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Measuring the magnitude of internal motion in a complex hexasaccharide
Author(s) -
Ganguly Soumya,
Xia Junchao,
Margulis Claudio,
Stanwyck Liz,
Bush C. Allen
Publication year - 2011
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.21532
Subject(s) - chemistry , conformational isomerism , dihedral angle , glycosidic bond , residual dipolar coupling , molecular dynamics , dipole , magnetic dipole–dipole interaction , computational chemistry , crystallography , nuclear magnetic resonance spectroscopy , stereochemistry , molecule , organic chemistry , hydrogen bond , enzyme
For the development of a scheme for quantitative experimental estimation of internal motion in the complex human milk hexasaccharide lacto‐ N ‐di‐fuco hexose I (LNDFH I), we measured a large number of experimental residual dipolar couplings in liquid crystal orienting media. We present a total of 40 13 C 1 H and 1 H 1 H dipolar coupling values, each representing distinct directions of internuclear vectors. The NMR data were interpreted with established methods for analysis of rigid subdomains of the oligosaccharide as well as a novel method in which dipolar couplings were calculated over an ensemble of conformers from a solvent Molecular Dynamics trajectory using multiple linear regression analysis. The Lewis b epitope region of LNDFH I assumed a single unique conformation with internal motion described by fluctuations of 5–10° in glycosidic dihedral angles consistent with previous studies. Greater flexibility was observed for the remaining GlcNAc1→3‐β‐ D ‐Gal and β‐ D ‐Gal1→4Glc linkages, with the former glycosidic linkage existing in a conformational exchange among three states. The results were also supported by similar results of calculations carried out with conformers obtained from a simple Monte Carlo simulation without explicit solvent. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 39–50, 2011.