scholarly journals NMR solution conformation of heparin-derived tetrasaccharide

1996 ◽  
Vol 318 (1) ◽  
pp. 93-102 ◽  
Author(s):  
Dmitri MIKHAILOV ◽  
Kevin H. MAYO ◽  
Ioncho R. VLAHOV ◽  
Toshihiko TOIDA ◽  
Azra PERVIN ◽  
...  
Keyword(s):  
Chair Conformation ◽  
Coupling Constants ◽  
Solution Conformation ◽  
1H And 13C Nmr ◽  
Small Deviations ◽  
J Coupling Constants ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Dynamics Simulations ◽  
Ring Conformations

The solution conformation of the homogeneous, heparin-derived tetrasaccharide ΔUA2S(1 → 4)-α-d-GlcNpS6S(1 → 4)-α-l-IdoAp2S(1 → 4)-α-d-GlcNpS6S (residues A, B, C and D respectively, where IdoA is iduronic acid) has been investigated by using 1H- and 13C-NMR. Ring conformations have been defined by J-coupling constants and inter-proton nuclear Overhauser effects (NOEs), and the orientation of one ring with respect to the other has been defined by inter-ring NOEs. NOE-based conformational modelling has been done by using the iterative relaxation matrix approach (IRMA), restrained molecular dynamics simulations and energy minimization to refine structures and to distinguish between minor structural differences and equilibria between various ring forms. Both glucosamine residues B and D are in the 4C1 chair conformation. The 6-O-sulphate group is oriented in the gauche–trans configuration in the D ring, whereas in the B ring the gauche–gauche rotomer predominates. Uronate (A) and iduronate (C) residues are mostly represented by 1H2 and 2S0 twisted boat forms, respectively, with small deviations in expected coupling constants and NOEs suggesting minor contributions from other A and C ring conformations.

scholarly journals NMR solution conformation of heparin-derived hexasaccharide

1997 ◽  
Vol 328 (1) ◽  
pp. 51-61 ◽  
Author(s):  
Dmitri MIKHAILOV ◽  
J. Robert LINHARDT ◽  
H. Kevin MAYO
Keyword(s):  
Energy Minimization ◽  
Conformational Stability ◽  
Chair Conformation ◽  
Coupling Constants ◽  
Solution Conformation ◽  
Explicit Solvent ◽  
J Coupling Constants ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
A Minor

The solution conformation of homogeneous, heparin-derived hexasaccharide (residues A, B, C, D, E, F) has been investigated by using 1H-NMR spectroscopy. Intra-ring conformations have been defined by J-coupling constants and inter-proton nuclear Overhauser effects (NOEs), and the orientation of one ring with respect to the other has been defined by inter-ring NOEs. NOE-based conformational modelling has been done by using the iterative relaxation matrix approach (IRMA), restrained energy minimization to refine structures and to distinguish between minor structural differences and equilibria between various intra-ring forms. All glucosamine residues B, D and F are in the 4C1 chair conformation. The uronate (A) residue is mostly represented by the 1H2 form, whereas internal iduronates (C and E) exist in equilibrium between the chair and skewed boat forms. Deviations in some NOEs indicate a minor contribution of the 2H1 form to the A ring. Glycosidic dihedral angles, which define the overall oligosaccharide conformation, were further refined by combining in vacuo energy map calculations and restrained energy minimization in explicit solvent water. Conformational stability was further assessed by subjecting NOE and IRMA-derived structures to 600 ps of unrestrained molecular dynamics in explicit solvent.

Structural studies of digitoxin and related cardenolides by two-dimensional NMR

1990 ◽  
Vol 68 (2) ◽  
pp. 272-277 ◽  
Author(s):  
Torbjörn Drakenberg ◽  
Peter Brodelius ◽  
Deane D. McIntyre ◽  
Hans J Vogel
Keyword(s):  
Nmr Spectroscopy ◽  
Nmr Spectra ◽  
Chair Conformation ◽  
Coupling Constants ◽  
Two Dimensional ◽  
Structural Studies ◽  
Solution Conformation ◽  
Phase Sensitive ◽  
Multiple Relay ◽  
C Nmr

The 1H and 13C NMR spectra of the cardenolides digitoxigenin, digoxigenin, digitoxin, and mono- and bis-digitoxigenin digitoxosides have been completely assigned by two-dimensional NMR spectroscopy. The techniques used include phase-sensitive COSY, multiple relay COSY, and carbon–proton correlation (HETCOR and HMQC) spectra. Various aspects of the solution conformation of the steroid moiety of digitoxin and digoxigenin could be determined from coupling constants and NOE difference experiments and they are indicative of an all-chair conformation. The carbohydrate rings in digitoxin and the mono- and bis-digitoxigenin digitoxosides are also in the chair conformation. Keywords: cardenolides, digitoxigenin, digitoxin, 2-dimensional NMR, conformational analysis.

