Paper Citing NAMD - Abstract
Nishima, Wataru; Miyashita, Naoyuki; Yamaguchi, Yoshiki; Sugita, Yuji; Re, Suyong
Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8504-8512, JUL 26 2012
The introduction of bisecting GlcNAc and core fucosylation in N-glycans is essential for fine functional regulation of glycoproteins. In this paper, the effect of these modifications on the conformational properties Of N-glycans is examined at the atomic level by performing replica exchange molecular dynamics (REMD) simulations. We simulate four biantennary complex type N-glycans, namely, unmodified, two single substituted with either bisecting GlcNAc or core fucose, and disubstituted forms. By using REMD as an enhanced sampling technique, five distinct conformers in solution, each of which is characterized by its local orientation of the Man alpha 1-6Man glycosidic linkage, are observed for all four N-glycans. The chemical modifications significantly change their conformational equilibria. The number of major conformers is reduced from five to two and from five to four upon the introduction of bisecting GlcNAc and core fucosylation; respectively, The population change is attributed to specific inter residue hydrogen bonds, including water mediated Ones. The experimental NMR data, including nuclear Overhauser enhancement and scalar J-coupling constant's, are well reproduced; taking the multiple conformers into account Our structural model supports the concept of "conformer selection"; which emphasize the, conformational flexibility of N-glycans in protein-glycan interactions.
