Directed evolution of a beta-lactamase samples a wide variety of conformational states

In directed evolution, enzyme activity is improved in successive generations of laboratory evolution, which can be described by a simple stepwise climb toward a peak in the fitness landscape. In a naive model of evolution, it can be assumed that each enzyme variant along this path is in a single, well-defined state that differs slightly from the previous one. We analyzed the structural changes in mutants of the β-lactamase BlaC from Mycobacterium tuberculosis obtained via directed evolution for increased ceftazidime hydrolysis activity. Crystal structures of three successive mutants only show an increase in the dynamics of a loop that lines the active site (Ω-loop), enabling better access of the large substrate. However, NMR spectra of wild type and nine mutants of different branches of the directed evolution experiment show a much more diverse and complex picture of the conformational effects. Many mutants show micro-millisecond dynamics for certain regions and most show peak doubling, indicative of two or more conformations being populated. Thus, the straightforward climb to increased ceftazidime activity in the fitness landscape masks a complex trajectory in the conformational landscape, emphasizing the complex and epistatic interplay that single mutations can have on the structure and dynamics of enzymes.