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Ion binding landscapes and molecular dynamics of phospholipid membranes
| Content Provider | Semantic Scholar |
|---|---|
| Author | Yang, Jing |
| Copyright Year | 2015 |
| Abstract | This thesis aims at studying the physical-chemical properties of model lipid bilayers in physiological environments. Since in such conditions biological membranes composed of phospholipids and cholesterol are surrounded by electrolyte solutions, understanding the interactions of phospholipids with cholesterol, lipid bilayers with surrounding ions, and lipid bilayers with interfacial water are of great fundamental importance. Moreover, phospholipids are classified into saturated ones and unsaturated ones according to the tail saturation. Therefore, considering the tail saturation is another important issue when studying lipid bilayers. The lipids involved in this thesis include the saturated phospholipids di-myristoil-phosphatidyl-choline (DMPC) and di-palmytoil-phosphatidyl-choline (DPPC), the unsaturated phospholipid palmytoiloleoil-phosphatidyl-coline (POPC) and cholesterol. Classical molecular dynamics simulations and well-tempered metadynamics simulations have been applied in this thesis. By applying well-tempered metadynamics simulations, we have performed systematic free energy calculations of Na+, K+, Ca2+, and Mg2+ bound to DMPC phospholipid membrane surfaces for the first time. Free energy landscapes unveil specific binding behaviors of metal cations at phospholipid membranes. This work provides a general methodology to explore the free energy landscapes for ions at complex biological interfaces which can be extended to study other interactions of interest between ions and charged headgroups in colloidal chemistry and biology. We further applied this methodology to cholesterol-containing membranes by means of systematic free energy calculations of Na+ bound to DMPC phospholipid membranes of several cholesterol concentrations. The resulting free energy landscapes further validate our methodology at membrane interfaces with higher complexity and unveil the cholesterol effects on Na+ binding at phospholipid membranes. We also studied the microscopic structure and dynamics of water and lipids in a DMPC phospholipid membrane in the liquid-crystalline phase by classical molecular dynamics simulations. Structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The physical meaning of all spectral features from lipid atomic sites is analyzed and correlated with experimental data. We have performed microsecond molecular dynamics simulations on the ternary mixtures of DPPC/POPC/cholesterol to systematically examined lipid-lipid and lipid-cholesterol interactions in the liquid-ordered and the liquid-disordered phases. The results show that the interactions of lipid-lipid and lipid-cholesterol are nontrivial properties depending on the lipid saturation and also on the mixture phase. The results are consistent with the push-pull forces derived from experiments and give systematical descriptions of the mutual interactions between various like or unlike species in different phases. |
| File Format | PDF HTM / HTML |
| Alternate Webpage(s) | http://upcommons.upc.edu/bitstream/handle/2117/96067/TJY1de1.pdf;jsessionid=D20336C9988FCC9505379566FD117BCD?sequence=1 |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
