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

• Published in: Nature communications 2021-03, Vol.12 (1), p.1852-1852, Article 1852
• Main Authors: Modi, Tushar, Risso, Valeria A., