title: Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics.
abstract: Molecular dynamics (MD) simulation of a N-glycan in solution is challenging because of high-energy barriers of the glycosidic linkages, functional group rotational barriers, and numerous intra- and intermolecular hydrogen bonds. In this study, we apply different enhanced conformational sampling approaches, namely, metadynamics (MTD), the replica-exchange MD (REMD), and the recently proposed replica state exchange MTD (RSE-MTD), to a N-glycan in solution and compare the conformational sampling efficiencies of the approaches. MTD helps to cross the high-energy barrier along the ω angle by utilizing a bias potential, but it cannot enhance sampling of the other degrees of freedom. REMD ensures moderate-energy barrier crossings by exchanging temperatures between replicas, while it hardly crosses the barriers along ω. In contrast, RSE-MTD succeeds to cross the high-energy barrier along ω as well as to enhance sampling of the other degrees of freedom. We tested two RSE-MTD schemes: in one scheme, 64 replicas were simulated with the bias potential along ω at different temperatures, while simulations of four replicas were performed with the bias potentials for different CVs at 300 K. In both schemes, one unbiased replica at 300 K was included to compute conformational properties of the glycan. The conformational sampling of the former is better than the other enhanced sampling methods, while the latter shows reasonable performance without spending large computational resources. The latter scheme is likely to be useful when a N-glycan-attached protein is simulated.
authors.affiliation: RIKEN Theoretical Molecular Science Laboratory , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
authors.forename: Raimondas
authors.initials: R
authors.lastname: Galvelis
authors.affiliation: RIKEN Theoretical Molecular Science Laboratory , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.|RIKEN Quantitative Biology Center , Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Suyong
authors.initials: S
authors.lastname: Re
authors.affiliation: RIKEN Theoretical Molecular Science Laboratory , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.|RIKEN iTHES, 2-1 Hirosawa , Wako-shi, Saitama 351-0198, Japan.|RIKEN Advanced Institute for Computational Science , Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.|RIKEN Quantitative Biology Center , Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Yuji
authors.identifier: http://orcid.org/0000-0001-9738-9216
authors.initials: Y
authors.lastname: Sugita
mesh_terms: D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011134:Polysaccharides / Q000737:chemistry*; D012996:Solutions; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011134:Polysaccharides; D012996:Solutions