scholarly journals Conformation and dynamics of the deoxyribose rings of a (nogalamycin)2–d (5′-GCATGC)2 complex studied in solution by 1H-n.m.r. spectroscopy

1990 ◽  
Vol 269 (2) ◽  
pp. 341-346 ◽  
Author(s):  
M S Searle ◽  
L P Wakelin
Keyword(s):  
Base Pair ◽  
Dynamic Equilibrium ◽  
Graphical Analysis ◽  
Correlation Spectroscopy ◽  
Coupling Constants ◽  
Double Quantum ◽  
Two Dimensional ◽  
Coherence Transfer ◽  
Data Set ◽  
Base Pair Stacking

The conformation and dynamics of the deoxyribose rings of a (nogalamycin)2-d(5′-GCATGC)2 complex have been determined from an analysis of 1H-1H vicinal coupling constants and sums of coupling constants (J1′-2′,J1′-2″,epsilon 1′, epsilon 2′ and epsilon 2″) measured from one-dimensional n.m.r. spectra and from H-1′-H-2′ and H-1′-H-2″ cross-peaks in high-resolution phase-sensitive two-dimensional correlation spectroscopy (COSY) and double-quantum-filtered correlation spectroscopy (DQF-COSY) experiments. The value of J3′-4′ has also been estimated from the magnitude of H-3′-H-4′ cross-peaks in DQF-COSY spectra and H-1′-H-4′ coherence transfer cross-peaks in two-dimensional homonuclear Hartman-Hahn spectroscopy (HOHAHA) spectra. The data were analysed, in terms of a dynamic equilibrium between North (C-3′-endo) and South (C-2′-endo) conformers, by using the graphical-analysis methods described by Rinkel & Altona [(1987) J. Biomol. Struct. Dyn. 4,621-649]. The data reveal that the sugars of the 2C-5G and 3A-4T base-pairs, which form the drug-intercalation site, have strikingly different properties. The deoxyribose rings of the 2C-5G base-pair are best described in terms of an equilibrium heavily weighted in favour of the C-2′-endo geometry (greater than 95% ‘S’), with a phase angle, P, lying in the range 170-175 degrees and amplitude of pucker between 35 and 40 degrees, as typically found for B-DNA. For the deoxyribose rings of the 3A-4T base-pair, however, the analysis shows that, for 3A, the C-2′-endo and C3′-endo conformers are equally populated, whereas a more limited data set for the 4T nucleotide restricts the equilibrium to within 65-75% C-2′-endo. The deoxyribose rings of the 1G-6C base-pair have populations of 70-80% C-2′-endo, typical of nucleotides at the ends of a duplex. Although drug-base-pair stacking interactions are an important determinant of the enhanced duplex stability of the complex [Searle, Hall, Denny, & Wakelin (1988) Biochemistry 27, 4340-4349], the current findings make it clear that the same interactions can be associated with considerable variations in the degree of local structural dynamics at the level of the sugar puckers.

scholarly journals Bivalent-metal binding to CheY protein. Effect on protein conformation

1992 ◽  
Vol 287 (2) ◽  
pp. 521-531 ◽  
Author(s):  
L Kar ◽  
P Matsumura ◽  
M E Johnson
Keyword(s):  
Metal Ions ◽  
Conformational Change ◽  
Metal Binding ◽  
Bound States ◽  
Aromatic Proton ◽  
Double Quantum ◽  
Two Dimensional ◽  
Coherence Transfer ◽  
Bivalent Metal ◽  
Metal Free

CheY is a 14 kDa cytoplasmic protein that is activated by the transfer of a phosphoryl moiety to Asp-57 from phosphoCheA during signal transduction in bacterial chemotaxis. It has been established that metal ions are necessary for the autophosphorylation of CheA, the transfer of phosphate from phosphoCheA to CheY and the autodephosphorylation of phosphoCheY. In this work, paramagnetic relaxation enhancement has been used in conjunction with one- and two-dimensional n.m.r. to study the interaction of CheY with bivalent metal ions. These studies have led to the discovery of two conformations of the protein in water, corresponding to the metal-free and the metal-bound states. Binding of bivalent cations like Mg2+, Ca2+, Sr2+, Zn2+ and Mn2+ results in a conformational change from the metal-free to the metal-bound state. Preliminary assignments of the aromatic proton resonances are reported. Comparison of phase-sensitive double-quantum-filtered COSY, homonuclear Hartmann-Hahn coherence transfer and nuclear Overhauser enhancement spectra from the metal-bound and metal-free protein indicates that Trp-58, Thr-87 and Tyr-106 are particularly affected by the conformational change involved, and that this change is limited to a small number of residues. In addition, homonuclear Hartmann-Hahn coherence transfer experiments with paramagnetic Mn2+ show significant suppression of cross-peaks associated with Trp-58 and several neighbouring residues. Comparison of the distances estimated using n.m.r. with the CheY crystal structure indicates that the n.m.r. results are consistent with bivalent metal binding at the cluster of aspartic acid residues that includes Asp-13 and Asp-57. These studies also demonstrate the utility of paramagnetic metal-induced relaxation in conjunction with two-dimensional n.m.r. measurements for exploring ligand-binding sites.

