Structural stabilization of protein nano-capsules via modification of protein-protein interactions.

Self-assembly of protein nano-structure is an essential and ubiquitous phenomenon which plays a role in a wide range of biological processes. In this work, we have re-engineered the E. coli Bacterioferritin (EcBfr), which is a protein cage of nano dimensionality, to self-assemble into a more stable complex. The designed protein is more thermally stable and forms a higher percentage of assembled cage than the wild-type protein. To achieve this, different methods, a) alignment-based design, b) protein grafting, and c) computational protein design, were all applied to investigate and to optimize the role protein-protein interactions play in the stability and the self-assembly of this protein. The protein designed based on alignment with homologues from thermophlic organisms did not fold properly in a water soluble form and was therefore unable to be purified and characterized. Next, three proteins were designed by grafting the protein-protein interfacial residues from a thermophilic homolog onto the EcBfr scaffold. None of these proteins exhibited an increased stability. Guided by the insights made from the results of these initial two designs, computational methods were used to analyze the self-assembly of two icosatetrameric protein complexes of the ferritin superfamily. Among this group of proteins, we have determined that the thermostability of a ferritin derived from a hyperthermophilic organism does not necessarily arise from the conformational stability of the monomer but due to the stronger intermolecular interactions at the dimer interface. To investigate the possibility of engineering EcBfr for modified thermostability and oligomerization, we have used a semi-empirical method to virtually explore the energy differences of the 480 possible mutants of the C2 interface relative to the wild type EcBfr. In agreement with the calculated results, by replacement of two water-bridged asparagine residues with two edge-to-edge stacked phenylalanines at the dimer interface, the thermal unfolding midpoint of the complex increases by 15.8 °C and facilitates oligomerization into the nano-cage.Master of Scienc