Insight from designing ideal αβ monomers and homo-oligomers

Thesis (Ph.D.)--University of Washington, 2017-06Previously, general principles relating secondary structure patterns to tertiary packing motifs enable design of different protein topologies stabilized by consistent local and non-local interactions. With the goal to achieve fine control over protein shape and size within a particular topology, the first part of my thesis extended the design rules by systematically analyzing the co-dependencies between the lengths and packing geometry of successive secondary structure elements and the backbone torsion angles of the loop linking them. I then demonstrated the fine control by the applying the extended set of rules to design series of proteins with the same fold but considerable variation in secondary structure length, loop geometry, registry between β-strands and overall shape. Solution NMR structures of four designed proteins for two different folds showed that protein shape and size can be precisely controlled within a given protein fold. These extended design principles can provide the foundation for custom design of protein structures performing desired functions. The second part of my thesis focused on homo-oligomer design. Proteins in cells often form oligomers through non-covalent interaction to execute various biological properties. Natural oligomeric proteins involve scaffold support, enzymatic reactions, signaling transduction, etc. Moreover, the intrinsic protein flexibility often facilitates protein structural changes upon oligomerization. To understand how αβ- proteins interact to form oligomers and to enable future de novo protein applications in biomaterial or molecular machinery, the second part of my thesis investigated the design of cyclic homo-oligomers using de novo proteins as building blocks and experimented with introducing flexible backbone design strategies to oligomer design process. The results suggested that de novo proteins undergo structural change for oligomerization and for homo-oligomers formed from globular building blocks, pre-organized hydrogen bonds between amines and carbonyl groups of beta strands are more effective in achieving protein interaction and shape complementarity between subunits with higher specificity