Molecular Determinants for Drug-Receptor Interactions. 6. Proton 500 MHz NMR Spectra of the Narcotic Antagonists Naloxone and Naltrexone by Two-Dimensional 1H–1H Chemical Shift Correlation Spectroscopy

1986 ◽  
Vol 41 (2) ◽  
pp. 231-238 ◽  
Author(s):  
Bruno Perly ◽  
Giuseppe C. Pappalardo ◽  
Antonio Grassi
Keyword(s):  
Nmr Spectra ◽  
Chemical Shifts ◽  
Relaxation Times ◽  
Chair Conformation ◽  
Correlation Spectroscopy ◽  
Coupling Constants ◽  
Piperidine Ring ◽  
Two Dimensional ◽  
Spectral Parameters ◽  
Narcotic Antagonists

The full analysis of the 1H NMR spectra of naloxone and naltrexone (hydrochloride salts, in 2H2O solution) was performed by using an high-frequency (500 MHz) spectrometer and the recent technique of two-dimensional (2D ) homonuclear shift spectroscopy. The 1H-1H connectivities allowed detection of correlated resonances and assignments of multiplets. The shapes of the contour levels of the COSY 45 spectra were also used to check the relative signs of coupling constants. The refinement of spectral parameters of some component spin-systems of the complex spectra was performed by computerized iterative simulation of patterns.The spectral analysis provided proton coupling constants that allowed to establish a slightly distorted-chair conformation of the piperidine ring in both compounds.The magnetic non-equivalence found for the protons bonded to C-17 atom (part of the N-alkyl fragment) was found to be larger in naltrexone than in the analogous naloxone. This fact, while no significant differences were observable in the chemical shifts of corresponding protons of the rigid molecular backbone of the two narcotic antagonists under study, was assigned to smaller degree of internal conformational flexibility of the N-methylcyclopropyl group in naltrexone with respect to that of the N-methylallyl group in naloxone.The above findings appeared in good agreement with our previously proposed views based on results from 13C relaxation times studies, which suggested the possible correlation of the motional rates of the N-methyl-R group to the pharmacological activity of antagonist compounds. This would consist in a direct correlation between decreasing flexibility of the N-bonded fragment and increasing antagonistic potency.

scholarly journals 1H- and 13C-n.m.r. studies of the antitumour antibiotic luzopeptin. Resonance assignments, conformation and flexibility in solution

1988 ◽  
Vol 256 (1) ◽  
pp. 271-278 ◽  
Author(s):  
M S Searle ◽  
J G Hall ◽  
P G Wakelin
Keyword(s):  
Hydrogen Bonds ◽  
Nuclear Overhauser Effect ◽  
Resonance Assignments ◽  
Carbonyl Oxygen ◽  
Correlation Spectroscopy ◽  
Spin Lattice Relaxation ◽  
Double Quantum ◽  
Two Dimensional ◽  
Relaxation Data ◽  
Oxygen Atoms

