Participant: PROMISE AGEP Research Symposium, 2014
Department: Chemical and Biomolecular Engineering, A. James Clark School of Engineering
Institution: University of Maryland, College Park
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 my family moved to the United States over seven years ago. During my high school years I enjoyed participating in math and chemistry competitions, and decided to pursue a career in Engineering. I enrolled in Chemical Engineering at Montgomery College, and transfer to the University of Maryland (UMD) to complete my degree. Starting my undergraduate education I did not anticipate going to graduate school. However, participating in research projects with my faculty advisor as well as an REU (Research Experience for Undergraduates) increased my interest on graduate studies. My research experience has been on computational simulations of biological systems, I hope to gain experimental experience as I progress in the PhD program. My graduate mentor has helped me develop scientific writing and oral presentation skills. I have presented my work in 3 professional meetings as well as at local symposia at UMD; some of them sponsored by the LSAMP program, both graduate and undergraduate branches, which has also supported my studies through scholarships and fellowships. I would like to follow a career on academia, and get an early hands-on experience participating on the Future Faculty Program available in my school. This preparation along with mentoring of undergraduates in my lab, and participation on professional meetings will give me a strong foundation on which to build a career as a scientist and educator. Outside of school I am an active youth leader at my local Seventh Day Adventist Church, and enjoy doing crafts.
GENERAL SUMMARY OF GRADUATE RESEARCH
I continued my graduate studies at UMD under my undergraduate advisor’s mentoring. My research has focused on the study of physical properties of biological membrane models. These models will be used to better understand the biding mechanism and function of peripheral membrane proteins, such as the oxysterol-binding protein homologue (Osh-) family in yeast cells. The first portion of my work is the basis of my MS thesis and focuses on organelle-specific yeast membrane models that account for the correct lipid type and concentration in three membranes of yeast cells. I have presented this work at the AIChE national meeting on November 2013, and will expand it at the Biophysical meeting this February. Another portion of my studies, leading to my PhD work, includes a small peptide (ALPS motif) of peripheral protein Osh4. The function of this protein is not yet well understood, learning more about the ALPS peptide binding mechanism will give us more insight about the entire protein interaction with membrane bilayers. Computational resources from the High-Performance Computing Cluster (HPCC) at UMD, Kraken and Stampede at XSEDE (NSF grants), and time at the ANTON machine make my research possible. I currently use CHARMM, NAMD, and VMD software packages to run and analyze molecular dynamic simulations of my systems. Collaboration with the Im research group at the University of Kansas has given me the opportunity to contribute in the testing and improvement of user-friendly tools to build and/or analyze simulations trajectories, such as CHARMM-GUI and ST-Analyzer.
SELECTED LIST OF PRESENTATIONS AND PUBLICATIONS
- J.B. Klauda, V. Monje, T. Kim, W. Im. Improving the CHARM Force Field for Polyunsaturated Fatty Acid Chains. J. Phys. Chem. B, 2012, 116(31), pp 9424-9431.
- V. Monje. Improved Charmm Force Field for Polyunsaturated Fatty Acid Chains, a Study on DAPC Membranes. (poster presentation). Biophys. J.-Abstracts Issue, 2013, 104(2), pp 590a.
- V. Monje-Galvan, J.B. Klauda. Simulation studies on organelle-specific yeast membrane models and amphipathic lipid packing sensor motif binding mechanism. Model Development for Biomolecular Systems Section (AIChE National Meeting, 2013, talk #261c)
- J.D. Spencer, et al. Design of a combined heat, hydrogen, and power plant from university campus waste streams. Int. J. of Hydrogen Energy, 2013, 38(12), pp 4889-4900.
- J. Cheol Jeong, et al. ST-analyzer: A Web-based User Interface for Simulation Trajectory Analysis. (manuscript under revision at the Journal of Computational Chemistry)
- E.L. Wu, et al. CHARMM_GUI Membrane Builder Toward Realistic Biological Membrane Simulations. (manuscript submitted)
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