Self-Assembly and Crystallization of Proteins

Self-assembly - the spontaneous and reversible organization of matter into ordered arrangements without any external direction - is the principle that governs the structure formation in living systems. The structures arising from self-assembly are ubiquitous in nature and diverse ranging from virus capsids that spontaneously reconstitute themselves from their molecular components and the tertiary structure of proteins resulting from protein folding to one of the simplest self-assembling systems in nature: S-layers which are two-dimensional crystalline envelopes of procaryotic organisms. In materials science, self-assembly is exploited to create functional nanostructures important for technological applications. A new class of materials is emerging which consists of building blocks that are designed with desired features, the final structure of the material being determined by the shape and properties of the designed building blocks. However, the understanding of how self-assembly actually works is still incomplete and understanding how specific interactions lead to a specific target structure is necessary for a bottom-up construction of novel materials. This will be investigated in the present project. Theoretical methods and computer simulations will be applied to gain insight into the physical mechanisms that determine the different structures being formed and the mechanisms that drive the transitions from one structure to another one. Simplified models, so-called patchy models, i.e., models of particles that interact via localized and directional interactions, will be employed in the study. Patchy models have been used to study numerous phenomena in molecular and colloidal systems. Here, we will develop a patchy model for S-layer proteins that self-assemble into different two-dimensional crystalline structures. While the first part of the project focuses on the study of the structural properties of the self-assembled materials, the second part will concentrate on the kinetic properties of the self-assembly process, i.e., how does self-assembly proceed and which intermediate structures are formed during the self-assembly process? In particular, I intend to study at a microscopic level the phenomenon of protein crystal nucleation in which a protein crystal is born out of a metastable supersaturated fluid phase. In order to bridge the time-scale gap that is typical for computer simulations of activated processes like nucleation and to cope with the lack of knowledge of an appropriate reaction coordinate, I will apply transition path sampling - an advanced computer simulation technique based on a statistical mechanics of trajectories which was developed for the simulation of rare but important events in complex systems. Analysis of the transition states will give me insight into the mechanism of the structural organization process. Understanding the mechanism of self-assembly and crystallization of proteins, from a theoretical point of view, is not only of fundamental interest but also of technological relevance. Applications are numerous ranging from drug design and drug delivery vehicles to devices for photonics, microelectronic systems and sensors.

The goal of the project has been the study of various self-assembly processes the spontaneous and reversible organization of matter into ordered arrangements without any external direction. The structures arising from self-assembly are diverse and we have studied different self-assembly mechanisms using various techniques based on the principles of statistical mechanics. On the one hand we have focused on the self-assembly of simple building blocks like macromolecules into bulk thermodynamic phases such as fluids or vapours, i.e. we investigated phase transitions in these systems. Studying the phase behaviour of macromolecules such as proteins or colloids has turned out to be a big challenge both for computer simulations and for theoretical models since the range of the effective interaction between the molecules is significantly smaller than the size of the building blocks and an accurate localization of the coexistence curve and the critical point becomes extremely difficult. Using simple model systems and a rather sophisticated theoretical approach we have been able to accurately predict the liquid-vapour transition of protein and colloidal suspensions and we confirmed Noro-Frenkel's extended law of scaling according to which the properties of a short-ranged system at a given temperature and density are independent of the detailed form of the interaction, but just depend on the value of the second virial coefficient that can be regarded as an integral over the interaction.In the second part of the project we have studied the self-assembly using computer simulations. In particular, we have been using molecular dynamics simulations to study the self-assembly of liposomes. These systems have become established as one of the most reliable drug delivery systems. Lipsomes are self-assembled spherical vesicles, that are typically 100nm in diameter, consisting of a lipid bilayer that is surrounding an aqueous core. The great advantage of liposomes which renders them particularly attractive for drug delivery systems is their ability to both encapsulate hydrophobic cargo in the lipid membrane interior and hydrophilic cargo in the aqueous lumen or attached to the surface of the vesicle. In computer simulations we have seen both the formation of (metastable) spherical micelles and the formation of (stable) liposomes. It turned out that the final assembly is highly sensitive to the starting configuration of the simulations and depends strongly on the water concentration. In particular, we have observed the formation of a hemifused vesicle, i.e. a vesicle obtained by fusion of lipid vesicles, where the aqueous interiors of the two initial vesicles are left unmixed.