Open AccessTheoretical and NMR-based Conformational Analysis of Phosphodiester-linked Disaccharides
Author(s) -
Alexey G. Gerbst,
Andrei V. Nikolaev,
Dmitry V. Yashunsky,
Alexander S. Shashkov,
Andrey S. Dmitrenok,
Nikolay E. Nifantiev
Publication year - 2017
Publication title -
scientific reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.24
H-Index - 213
ISSN - 2045-2322
DOI - 10.1038/s41598-017-09055-x
Subject(s) - phosphodiester bond , molecular dynamics , chemistry , molecule , molecular model , nuclear magnetic resonance spectroscopy , linker , computational chemistry , stereochemistry , crystallography , organic chemistry , biochemistry , rna , gene , computer science , operating system
The conformational behaviour of three phosphate-bridged dimannosides was studied by means of NMR and computational molecular modelling. First, the conformations of the phosphodiester linker were determined by quantum chemistry methods using dimethyl phosphate as a model. Then, a series of conformations was constructed for each of the studied molecules. Preliminary molecular dynamics (MD) simulations revealed that the inclusion of a cation had a drastic influence on the obtained results. Additionally, triethylammonium had the same effect as sodium as the counter-ion. After that, another series of MD simulations was run. The resulting MD trajectories were used to define the conformations responsible for the observed nuclear Overhauser effects and inter-nuclear coupling.