Molecular modelling of quatsome nanovesicles

Abstract

This thesis is devoted to the theoretical and computational study at atomistic and molecular scales of the properties of novel organic nanoparticles called “Quatsomes” (vesicles made by mixing CTAB cationic surfactant and cholesterol) as well as the interactions of Quatsomes with different types of fluorescent molecules. The methodology employed is computational molecular modelling. It includes modelling of the interactions between molecules at different scales and resolutions (DFT electronic structure calculations, atomistic molecular mechanics force fields and coarse-grain molecular mechanics force fields) and molecular dynamics simulations at atomistic and coarse-grain molecular resolutions. Most of the results have observable consequences that have been confirmed experimentally.

The thesis is divided into an Introduction to the topic (with a brief explanation of the main experimental results and the main theoretical concepts), a chapter describing in detail the methods to be employed in the thesis, four chapters containing new results and a chapter with conclusions and perspectives.

The results of the thesis are presented in two parts. The first part (Chapters 3 and 4) contains the results concerning the simulations and calculations of structure and properties of the Quatsome vesicle from atomistic and coarse-grain molecular simulations. The second part (Chapters 5 and 6) contains the simulation study of the interaction of Quatsome vesicles with different types of dyes. The atomistic simulation results presented in Chapter 3 provide a detailed characterization of the properties of the Quatsome bilayer. The molecular organization of the components across the bilayer (positioning, orientation and diffusion of the component molecules) was studied as well as mechanical properties such as bending modulus and area expansion modulus. The effect of temperature and added salt was also analyzed. Remarkably, it was found that the orientation of the molecules has a spontaneous symmetry breaking between the two leaflets of the bilayer and states with different orientations coexist, a theoretical prediction that has been tested experimentally. In Chapter 4 two coarse-grain Martini-type parametrizations of a force field for CTAB surfactant (one for explicit solvent and one for implicit solvent simulations) was developed and successfully tested against atomistic simulations. The model was further employed to perform simulations of full Quatsome vesicles. These simulations revealed that the Quatsome vesicle is made of planar faces linked by curved defects, a kind of vesicle organization never found before. These predictions were confirmed by experimental Cryo-TEM images. Chapters 5 and 6 start by developing (from DFT) CHARMM compatible atomistic force fields for simulation of different dyes (fluorescein in Chapter 4 and DiD and DiI in Chapter 5). These force fields were employed in molecular dynamics simulations of the interactions of these dyes with Quatsomes. The results demonstrate that despite the hydrophilic fluorescein dye interacts strongly with Quatsome (via electrostatic interactions), the adsorption of the dye competes with the more favorable formation of soluble molecular clusters. Hence, a more suitable approach is to employ hydrophobic dyes such as DiI and DiD. The simulations reported in the thesis show that these dyes are integrated in the bilayer without deforming or altering the Quatsome and without aggregating inside the Quatsome bilayer, thus providing suitable alternatives for developing fluorescent vesicles.

The conclusions and perspectives section shows that the thesis not only present many new results but also has many possible future perspectives in different directions: vesicles with resonant energy transfer, conceptual aspects regarding the spontaneous self-assembly of vesicles, possibility of replacing the components by other different bilayer components. All these options have been initially explored and all of them are very promising.