scholarly journals Chemical Tagging with tert -Butyl and Trimethylsilyl Groups for Measuring Intermolecular Nuclear Overhauser Effects in a Large Protein-Ligand Complex

2017 ◽  
Vol 23 (53) ◽  
pp. 13033-13036 ◽  
Author(s):  
Shereen Jabar ◽  
Luke A. Adams ◽  
Yao Wang ◽  
Luigi Aurelio ◽  
Bim Graham ◽  
...  
Keyword(s):  
Large Protein ◽  
Ligand Complex ◽  
Tert Butyl ◽  
Chemical Tagging ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Trimethylsilyl Groups

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.

Structure assignment of some 3,4′-diquinolinyl sulfides studied by Nuclear Overhauser Effects, X-ray analysis and reactions with sodium methoxide

2010 ◽  
Vol 109 (10) ◽  
pp. 509-514 ◽  
Author(s):  
Stanislaw Boryczka ◽  
Andrzej Maślankiewicz ◽  
Miroslaw Wyszomirski ◽  
Teresa Borowiak ◽  
Maciej Kubicki
Keyword(s):  
Sodium Methoxide ◽  
X Ray ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Structure Assignment

scholarly journals Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations

2020 ◽  
Vol 21 (20) ◽  
pp. 7626
Author(s):  
Victor Stroylov ◽  
Maria Panova ◽  
Philip Toukach
Keyword(s):  
Density Functional ◽  
Structural Features ◽  
Functional Theory ◽  
Conformational Ensembles ◽  
Explicit Solvent ◽  
Empirical Force Field ◽  
Automated Simulation ◽  
Nuclear Overhauser ◽  
Nuclear Overhauser Effects ◽  
Accuracy Speed

Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser effects (NOEs) from conformational ensembles obtained from 50 to 100 ns molecular dynamics (MD) trajectories and their comparison to the published experimental data. Using various ranking schemes, it was concluded that explicit solvent MM3 MD yielded non-inferior NOE accuracy with newer GLYCAM-06, and ultimately PBE0-D3/def2-TZVP (Triple-Zeta Valence Polarized) Density Functional Theory (DFT) simulations. For seven of eleven molecules, at least one empirical force field with explicit solvent outperformed DFT in NOE prediction. The aggregate of characteristics (accuracy, speed, and compatibility) made MM3 dynamics with explicit solvent at 300 K the most favorable method for bulk generation of disaccharide conformation maps for massive database filling.

Sign in / Sign up

Export Citation Format

Share Document