Modeling Yeast Organelle Membranes and How Lipid Diversity
Influences Bilayer Properties
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Abstract
Membrane
lipids are important for the health and proper function
of cell membranes. We have improved computational membrane models
for specific organelles in yeast <i>Saccharomyces cerevisiae</i> to study the effect of lipid diversity on membrane structure and
dynamics. Previous molecular dynamics simulations were performed by
Jo et al. [(2009) <i>Biophys J.</i> <i>97</i>,
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
(<i>S</i><sub>CD</sub>), electron density profiles (EDPs),
and lipid packing. The average surface area per lipid decreased from
63.8 ± 0.4 Å<sup>2</sup> in the ER to 47.1 ± 0.3 Å<sup>2</sup> in the PM, while the compressibility modulus (<i>K</i><sub>A</sub>) varied in the opposite direction. The high <i>S</i><sub>CD</sub> 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 (2<i>D</i><sub>C</sub>) 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
