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.

Conformational analysis of key disaccharide components of Brucella A and M antigens

1990 ◽  
Vol 68 (7) ◽  
pp. 979-988 ◽  
Author(s):  
Thomas Peters ◽  
Jean-Robert Brisson ◽  
David R. Bundle
Keyword(s):  
Conformational Analysis ◽  
Boltzmann Distribution ◽  
Coupling Constants ◽  
Resonance Spectroscopy ◽  
Structural Elements ◽  
Torsion Angles ◽  
Proton Proton ◽  
Vicinal Proton ◽  
Polysaccharide Antigens ◽  
Nuclear Overhauser

The synthetic α 1,2 and α 1,3 disaccharide methyl glycosides of 4-amino-4,6-dideoxy-D-mannose 1–6 that constitute key structural elements of Brucella A and M antigens were analyzed by 1H and 13C nuclear magnetic resonance spectroscopy. A detailed conformational analysis was performed for the N-acetylated derivatives 1 and 4 as well as for the amino derivatives 2 and 5. Potential energy calculations using the GESA program established the global minima for the disaccharides 1, 2, 4, and 5, and mapped the energy surface as a function of the glycosidic torsion angles [Formula: see text] and ψ. Ensemble averaged nuclear Overhauser enhancements, weighted according to the Boltzmann distribution function, were derived for each of the four disaccharides. This procedure improved the fit between experimentally and theoretically derived nOe values, when compared to interpretations based on a single conformer model. The Brucella A and M antigens are homopolymers of 4-formamido-4,6-dideoxy-D-mannose and, as.N-formyl groups (saccharides 3, 6, and 8) are essential for the binding of these antigens to their respective antibodies, amide conformation was analyzed by examination of the vicinal proton–proton and proton–carbon coupling constants of the model monosaccharide 8. The conformational properties of the model compounds 1–8 were used to model the Brucella A and M polysaccharide antigens. Keywords: conformational analysis, disaccharide conformation, nuclear Overhauser measurements, molecular modeling, Brucella antigen.

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 Characterization of the structure and redox behaviour of cytochrome c3 from Desulfovibrio baculatus by 1H-nuclear-magnetic-resonance spectroscopy

1993 ◽  
Vol 294 (3) ◽  
pp. 899-908 ◽  
Author(s):  
I B Coutinho ◽  
D L Turner ◽  
J LeGall ◽  
A V Xavier
Keyword(s):  
Chemical Shifts ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Resonance Spectroscopy ◽  
Cytochrome C3 ◽  
X Ray ◽  
1H Nuclear Magnetic Resonance ◽  
Proton Resonances ◽  
Nuclear Overhauser

Complete assignment of the aromatic and haem proton resonances in the cytochromes c3 isolated from Desulfovibrio baculatus strains (Norway 4, DSM 1741) and (DSM 1743) was achieved using one- and two-dimensional 1H n.m.r. Nuclear Overhauser enhancements observed between haem and aromatic resonances and between resonances due to different haems, together with the ring-current contributions to the chemical shifts of haem resonances, support the argument that the haem core architecture is conserved in the various cytochromes c3, and that the X-ray structure of the D. baculatus cytochrome c3 is erroneous. The relative orientation of the haems for both cytochromes was determined directly from n.m.r. data. The n.m.r. structures have a resolution of approximately 0.25 nm and are found to be in close agreement with the X-ray structure from D. vulgaris cytochrome c3. The proton assignments were used to relate the highest potential to a specific haem in the three-dimensional structure by monitoring the chemical-shift variation of several haem resonances throughout redox titrations followed by 1H n.m.r. The haem with highest redox potential is not the same as that in other cytochromes c3.

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.

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.

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.

Sign in / Sign up

Export Citation Format

Share Document