Physics
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Item LIPID FORCE FIELD PARAMETERIZATION FOR IMPROVED MODELING OF ION-LIPID INTERACTIONS AND ETHER LIPIDS, AND EVALUATION OF THE EFFECTS OF LONG-RANGE LENNARD-JONES INTERACTIONS ON ALKANES(2019) Leonard, Alison N; Klauda, Jeffery B; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Chemical specificity of lipid models used in molecular dynamics simulations is essential to accurately represent the complexity and diversity of biological membranes. This dissertation discusses contributions to the CHARMM36 (C36) family of lipid force fields, including a revised model for the glycerol-ether linkage found in plasmalogens and archaeal membranes; interaction parameters between ions and lipid oxygens; and evaluation of the effects of long-range Lennard-Jones parameters on alkanes. Long-range Lennard-Jones interactions have a significant impact on structural and thermodynamic properties of systems with nonpolar regions such as membranes. Effects of these interactions on properties of alkanes are investigated. Implementation of the Lennard-Jones particle-mesh Ewald (LJ-PME) method with the C36 additive and Drude polarizable force fields improves agreement with experiment for thermodynamic and kinetic properties of alkanes, with Drude outperforming the additive FF for nearly all quantities. Trends in the temperature dependence of the density and isothermal compressibility are also improved. Phospholipids containing an ether linkage between the glycerol backbone and hydrophobic tails are prevalent in human red blood cells and nerve tissue. Ab initio results are used to revise linear ether parameters and develop new parameters for the glycerol-ether linkage in lipids. The new force field, called C36e, more accurately represents the dihedral potential energy landscape and improves solution properties of linear ethers. C36e allows more water to penetrate an ether-linked lipid bilayer, increasing the surface area per lipid compared to simulations carried out with the original C36 parameters and improving structural properties. In addition to modulating membrane structure, lipid-ion interactions influence protein-ligand binding and conformations of membrane-bound proteins. Interaction parameters are introduced describing Be2+ affinity for binding sites on lipids. Experimental binding affinities reveal that Be2+ strongly binds to phosphoryl groups. Revised interaction parameters reproduce binding affinities in solution simulations. In a separate effort, experimental results for the radius of gyration (R_g) of polyethylene glycol (PEG) in various concentrations of KCl reveal that, while C36e parameters reproduce experimental R_g of PEG in the absence of KCl, adding salt results in underestimation of〖 R〗_g. It is found that the water shell around PEG affects R_g calculated from neutron scattering experiments, and K+-PEG interactions increase the gauche character of PEG.Item Structure and Dynamics of Microtentacles(2016) Ory, Eleanor Claire-higgins; Losert, Wolfgang; Martin, Stuart; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)While modern cancer diagnostics and treatments are often interpreted through a biomolecular perspective, cancer abounds with many mechanically interesting characteristics and questions. Metastasis, the process by which a primary tumor spreads and forms a second tumor in a distant site is currently responsible for 90% of cancer fatalities [1–3]. One of the key limiting steps in metastasis is extravasa- tion; the process by which a circulating tumor cell (CTC) moves from the blood- stream into surrounding tissue. So far, most in vitro studies in metastasis focus on cell migration and invasiveness with few focused on reattachment of cells to a blood vessel wall, and extravasation. One possible attachment mechanism involves tubulin-based structures called microtentacles, which have been observed to poke into crevices between cells that line blood vessels. Based on biomolecular assays, the current hypothesis is that microtentacles are formed as the result of unbalanced, mechanical interactions between microtubules and actin, allowing microtubules to push the plasma membrane beyond the cell body. The focus of my thesis is to gain insights into the dynamics and mechanical properties of microtentacles and evaluate how microtentacles may be altered by cytoskeletal drugs. In this thesis, I will measure changes in microtubule dynamics using cytoskele- tal drugs to the actomyosin cortex and microtubules. The first study presented examines how drug treatments targeting the actomyosin cortex impact microtubule dynamics for attached cells. The results of the first study demonstrate that weaken- ing the actomyosin cortex allows microtubule end-binding-protein-1 (EB1) to move beyond the cell body boundary. Weakening the actomyosin cortex also results in changes to the speed and straightness of microtubule growth. In the second study, an image analysis framework is presented to quantify microtentacles as well as an eval- uation of the dynamics of microtubules in suspended cells. The study demonstrates a successful image analysis technique that can evaluate microtentacle phenotype for both free-floating and tethered cells as well as dynamics for tethered cells. This second study shows that while microtubule stabilizing drug treatment with Taxol increases total microtentacle phenotype, it also reduces microtentacle dynamics. On the other hand, while microtubule destabilizing drug treatment Colchicine decreases total microtentacle phenotype, Colchicine also reduces microtentacle dynamics. As a summary and outlook, I present a mechanical framework and present hypotheses for 4 different genetic modifications spanning a spectrum of different cytoskeletal states. I also show preliminary, qualitative results for 3 out of the 4 different cell lines. Critical to evaluating microtentacles within this physical framework is a direct mechanical assay; here, I show preliminary work taken at the University of Leipzig on an optical stretcher. Given that microtentacles have demonstrated to be a sufficient prerequisite for reattachment, better understanding of what circumstances lead to microtentacles is a critical basic research question. My work applies a physical perspective to the bal- ance between the actomyosin cortex and microtubules and demonstrates changes in microtubule dynamics. Such work contributes towards the possibility of identifying morphological and dynamics signatures of CTCs with higher metastatic potential.