inhibitor. It is suggested that these techniques could serve quite generally to obtain individual resonance assignments in beta-sheet secondary structures of proteins. Combination of nuclear Overhauser studies with spin decoupling further resulted in individual assignments of the gamma-methyl resonances of the two isoleucines and numerous Calpha and Cbeta protons.     

Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: Application to HU protein from Bacillus stearothermophilus

A computer-assisted procedure, based upon a branch of mathematics known as graph theory, has been developed to recognize secondary structure elements in proteins from their corresponding nuclear Overhauser effect spectroscopy (NOESY)-type spectra and to carry out their sequential assignment. In the method, NOE connectivity templates characteristic of regular secondary structures are identified in the spectra. Resonance assignment is then achieved by connecting these NOE patterns of secondary structure together, and thereby matching connected spin systems to specific parts of the primary sequence. The range of NOE-graph templates of secondary structure motifs, incorporating α-helices and β-strand motifs, has been examined for reliability and extent of secondary structure identification in a data base composed of the high resolution structures of 20 proteins. The analysis identified several robust NOE-graph templates and supports the implementation of an ordered search strategy. The method, known as SERENDIPITY, has been applied to the analysis of nuclear Overhauser effect data from a three-dimensional time-shared nuclear Overhauser effect spectroscopy (¹³C, ¹⁵N) heteronuclear single quantum correlation spectrum of the (α + β) type protein HU from Bacillus stearothermophilus. The arrangement of the elucidated elements of secondary structure is very similar to that of the x-ray and nmr structures of HU. In addition, our analysis revealed a pattern of interstrand nuclear Overhauser effect in the β-arm region (residues 53–76) of HU, which suggest irregularities, not reported in the x-ray structure, in both strands of the β-arm at Ala57 and Pro72, respectively. At these residues, both strands of the β-arm appear to flip inside out before continuing as a regular antiparallel β-sheet. © 1996 John Wiley & Sons, Inc.     

1H and15N resonance assignments and secondary structure of the human thioredoxin C62A,C69A,C73A mutant

Summary The complete assignment of¹H and¹⁵N backbone resonances and near-complete¹H side-chain resonance assignments have been obtained for the reduced form of a mutant of human thioredoxin (105 residues) in which the three non-active site cysteines have been substituted by alanines: C62A, C69A, C73A. The assignments were made primarily on the basis of three-dimensional.¹⁵N-separated nuclear Overhauser and Hartmann-Hahn spectroscopy, in conjunction with two-dimensional homonuclear and heteronuclear correlation experiments. Based on comparisons of short-range and interstrand nuclear Overhauser effects, patterns of amide exchange, and chemical-shift differences, the structure appears essentially unchanged from that of the previously determined solution structure of the native protein [Forman-Kay. J.D. et al. (1991)Biochemistry, 30, 2685–2698). An assay for thioredoxin shows that the C62A, C69A, C73A mutant retains activity. The assignment of the spectrum for this mutant of human thioredoxin constitutes the basis for future studies aimed at comparing the details of the active-site conformation in the reduced and oxidized forms of the protein.