Paper Citing NAMD - Abstract
Monje-Galvan, Viviana; Klauda, Jeffery B.
Modeling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties
BIOCHEMISTRY, 54:6852-6861, NOV 17 2015
Membrane lipids are important for the health and proper function of cell membranes. We have improved computational membrane models for specific organelles in yeast Saccharomyces cerevisiae to study the effect of lipid diversity on membrane structure and dynamics. Previous molecular dynamics simulations were performed by Jo et al. [(2009) Biophys J. 97, 50-58] on yeast membrane models having six lipid types with compositions averaged between the endoplasmic reticulum (ER) and the plasma membrane (PM). We incorporated ergosterol, phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol lipids in our models to better describe the unique composition of the PM, ER, and trans-Golgi network (TGN) bilayers of yeast. Our results describe membrane structure based on order parameters (S-CD), electron density profiles (EDPs), and lipid packing. The average surface area per lipid decreased from 63.8 +/- 0.4 angstrom(2) in the ER to 47.1 +/- 0.3 angstrom(2) in the PM, while the compressibility modulus (K-A) varied in the opposite direction. The high S-CD, values for the PM lipids indicated a more ordered bilayer core, while the corresponding lipids in the ER and TGN models had lower parameters by a factor of at least 0.7. The hydrophobic core thickness (2D(c)) as estimated from EDPs is the thickest for PM, which is in agreement with estimates of hydrophobic regions of transmembrane proteins from the Orientation of Proteins in Membranes database. Our results show the importance of lipid diversity and composition on a bilayer's structural and mechanical properties, which in turn influences interactions with the proteins and membrane-bound molecules.
