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.
Highlights
TEM-1 β-lactamase degrades β-lactam antibiotics with a strong preference for penicillins
This study provided us with sequences and structures of enterobacteria (ENCA), the last common ancestor of various Gram-negative bacteria (GNCA), and the last common ancestor of Gram-positive and Gram-negative bacteria (PNCA)
We propose a detailed mechanism, according to which selected substitution mutations are applied to GNCA, which gradually drives its dynamics (DFI profile) towards that of TEM-1 β-lactamase
Summary
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. A complete understanding of the blueprint of their functional behavior (i.e., the relationship between their sequence, structure, dynamics, and function) and how it evolves with time could dramatically expand our ability to develop protein-based catalysts with potentially far-reaching applications to fields including chemistry, biotechnology, and medicine. One such popular target of evolutionary studies is the TEM-1 β-lactamase. This study provided us with sequences and structures of enterobacteria (ENCA), the last common ancestor of various Gram-negative bacteria (GNCA), and the last common ancestor of Gram-positive and Gram-negative bacteria (PNCA)
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