Tubular biological micro- and nanostructures : Physical mechanisms of self-assembly and functioning

Applications of classical solid state physics methods such as X-ray diffraction analysis and electron microscopy allowed making a giant step in understanding of cellular membranes’ structure. Today since their composition and structure are well known, the focus of research has shifted to active processes involving cell membranes. As we know, such processes as endocytosis involve substantial shape changes of cell membranes, which are performed by curvature-inducing proteins. One of the most popular methods to study how these proteins interact with lipid membranes and each other is TLM-pulling experiment, where tubular lipid membrane (TLM) is formed from the vesicle by pulling. Similar structures connect endocytic vesicles with the donor compartments and serve as channels for the matter transfer within the cell and between adjacent cells establishing cell-to-cell communication pathway. Such systems formed in vitro due to their simplicity and high homogeneity can be accurately described by the means of theoretical physics.In the first part of the present thesis, we develop a theoretical model of the TLM pulled out of the vesicle on the basis of classical mechanics and thermodynamics and apply it to the TLM-pulling experiments with curvature-inducing proteins adsorption. The developed model takes into account asymmetry of the lipid bilayer, surface tension, longitudinal force applied to the TLM and pressure difference in the system. We model the action that proteins exert on TLM via sets of forces normal to the membrane’s surface and satisfying conditions of mechanical equilibrium. This novel force multipole approach allows us to model anisotropic interactions between proteins adsorbed at the membrane surface that are induced by the membrane deformation. Our theory describes early stages of protein scaffolds formation i.e. characteristic arrangement of proteins and their high affinity to the membrane ends. Collective behavior of curvature-inducing proteins is extremely important for performing large scale deformations of lipid membranes during such processes as endo and exocytosis, virus entry in the host cell as well as formation and exit of daughter virions later on. Studying of the latter process can possibly lead to the development of fundamentally new methods of viral disease treatment.The second part of the thesis is devoted to the study of zebrafish embryo’s dorsal aorta (DA). It focuses on DA’s shape evolution during the Endothelio-Haematopoietic Transition (EHT). The EHT process leads to the extrusion of haematopoietic stem/progenitor cells (HSPCs) which will later on colonize haematopoietic organs allowing haematopoiesis throughout adult life. This process seems to be universal and should also apply for both mammals and birds, which makes its investigation a fundamental problem of embryology.DA has a cylindrical geometry that makes it similar to the TLM’s, however at the same time DA is much bigger than lipid tubes, has a non-zero share modulus and is embedded in the matrix of surrounding tissues, which makes it a much more complex system from the mechanical perspective. We relate the global shape changes of the aorta during EHT to generic principles of mechanics and show that mechanical instabilities leading to the aorta shape evolution are invoked by different stresses resulting from the growth inhomogeneities and interaction with surrounding tissues. Based on the performed theoretical analysis and the data obtained with a help of 4D confocal microscopy we propose a detailed scheme of the process and postulate that mechanical instabilities prepare and support the whole EHT process prior to its specific genetic control. Our interpretation suggests a universal and self-organized mechanism underlying collective tissue reorganization processes in the growing organisms such as EHT.