title: Exploration of conformational spaces of high-mannose-type oligosaccharides by an NMR-validated simulation.
abstract: Exploration of the conformational spaces of flexible biomacromolecules is essential for quantitatively understanding the energetics of their molecular recognition processes. We employed stable isotope- and lanthanide-assisted NMR approaches in conjunction with replica-exchange molecular dynamics (REMD) simulations to obtain atomic descriptions of the conformational dynamics of high-mannose-type oligosaccharides, which harbor intracellular glycoprotein-fate determinants in their triantennary structures. The experimentally validated REMD simulation provided quantitative views of the dynamic conformational ensembles of the complicated, branched oligosaccharides, and indicated significant expansion of the conformational space upon removal of a terminal mannose residue during the functional glycan-processing pathway.
authors.affiliation: Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan); Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603 (Japan); School of Physical Sciences, The Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan).
authors.forename: Takumi
authors.initials: T
authors.lastname: Yamaguchi
authors.forename: Yoshitake
authors.initials: Y
authors.lastname: Sakae
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.forename: Sayoko
authors.initials: S
authors.lastname: Yamamoto
authors.forename: Yuko
authors.initials: Y
authors.lastname: Okamoto
authors.forename: Koichi
authors.initials: K
authors.lastname: Kato
mesh_terms: D002236:Carbohydrate Conformation; D028581:Lanthanoid Series Elements / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008358:Mannose / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009844:Oligosaccharides / Q000737:chemistry*
chemical_list: D028581:Lanthanoid Series Elements; D009844:Oligosaccharides; D008358:Mannose
keywords: NMR spectroscopy; lanthanides; molecular dynamics; oligosaccharides; paramagnetic effects