Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity

W.D.V.H. acknowledges support from National Institutes of Health (Grant: R01GM112077). S.B.O. acknowledges support from the Gordon and Betty Moore Foundations and National Science Foundation (Awards: 1715591 and 1901709). J.M.S.R. acknowledges support from Spanish Ministry of Economy and Competitiveness/FEDER Funds (Grants BIO2015-66426-R and RTI2018-097142-B-100) and the Human Frontier Science Program (Grant RGP0041/2017). V.A.R. acknowledges support from FEDER/Junta de Andalucia-Consejeria de Economia y Conocimiento (Grant E.FQM.113.UGR18). We would like to thank the beamline staff of ID30B of the ESRF (European Synchrotron Radiation Facility, Grenoble, France) for their assistance during data collection and the ESRF for the provision of time through proposals MX-2064.
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.
United 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