THE DESIGN OF TWO PROTEINS THAT HAVE 100% SEQUENCE IDENTITY BUT ENCODE DIFFERENT FOLDS

Abstract

It is well-established that proteins adopt specific three-dimensional structures. However, examples of proteins that can adopt more than one folded state have become increasingly more common. The objective of this thesis is to determine how three common, small folds are connected in sequence space. The folds this work focuses on are a 3-α-helix bundle, an α/β plait, and a 4β+α fold. Topological alignment and site-directed mutagenesis were used to develop engineered variants of the 3-α-helix bundle and the α/β plait folds that maintain their highly distinct native folds even though their sequences are 100% identical. CD and NMR data suggest that both proteins were stable and folded. This engineered fold switch demonstrates that the fold preference of a sequence is dependent upon stabilizing interactions within the context of the protein. These fold switching proteins have important implications in areas such as protein design, human disease, and structural biology.