Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity
Tushar Modi, Valeria A. Risso, Sergio Martínez‐Rodríguez, Jose A. Gavira, Mubark D. Mebrat, Wade D. Van Horn, José M. Sánchez‐Ruiz, S. Banu Ozkan
Abstract
TEM-1 β-lactamase degrades β-lactam antibiotics with a strong preference for penicillins. Sequence reconstruction studies indicate that it evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency. This generalist to specialist conversion involved more than 100 mutational changes, but conserved fold and catalytic residues, suggesting a role for dynamics in enzyme evolution. Here, we develop a conformational dynamics computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism. By deliberately weighting and altering the conformational dynamics of a putative Precambrian β-lactamase, we engineer enzyme specificity that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements. Our conformational dynamics design thus re-enacts the evolutionary process and provides a rational allosteric approach for manipulating function while conserving the enzyme active site.