Biomaterial Database

Molecular-dynamics simulation of a ceramide bilayer. 2006

Sagar A Pandit, and H Larry Scott

Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA. pandit@iit.edu

Ceramide is the simplest lipid in the biologically important class of glycosphingolipids. Ceramide is an important signaling molecule and a major component of the strateum corneum layer in the skin. In order to begin to understand the biophysical properties of ceramide, we have carried out a molecular-dynamics simulation of a hydrated 16:0 ceramide lipid bilayer at 368 K (5 degrees above the main phase transition). In this paper we describe the simulation and present the resulting properties of the bilayer. We compare the properties of the simulated ceramide bilayer to an earlier simulation of 18:0 sphingomyelin, and we discuss the results as they relate to experimental data for ceramide and other sphingolipids. The most significant differences arise at the lipid/water interface, where the lack of a large ceramide polar group leads to a different electron density and a different electrostatic potential but, surprisingly, not a different overall "dipole potential," when ceramide is compared to sphingomyelin.

UI	MeSH Term	Description	Entries
D008051	Lipid Bilayers	Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.	Bilayers, Lipid,Bilayer, Lipid,Lipid Bilayer
D008055	Lipids	A generic term for fats and lipoids, the alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. They comprise the fats, fatty oils, essential oils, waxes, phospholipids, glycolipids, sulfolipids, aminolipids, chromolipids (lipochromes), and fatty acids. (Grant & Hackh's Chemical Dictionary, 5th ed)	Lipid
D008956	Models, Chemical	Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.	Chemical Models,Chemical Model,Model, Chemical
D008968	Molecular Conformation	The characteristic three-dimensional shape of a molecule.	Molecular Configuration,3D Molecular Structure,Configuration, Molecular,Molecular Structure, Three Dimensional,Three Dimensional Molecular Structure,3D Molecular Structures,Configurations, Molecular,Conformation, Molecular,Conformations, Molecular,Molecular Configurations,Molecular Conformations,Molecular Structure, 3D,Molecular Structures, 3D,Structure, 3D Molecular,Structures, 3D Molecular
D010767	Phosphorylcholine	Calcium and magnesium salts used therapeutically in hepatobiliary dysfunction.	Choline Chloride Dihydrogen Phosphate,Choline Phosphate Chloride,Phosphorylcholine Chloride,Choline Phosphate,Phosphocholine,Chloride, Choline Phosphate,Chloride, Phosphorylcholine,Phosphate Chloride, Choline,Phosphate, Choline
D002518	Ceramides	Members of the class of neutral glycosphingolipids. They are the basic units of SPHINGOLIPIDS. They are sphingoids attached via their amino groups to a long chain fatty acyl group. They abnormally accumulate in FABRY DISEASE.	Ceramide
D003198	Computer Simulation	Computer-based representation of physical systems and phenomena such as chemical processes.	Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D004583	Electrons	Stable elementary particles having the smallest known negative charge, present in all elements; also called negatrons. Positively charged electrons are called positrons. The numbers, energies and arrangement of electrons around atomic nuclei determine the chemical identities of elements. Beams of electrons are called CATHODE RAYS.	Fast Electrons,Negatrons,Positrons,Electron,Electron, Fast,Electrons, Fast,Fast Electron,Negatron,Positron
D013109	Sphingomyelins	A class of sphingolipids found largely in the brain and other nervous tissue. They contain phosphocholine or phosphoethanolamine as their polar head group so therefore are the only sphingolipids classified as PHOSPHOLIPIDS.	Sphingomyelin
D013696	Temperature	The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.	Temperatures