The depsipeptide DNA-intercalating antibiotic luzopeptin was studied in solution by n.m.r. methods. Two-dimensional 1H double-quantum-filtered correlation spectroscopy (DQF-COSY) and nuclear-Overhauser-effect spectroscopy (NOESY) confirm the primary structure and twofold symmetry of luzopeptin and provide details of its three-dimensional conformation in solution. Trans-annular hydrogen bonds between the glycine NH groups and carbonyl oxygen atoms have been identified in the crystalline state [Arnold & Clardy (1981) J. Am. Chem. Soc. 103, 1243-1244], and are important in maintaining an antiparallel beta-sheet conformation. The n.m.r. data indicate that the glycine NH protons are appreciably shielded from the solvent molecules, which suggests that these hydrogen bonds are maintained in solution. The orientation of the quinoline chromophores is defined by two-dimensional NOE cross-peaks that position the N-methyl group of the L-beta-hydroxyvaline residue close in space to both the quinoline H-8 and serine NH proton. This pattern of NOEs is in accord both with the chromophore configuration found in the crystal and one where the quinoline rings are aligned in a parallel manner at right-angles to the depsipeptide ring. The n.m.r. data are consistent with a hydrogen bond between the quinoline hydroxy groups and the quinoline carbonyl oxygen atoms. The pyridazine acetylmethyl groups give NOEs to the C(alpha)H groups of the beta-hydroxy-N-methylvaline residues, showing that the acetyl groups, for at least some of the time, stretch over the depsipeptide ring, occluding one face of the molecule. Both of the latter features are also found in the crystal structure. Resonances in the 13C-n.m.r. spectrum of luzopeptin have been assigned by transferring 1H assignments to their covalently bonded carbon atoms via a heteronuclear shift-correlation experiment (HETCOR). The measurement of spin-lattice relaxation times and 1H-13C NOEs at specific sites in the molecule has led us to conclude that segmental motions within the depsipeptide ring are restricted and that the 13C relaxation data for luzopeptin's protonated carbon atoms are adequately described by isotropic tumbling in solution. Furthermore, relaxation data for the carbon atoms of the quinoline chromophores show that these rings exhibit similar motion to the depsipeptide ring and are not rotating rapidly with respect to it. Taken together all the data imply that luzopeptin is fairly rigid in solution, on the time scale of molecular tumbling, and has, or can readily attain, a staple-like structure suitable for bisintercalation.(ABSTRACT TRUNCATED AT 400 WORDS)

Structural characterization, by two-dimensional NMR spectroscopy and fast-atom-bombardment mass spectrometry, of a highly acylated trirhamnoside from Mezzettialeptopoda (Annonaceae)

1990 ◽  
Vol 68 (7) ◽  
pp. 1044-1050 ◽  
Author(s):  
Donald A. Powell ◽  
William S. York ◽  
Herman van Halbeek ◽  
Joseph T. Etse ◽  
Alexander I. Gray ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Fast Atom Bombardment ◽  
Multiple Bond ◽  
Stem Bark ◽  
Correlation Spectroscopy ◽  
Double Quantum ◽  
Two Dimensional ◽  
Complex Carbohydrate ◽  
Heteronuclear Multiple Bond Correlation

The structure of Mezzettiaside 3, a highly acylated trisaccharide obtained from the stem bark of Mezzettialeptopoda, was determined by a combination of double-quantum-filtered {1H,1H} correlation spectroscopy, two-dimensional homonuclear Hartmann–Hahn, and 1H-detected {1H,13C} one-bond and multiple-bond shift correlation nuclear magnetic resonance experiments, in conjunction with fast-atom-bombardment mass spectrometry. Mezzettiaside 3 was found to be the α-(n-octyl)glycoside of 3,4-di-O-acetyl-L-rhamnopyranosyl-α(1 → 3)-2,4-di-O-acetyl-L-rhamnopyranosyl-α(1 → 3)-4-O-hexanoyl-L-rhamnopyranose. The heteronuclear multiple-bond correlation NMR technique proved to be invaluable in establishing the location of the O-acyl groups in this complex carbohydrate. Keywords: oligosaccharide, HMBC, HMQC, HOHAHA, FAB-MS.

PC 2D-COS: A Principal Component Base Approach to Two-Dimensional Correlation Spectroscopy

2020 ◽  
Vol 74 (4) ◽  
pp. 460-472 ◽  
Author(s):  
Julian Hniopek ◽  
Michael Schmitt ◽  
Jürgen Popp ◽  
Thomas Bocklitz
Keyword(s):  
Computational Cost ◽  
Principal Component ◽  
Correlation Spectroscopy ◽  
High Spectral Resolution ◽  
Data Sets ◽  
Two Dimensional ◽  
Real World Data ◽  
Data Set ◽  
Multiple Data Sets ◽  
2D Correlation Spectroscopy

This paper introduces the newly developed principal component powered two-dimensional (2D) correlation spectroscopy (PC 2D-COS) as an alternative approach to 2D correlation spectroscopy taking advantage of a dimensionality reduction by principal component analysis. It is shown that PC 2D-COS is equivalent to traditional 2D correlation analysis while providing a significant advantage in terms of computational complexity and memory consumption. These features allow for an easy calculation of 2D correlation spectra even for data sets with very high spectral resolution or a parallel analysis of multiple data sets of 2D correlation spectra. Along with this reduction in complexity, PC 2D-COS offers a significant noise rejection property by limiting the set of principal components used for the 2D correlation calculation. As an example for the application of truncated PC 2D-COS a temperature-dependent Raman spectroscopic data set of a fullerene-anthracene adduct is examined. It is demonstrated that a large reduction in computational cost is possible without loss of relevant information, even for complex real world data sets.

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