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Molecular dynamics simulations of carrabiose
Author(s) -
Ueda K.,
Brady J. W.
Publication year - 1997
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/(sici)1097-0282(199703)41:3<323::aid-bip7>3.0.co;2-u
Subject(s) - chemistry , molecular dynamics , adiabatic process , dimer , molecule , potential energy , aqueous solution , energy minimization , computational chemistry , disaccharide , molecular mechanics , chemical physics , thermodynamics , stereochemistry , classical mechanics , physics , organic chemistry
Molecular mechanics calculations have been performed for the disaccharide carrabiose, one of the repeat units of β‐carrageenan, as a general model for the (1→4)‐linkage in the carrageenans. An adiabatic conformational energy map for this unsulfated molecule was prepared by constrained energy minimization and compared to a previously reported rigid‐residue energy map for the sulfated molecule and to a similar adiabatic map for neocarrabiose, the related (1→3)‐linked dimer repeat unit of β‐carrageenan. Molecular dynamics simulations of this molecule in vacuo and in an aqueous (TIP3P) solution were calculated, and the observed motions were found to be generally consistent with the vacuum adiabatic energy map. Unlike the case observed in previous simulations of neocarrabiose, little salvation shift in the molecular conformation was observed for carrabiose. From the dynamics, the linkage was observed to be relatively flexible, as has been inferred from experiment on sulfated carrageenan polymers. © 1997 John Wiley & Sons, Inc.