COMPUTATIONAL STUDIES ON ORGANELLE-SPECIFIC YEAST MEMBRANE MODELS

Computational models were built for the endoplasmic reticulum (ER), trans-Golgi network (TGN), and plasma membranes (PM) of yeast Saccharomyces cerevisiae. Based on experimental data, ergosterol, phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol lipids were included. Lipid packing, order parameters (SCD), electron density profiles (EDPs), and lipid rotation were studied for each model. The average surface area per lipid decreased from 63.82±0.03 Å2 in the ER to 47.09±0.12 Å2 at the PM; while the compressibility modulus (KA) varied in opposite direction (PM>TGN>ER). The SCD values were higher (more ordered) for the PM lipids than the ER and TGN membranes by a factor of 1.5. The bilayer thickness estimated from EDPs was larger for the PM (43.9±0.1 Å) than the ER or TGN (37.6±0.1 Å). These properties followed expected experimental trends and were compared against a previous model built by Jo et al. (Biophys J. 2009, 97:50-58)

Computational Studies of Membrane Models and their Interaction with a Peripheral Protein in Yeast, and Disruption of the Water-Oil Interface by a Hydrotrope

Biological and non-biological interfaces were studied using all-atom molecular dynamics simulations to understand the interaction between different molecules at the atomic level. Simulation were run to analyze the dynamics and structure of cell membrane models and their interaction with a specific protein. Additionally, the effect of a small alcohol at the water-oil interface was examined as a model for amphiphilic molecules, which are relevant in chemistry and biology. Previously developed organelle-specific membrane models for yeast S. cerevisiae (Biochem. 54:6852-6861) were improved to reflect leaflet asymmetry of the trans-Golgi network (TGN) and plasma membranes. Each model was built based on experimental trends to study interleaflet coupling and lipid clustering. The (previous) symmetric endoplasmic reticulum (ER) and TGN models were further used to study the effect of sterol type in the structural properties of the membrane, and lipid-protein interactions with a lipid transport protein in yeast, Osh4. The protein’s phenylalanine loop was determined to have the strongest interaction with the bilayer among the protein’s six binding regions (BBA-Biomemb. 1858:1584-1593). The protein’s lid, the ALPS-like motif (Amphipathic Lipid Packing Sensor), was also simulated with simple (2-lipid) bilayers and with the symmetric ER and TGN models. Key residues for peptide-membrane interaction were identified based on their interaction energy, and a time scale of ~1µs determined for stable peptide binding. The interfacial dynamics between water and cyclohexane were examined in the presence of a hydrotrope - an amphiphilic molecule that reduces the interfacial tension between two liquids. Simulations were run for water-cyclohexane systems and all butanol isomers separately to understand the effect of this hydrotrope’s chemical structure on the interface. The results reproduced experimental data trends, showing that a hydrotrope concentration of as little as 0.6mol% in the aqueous phase reduces the interfacial tension to nearly half the value of a binary water-cyclohexane mixture. Tert-butanol was further compared with experimental studies showing that at low concentrations (< 10mol%) the simulations accurately reproduce experimental data. In addition, theoretical correlations from simulation data show the system follows van der Waals theory of smooth interfaces, and describe the crossover behavior of this hydrotrope from surfactant-like to co-solvent based on its concentration in solution, and describe the crossover behavior of this hydrotrope from surfactant-like to co-solvent based on its concentration in solution

CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations

This is the peer reviewed version of the following article: Wu, E. L., Cheng, X., Jo, S., Rui, H., Song, K. C., Dávila-Contreras, E. M., … Im, W. (2014). CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations. Journal of Computational Chemistry, 35(27), 1997–2004. http://doi.org/10.1002/jcc.23702, which has been published in final form at http://doi.org/10.1002/jcc.23702. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulation through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builderthat allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types such as phosphoinositides, cardiolipin, sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: cardiolipin lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments

