Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins.

ABSTRACT: N-linked glycans are on protein surfaces and have direct and water/ion-mediated interactions with surrounding amino acids. Such contacts could restrict their conformational freedom compared to the same glycans free in solution. In this work, we have examined the conformational freedom of the N-glycan core pentasaccharide moiety in solution using standard molecular dynamics (MD) simulations as well as temperature replica-exchange MD simulations. Both simulations yield the comparable conformational variability of the pentasaccharide in solution, indicating the convergence of both simulations. The glycoprotein crystal structures are analyzed to compare the conformational freedom of the N-glycan on the protein surface with the simulation result. Surprisingly, the pentasaccharide free in soluti

SUBMITTER: Jo S 

PROVIDER: S-EPMC4672150 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature