Participant: PROMISE AGEP Research Symposium
Department: Chemical and Biomolecular Engineering
Institution: University of Maryland College Park (UMD)
Asymmetric membrane models for the trans-Golgi Network and plasma membranes of yeast, an all-atom molecular dynamics study
We previously examined symmetric membrane models for the plasma (PM) and trans-Golgi-network (TGN) membranes of Saccharomyces cerevisiae (yeast) (Biochem 54:6852-6861). Although diverse in lipid nature and reflecting sterol compositions characteristic to those organelles, our models were not an accurate enough representation as they lacked sphingolipids (SM), relevant for membrane structure and dynamics. Once SM were parametrized for the CHARMM 36 lipid force field (BJ, 107:134-145), we included them in the new models and added lipid composition asymmetry to better reflect the complexity of these bilayers. The new models include inositol phosphoceramide (IPC) and mannose-(inositol-P)2-ceramide M(IP)2C lipids, both present in the non-cytosolic leaflets of the PM and TGN. We present a comparison study between the previous PM model and the more complex ones using common membrane properties such as surface area per lipid, bilayer thickness, deuterium order parameters, lipid diffusion constants, and lipid cluster formation. The last three properties will serve to investigate lipid phase coexistence and leaflet coupling in membrane order and diffusion. Our simulation trajectories were at least 2µs long for each of the three models (old-PM, PM, and TGN), for a total of 15 µs of simulation data run in the Anton machine at the Pittsburgh Supercomputing Center.
Binding of a curvature-sensing peptide in yeast, a molecular dynamics study
This work summarizes preliminary results in the study of a peripheral membrane protein’s (Osh4) binding mechanism. This protein is member of a family of seven homologue oxysterol binding proteins in yeast, and has six membrane binding regions (JMB 2012, 423:847-862). Nonspecific interactions with anionic lipids are an important driving force for the Osh4 attraction to membranes. The ALPS-like motif of Osh4, a 29 amino acid peptide that forms the lid to protect sterols, has been identified as a membrane curvature sensor that binds to membranes with surface-packing defects (NSMB 2007, 14(2):138-146; BJ 2013, 104:575-584). Initial results gave us insight on the binding mechanism of the peptide with charged and neutral bilayers containing different lipid types. Unsaturated lipids and increasing values of surface tension (γ) were implemented to increase the surface packing defects of our membrane models. The simplest model had only phosphatidylcholine (PC) lipids; phosphatidylserine (PS) and ergosterol (ERG) were added to model yeast membranes more closely. Finally, two complex yeast membrane models with phosphoinositol (PI) lipids (anionic) were also studied. Short simulations runs were done in triplicates, 200ns each, for pure (neutral) DOPC bilayers. The charged membranes were run on the Anton machine for 2µs per replicate run. Binding events were characterized through hydrogen bonding and binding energy calculations, finding SER8, ALA5, TYR4, and LYS15 as recurrent binding residues.
Molecular Dynamic Simulations of Organelle-Specific Yeast Membrane Models
The present study analyzes improved computational membrane models for specific organelles in yeast. Previous molecular dynamic (MD) simulations were performed on yeast membrane models having six lipid types with lipid composition averages between the endoplasmic reticulum (ER) and the plasma membrane (PM) (BJ. 97:50-58). The models studied in this research include ergosterol (ERG), phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylinositol (PI) lipids, with bilayer diversity ranging between six and eleven lipid types. MD simulations were used to equilibrate systems with lipid compositions characteristic to the ER, PM, and Golgi network (TGN) membranes based on experimental data (Yeast 15:1555-1564; Yeast 15: 601-614; JCB 146:741-754; JCB 185:601-612; ). Data analysis provided better understanding of membrane behavior, mechanical properties, order parameters, electron density profiles (EDPs), and lipid packing – the calculated properties follow expected trends. Selected models will be used to advance the study of peripheral membrane Osh4 binding mechanism and function.
I grew up in La Paz, Bolivia, and moved to the United States in 2007. I started my undergraduate studies in Chemical Engineering at Montgomery College, and transferred to the University of Maryland (UMD) to complete my degree. I volunteered as an undergraduate at my advisor’s lab doing molecular simulations and as a result decided to stay for graduate school. I completed my MS degree in December 2014, and have been blessed to present my work in several local, national, and international conferences or symposia. I am a former LSAMP Bridge to the Doctorate fellow, and enjoy participating in activities promoting minorities’ participation in science. My research focuses on the computational modeling of biological membranes using all-atom molecular dynamics. My career goal is to become a university professor at a research focused institution and establish collaboration with scientists in Latin-America to motivate computational scientific research in countries that may not have the resources or research-oriented programs to do so. Outside academics, I am an active member of my local Seventh-Day Adventist church, I enjoy watching a good movie with my husband, and I am a proud mom of a 6-month-old boy, Sebastian.
GENERAL SUMMARY OF GRADUATE RESEARCH
I developed organelle-specific membrane models for yeast S. cerevisiae to study the impact of lipid composition on bilayer properties (Biochem. 54:6852-6861). Then improved the trans-Golgi network (TGN) and plasma membrane models to reflect leaflet asymmetry and study lipid clustering modulated by sterol lipids. The endoplasmic reticulum (ER) and TGN models were later used to study lipid-protein interactions of Osh4, a lipid transport protein in yeast whose homologues in mammals have been linked to cancer cell activity. This protein transports ergosterol and phosphatidylinositol lipids between membranes, but its binding mechanism is not yet fully understood. I simulated the protein’s lid, the ALPS-like motif (Amphipathic Lipid Packing Sensor), with the ER and TGN membranes and a simpler model. I identified key residues for peptide-membrane interaction based on their interaction energy, and found ~1µs is needed for stable horizontal binding of the peptide with its hydrophobic face embedded at the lipids’ phosphate region. When simulating the full protein with the ER and TGN models, the Phenalanine loop had the strongest interaction among the protein’s six binding regions (BBA-Biomemb. 1858:1584-1593).
Additionally, I studied the effect of all butanol isomers at the water-cyclohexane interface. This small alcohol is a hydrotrope, i.e. a molecule that reduces the interfacial tension between two liquids. My simulations 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 mixture of water and cyclohexane. At low hydrotrope concentrations (< 10mol%) our simulations reproduce experimental data, but there is a need to improve simulations’ parameters to model the alcohol-oil interaction accurately at moderate to high alcohol concentrations.
SELECTED LIST OF PRESENTATIONS AND PUBLICATIONS
- Monje-Galvan, V.; Klauda, J.B. 2016. Peripheral Membrane Proteins: Tying the Knot between Experiment and Computation. BBA: Biomembranes, 1858: 1584-1593 (2016).
- Monje-Galvan, V.; Klauda, J.B. 2015. Modelling Yeast Organelle Membranes and How Lipid Diversity influences Bilayer Properties. 54(45), 6852-6861. DOI: 10.1021/acs.biochem.5b00718
- Wu, E.L.; Cheng, X.; Jo, S.; Rui, H.; Song, K.C.; Davila-Contreras, E.M.; Qi, Y.; Lee, J.; Monje-Galvan, V.; Venable, R.M.; Klauda, J.B.; Im, W. CHARMM_GUI Membrane Builder toward Realistic Biological Membrane Simulations. Comput. Chem. 35(27), 1997-2004 (2014).
- Monje-Galvan, V. & Klauda, J.B. “Lo/Ld Phase Coexistence and Interaction in Model Membranes with IPC Lipids.” Biophysical Society (2016)
- Monje-Galvan, V. & Klauda, J.B. “Interfacial Properties of Aqueous Solutions of TBA and Cyclohexane.” Congress of Theoretical Chemists of the Latin Expression, Chitel (2015, Poster in Spanish)
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