Molecular dynamics simulations of membrane- and protein-bound glycolipids using GLYCAM
1Department of Pathology and Laboratory Medicine, St. Paul's Hospital, University of British Columbia, 1081 Burrard St, Vancouver, BC, Canada, V6Z 1Y6, mdmrco@mail.ubc.ca.
Methods in Molecular Biology (Clifton, N.J.)
|March 11, 2015
Abstract:
This chapter outlines protocols for the preparation, execution, and analysis of molecular dynamics (MD) simulations of glycolipids in biologically relevant environments, i.e., imbedded in lipid bilayers or bound to proteins, with the goal of generating biologically relevant structural and dynamic information. Also included is a description of ensemble average (EA) charge set development consistent with the GLYCAM06 force field and its implementation using the AMBER molecular dynamics software suite.
Related Concept Videos
01:26Membrane Fluidity
18.3K
Membrane fluidity is explained by the fluid mosaic model of the cell membrane, which describes the plasma membrane structure as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character.
Mosaic nature of the membrane
The mosaic characteristic of the membrane helps the plasma membrane remain fluid. The integral proteins and lipids exist as separate but loosely-attached molecules in the membrane. The membrane is...
Mosaic nature of the membrane
The mosaic characteristic of the membrane helps the plasma membrane remain fluid. The integral proteins and lipids exist as separate but loosely-attached molecules in the membrane. The membrane is...
18.3K
01:23Membrane Fluidity
180.1K
Cell membranes are composed of phospholipids, proteins, and carbohydrates loosely attached to one another through chemical interactions. Molecules are generally able to move about in the plane of the membrane, giving the membrane its flexible nature called fluidity. Two other features of the membrane contribute to membrane fluidity: the chemical structure of the phospholipids and the presence of cholesterol in the membrane.
180.1K