Molecular dynamics simulations of glycoproteins using CHARMM.

Printer-friendly versionPrinter-friendly versionPDF versionPDF version
TitleMolecular dynamics simulations of glycoproteins using CHARMM.
Publication TypeJournal Article
Year of Publication2015
AuthorsMallajosyula, SS, Jo, S, Im, W, Mackerell, AD
JournalMethods Mol Biol
Volume1273
Pagination407-29
Date Published2015
ISSN1940-6029
KeywordsAspergillus, Glucan 1,4-alpha-Glucosidase, Glycoproteins, Molecular Dynamics Simulation, Software, Solvents, Water
Abstract

Molecular dynamics simulations are an effective tool to study the structure, dynamics, and thermodynamics of carbohydrates and proteins. However, the simulations of heterogeneous glycoprotein systems have been limited due to the lack of appropriate molecular force field parameters describing the linkage between the carbohydrate and the protein regions as well as the tools to prepare these systems for modeling studies. In this work we outline the recent developments in the CHARMM carbohydrate force field to treat glycoproteins and describe in detail the step-by-step procedures involved in building glycoprotein geometries using CHARMM-GUI Glycan Reader.

DOI10.1007/978-1-4939-2343-4_25
Alternate JournalMethods Mol. Biol.
PubMed ID25753723
PubMed Central IDPMC4537648
Grant ListR01 GM070855 / GM / NIGMS NIH HHS / United States
R01 GM072558 / GM / NIGMS NIH HHS / United States
GM070855 / GM / NIGMS NIH HHS / United States