Binding mechanism of the matrix domain of HIV-1 gag on lipid membranes

Specific protein-lipid interactions are critical for viral assembly. We present a molecular dynamics simulation study on the binding mechanism of the membrane targeting domain of HIV-1 Gag protein. The matrix (MA) domain drives Gag onto the plasma membrane through electrostatic interactions at its highly-basic-region (HBR), located near the myristoylated (Myr) N-terminus of the protein. Our study suggests Myr insertion is involved in the sorting of membrane lipids around the protein-binding site to prepare it for viral assembly. Our realistic membrane models confirm interactions with PIP2 and PS lipids are highly favored around the HBR and are strong enough to keep the protein bound even without Myr insertion. We characterized Myr insertion events from microsecond trajectories and examined the membrane response upon initial membrane targeting by MA. Insertion events only occur with one of the membrane models, showing a combination of surface charge and internal membrane structure modulate this process

Two sterols, two bilayers: insights on membrane structure from molecular dynamics

<p>Cholesterol (CHL) and ergosterol (ERG) are two predominant sterols in eukaryotic cells. The differences in their chemical structure can influence membrane structure and dynamics; this study discusses the effect CHL and ERG have on yeast membrane models with characteristic lipid composition for the endoplasmic reticulum (ER) and the trans-Golgi network (TGN) of yeast <i>Saccharomyces cerevisiae</i>. Molecular dynamics simulations were used to understand the atomic details of the sterols’ interaction with lipid bilayers that have both saturated and unsaturated tails as well as neutral and charged headgroups. Our models include phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine and phosphatidylinositol lipids to mimic the environment of the ER and TGN. The models for each organelle are identical, respectively, except for the sterol type. The overall surface area per lipid has no statistical difference between models for the same organelle, 63.6 ± 0.4 Å² in the ER and 60.9 ± 0.4 Å² in the TGN with either ERG or CHL. However, the compressibility modulus is approximately 30% lower in the models with ERG. We analyse this difference based on the sterols’ chemical structure and examine other membrane properties such as the lipid tails order parameters, bilayer thicknesses, sterol tilt angles and sterol spatial orientation with respect to the lipid tails to compare trends with existing data from simulation as well as experiment. This is the first study, to our knowledge, to examine the effect of sterol type on multi-lipid bilayer models with all-atom molecular dynamics.</p

Modeling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties

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>_CD), electron density profiles (EDPs), and lipid packing. The average surface area per lipid decreased from 63.8 ± 0.4 Ų in the ER to 47.1 ± 0.3 Ų in the PM, while the compressibility modulus (<i>K</i>_A) varied in the opposite direction. The high <i>S</i>_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 (2<i>D</i>_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

Cooperative Membrane Binding of HIV‑1 Matrix Proteins

The HIV-1 assembly process begins with a newly synthesized Gag polyprotein being targeted to the inner leaflet of the plasma membrane of the infected cells to form immature viral particles. Gag–membrane interactions are mediated through the myristoylated (Myr) N-terminal matrix (MA) domain of Gag, which eventually multimerize on the membrane to form trimers and higher order oligomers. The study of the structure and dynamics of peripheral membrane proteins like MA has been challenging for both experimental and computational studies due to the complex transient dynamics of protein–membrane interactions. Although the roles of anionic phospholipids (PIP2, PS) and the Myr group in the membrane targeting and stable membrane binding of MA are now well-established, the cooperative interactions between the MA monomers and MA-membrane remain elusive in the context of viral assembly and release. Our present study focuses on the membrane binding dynamics of a higher order oligomeric structure of MA protein (a dimer of trimers), which has not been explored before. Employing time-lagged independent component analysis (tICA) to our microsecond-long trajectories, we investigate conformational changes of the matrix protein induced by membrane binding. Interestingly, the Myr switch of an MA monomer correlates with the conformational switch of adjacent monomers in the same trimer. Together, our findings suggest complex protein dynamics during the formation of the immature HIV-1 lattice; while MA trimerization facilitates Myr insertion, MA trimer–trimer interactions in the immature lattice can hinder the same