Molecular basis of the evolution of new protein functions: Kemp elimination and phosphoryl transfer reactions

Abstract

This is a series of investigations into the molecular basis of the evolution of new protein functions. The broad objective of this work was to determine exactly how a series of single amino acid mutations, typical of an evolutionary trajectory, can result in dramatic changes in catalytic activity, specificity and protein solubility. Various strategies were employed to achieve this aim, including analysis of existing literature concerning the various models and theories relating to molecular evolution, protein crystallography, extensive enzyme kinetics and thermodynamic analysis, theoretical analysis of catalytic mechanisms and computational simulation of protein dynamics. Three model systems were investigated: the de novo designed Kemp Eliminase (KE07), the metallo-beta-lactamases NDM1 and VIM2, and the N-acyl-homoserine lactonase AiiA. Based on these studies, I was able to identify three clear phenomena that are important in molecular evolution: first, preorganization of the active sites residues is essential for efficient catalysis; second, remote mutations are capable of causing quite drastic rearrangements to the active site and substrate binding site by modulating the conformational landscape of a protein; third, intramolecular epistasis, the way that mutations interact with each other and the sequence background that they are introduced to, can constrain evolutionary trajectories and make the evolutionary potential of a protein contingent on its starting sequence. In Chapters 3-5 I focus on KE07, performing detailed kinetic analysis of hydrogenated and deuterated substrate, which revealed entropy-enthalpy compensation in the improvement in activity as well as an unusual change in the kinetic properties in the middle of the evolutionary trajectory. This is followed by comprehensive structural analysis, which reveals the enzyme has evolved to adopt a completely unexpected active site configuration via remote mutations. Finally, using computational simulations and solution fluorescence spectroscopy, I confirm that the in crystallo and kinetic observations are consistent with the behaviour of the protein in solution. Chapter 6 consists of a manuscript that describes the effects of conformational tinkering on the N-acyl-homoserine lactonase AiiA, specifically how remote mutations can have dramatic effects on activity by modulating the conformation of the active site. My contribution to this work included crystal structures and molecular dynamics simulations. Finally, Chapter 7 is a second manuscript that focuses on evolutionary contingency: by examining two related sub-families of the metallo-beta-lactamases, NDM1 and VIM2 we show that the evolvability of each is constrained by intramolecular epistasis and contingent on the starting sequence. To achieve the same final goal (greater whole cell activity), NDM1 evolved higher activity, while VIM2 evolved greater solubility. The crystals structures that I solved revealed the structural basis for the enhanced activity in NDM1 and that enhanced solubility in VIM2 is a result of an unprecedented (for an enzyme) structural rearrangement where the two halves of the alpha/beta sandwich metallo-beta-lactamase protein fold have separated and rearranged in an domain-swapped dimer.