Conformation of purine mononucleotides by H{H} and P{H} nuclear Overhauser effects

1983 ◽  
Vol 61 (7) ◽  
pp. 1456-1464 ◽  
Author(s):  
H. Santos ◽  
A. V. Xavier ◽  
C.F.G.C. Geraldes
Keyword(s):  
Aqueous Solution ◽  
Nuclear Overhauser Effect ◽  
Coupling Constants ◽  
Glycosidic Bond ◽  
Proton Proton ◽  
Proton Coupling ◽  
Vicinal Proton ◽  
Group A ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects

The proton–proton and phosphorus–proton nuclear Overhauser effect (nOe) of guanosine 5′-monophosphate (5′-GMP) was measured in aqueous solution at different pH values and in the presence of excess LaIII at acid pH. These data and nOe data from the literature for other mononucleotides were used together with vicinal proton–proton coupling constants to investigate the conformations of mononucleotides in aqueous solution, especially their rotational state about the glycosidic bond. Comparison of observed and calculated enhancements using various conformational models for the glycosidic bond gave predominantly anti conformations for 5′-AMP and 5′-GMP and a mixture of syn and anti conformations for 2′-AMP, 2′-GMP, 3′-AMP, and 3′-GMP. Protonation of 5′-GMP at N-7 of the guanine base alters the amplitude of its torsion angle within the anti range. The agreement between the glycosidic nucleotide conformations defined by nOe and by the lanthanide probe method is good but not perfect. As complexation of 5′-GMP with LaIII through the phosphate group has only a small effect on the conformation of its exocyclic group, a comparison of the two methods is justified.

A nuclear Overhauser effect difference study of the solution conformation of (6R)-prostaglandin I1

1980 ◽  
Vol 58 (23) ◽  
pp. 2649-2659 ◽  
Author(s):  
George Kotovych ◽  
Gerdy H. M. Aarts
Keyword(s):  
Proton Magnetic Resonance ◽  
Nuclear Overhauser Effect ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Solution Conformation ◽  
Magnetic Resonance Studies ◽  
Overhauser Effect ◽  
Complete Assignment ◽  
Effect Difference ◽  
Nuclear Overhauser

Proton magnetic resonance studies at 400 MHz allowed the complete assignment of the spectra for (6R)-prostaglandin I1 in phosphate buffer and in CDCl3 solutions. The spectral analysis was based on the nuclear Overhauser effect difference measurements, which also provide accurate chemical shifts and coupling constants. Conformational differences in the two solvents for the ring portion of the molecule are indicated.

A high field proton magnetic resonance study of the solution conformation of thromboxane B2

1980 ◽  
Vol 58 (11) ◽  
pp. 1111-1117 ◽  
Author(s):  
George Kotovych ◽  
Gerdy H. M. Aarts
Keyword(s):  
Magnetic Resonance ◽  
High Field ◽  
Double Resonance ◽  
Relaxation Times ◽  
Chair Conformation ◽  
Rotational Correlation Time ◽  
Coupling Constants ◽  
Solution Conformation ◽  
Dipolar Relaxation ◽  
Rotational Correlation

The solution conformation of thromboxane B2 (TXB2) has been studied using high-field nuclear magnetic resonance techniques. In CDCl3, both anomers are present in solution with 76% 11α-OH TXB2 and 24% 11β-OH TXB2. In CD3OD, the predominant anomer is 11β-OH TXB2 (80%) while the concentration of 11α-OH TXB2 is 20%. The proton resonances were assigned at 400 MHz using double resonance techniques. The analysis of the vicinal coupling constants indicates that the six-membered ring is present in solution in a chair conformation with both of the aliphatic side chains equatorial. Proton longitudinal relaxation times were measured at 25 °C in CDCl3 for H-2, H-11β, H-12, H-13, H-14, and H-17 to H-19, both at 200 MHz and at 400 MHz. From the frequency dependence of these dipolar relaxation times, the rotational correlation times were evaluated. Within experimental error, all of the values are similar in magnitude (~ 2.0 × 10−10 s) indicating that this is the molecular rotational correlation time.

