Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity
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AuthorModi, Tushar; Risso, Valeria Alejandra; Martínez Rodríguez, Sergio; Gavira Gallardo, José Antonio; Sánchez Ruiz, José Manuel
Modi, T., Risso, V.A., Martinez-Rodriguez, S. et al. Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity. Nat Commun 12, 1852 (2021). [https://doi.org/10.1038/s41467-021-22089-0]
SponsorshipUnited States Department of Health & Human Services National Institutes of Health (NIH) - USA R01GM112077; Gordon and Betty Moore Foundations; National Science Foundation (NSF) 1715591 1901709; Spanish Ministry of Economy and Competitiveness/FEDER Funds BIO2015-66426-R RTI2018-097142-B-100; Human Frontier Science Program RGP0041/2017; FEDER/Junta de Andalucia-Consejeria de Economia y Conocimiento E.FQM.113.UGR18
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.