Measuring the magnitude of internal motion in a complex hexasaccharide

• Published in: Biopolymers Vol. 95; no. 1; pp. 39 - 50
• Main Authors: Ganguly, Soumya, Xia, Junchao, Margulis, Claudio, Stanwyck, Liz, Bush, C. Allen
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.01.2011
• Subjects: Biopolymers; Carbohydrate Sequence; Computer Simulation; conformation; Couplings; dipolar coupling; flexibility; Humans; Linkages; Magnetic Resonance Spectroscopy; Mathematical analysis; Milk, Human; Molecular Sequence Data; Monte Carlo methods; Motion; NMR; oligosaccharide; Oligosaccharides - chemistry; Regression analysis; Solvents
• ISSN: 0006-3525; 1097-0282; 1097-0282
• DOI: 10.1002/bip.21532

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 13C1H and 1H1H 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 Lewisb 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.