Conformational and Structural characterization of carbohydrates and their interactions studied by NMR

2021 ◽  
Vol 28 ◽  
Author(s):  
Francisco Javier Cañada ◽  
Ángeles Canales ◽  
Pablo Valverde ◽  
Beatriz Fernández de Toro ◽  
Mónica Martínez-Orts ◽  
...  
Keyword(s):  
Structural Information ◽  
Theoretical Calculations ◽  
Chemical Shifts ◽  
Structural Complexity ◽  
Coupling Constants ◽  
Resonance Spectroscopy ◽  
Additional Information ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects

: Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.

scholarly journals A combined NMR, MD and DFT conformational analysis of 9-O-acetyl sialic acid-containing GM3 ganglioside glycan and its 9-N-acetyl mimic

Glycobiology ◽  
2020 ◽  
Vol 30 (10) ◽  
pp. 787-801 ◽  
Author(s):  
Wanqing Li ◽  
Marcos D Battistel ◽  
Hannah Reeves ◽  
Lisa Oh ◽  
Hai Yu ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Density Functional ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Functional Theory ◽  
Acetylneuraminic Acid ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Intramolecular Hydrogen

Abstract O-Acetylation of carbohydrates such as sialic acids is common in nature, but its role is not clearly understood due to the lability of O-acetyl groups. We demonstrated previously that 9-acetamido-9-deoxy-N-acetylneuraminic acid (Neu5Ac9NAc) is a chemically and biologically stable mimic of the 9-O-acetyl-N-acetylneuraminic acid (Neu5,9Ac2) of the corresponding sialoglycans. Here, a systematic nuclear magnetic resonance (NMR) spectroscopic and molecular dynamics (MD) simulation study was undertaken for Neu5,9Ac2-containing GM3 ganglioside glycan (GM3-glycan) and its Neu5Ac9NAc analog. GM3-glycan with Neu5Ac as the non-O-acetyl form of Neu5,9Ac2 was used as a control. Complete 1H and 13C NMR chemical shift assignments, three-bond 1H-13C trans-glycosidic coupling constants (3JCH), accurate 1H-1H coupling constants (3JHH), nuclear Overhauser effects and hydrogen bonding detection were carried out. Results show that structural modification (O- or N-acetylation) on the C-9 of Neu5Ac in GM3 glycan does not cause significant conformational changes on either its glycosidic dihedral angles or its secondary structure. All structural differences are confined to the Neu5Ac glycerol chain, and minor temperature-dependent changes are seen in the aglycone portion. We also used Density Functional Theory (DFT) quantum mechanical calculations to improve currently used 3JHH Karplus relations. Furthermore, OH chemical shifts were assigned at −10°C and no evidence of an intramolecular hydrogen bond was observed. The results provide additional evidence regarding structural similarities between sialosides containing 9-N-acetylated and 9-O-acetylated Neu5Ac and support the opportunity of using 9-N-acetylated Neu5Ac as a stable mimic to study the biochemical role of 9-O-acetylated Neu5Ac.

scholarly journals Secondary structure of neutrophil-activating peptide-2 determined by 1H-nuclear magnetic resonance spectroscopy

1994 ◽  
Vol 304 (2) ◽  
pp. 371-376 ◽  
Author(s):  
K H Mayo ◽  
Y Yang ◽  
T J Daly ◽  
J K Barry ◽  
G J La Rosa
Keyword(s):  
Solution Structure ◽  
Resonance Assignments ◽  
Coupling Constants ◽  
Resonance Spectroscopy ◽  
Heparin Binding ◽  
Structural Elements ◽  
Solution Conformation ◽  
Platelet Factor ◽  
1H Nuclear Magnetic Resonance ◽  
Nuclear Overhauser

Neutrophil-activating protein-2 (NAP-2) is a 72 residue protein demonstrating a range of proinflammatory activities. The solution structure of monomeric NAP-2 has been investigated by two-dimensional 1H-n.m.r. spectroscopy. Sequence-specific proton resonance assignments have been made and secondary structural elements have been identified on the basis of nuclear Overhauser data, coupling constants and amide hydrogen/deuteron exchange. The NAP-2 monomer consists of a triple-stranded anti-parallel beta-sheet arranged in a ‘Greek key’ and a C-terminal helix (residues 59-70) and is very similar to that found in the n.m.r. solution conformation of dimeric interleukin-8 and the crystal structure of tetrameric bovine platelet factor-4. Results are discussed in terms of heparin binding and neutrophil-activation properties of NAP-2.

Sign in / Sign up

Export Citation Format

Share Document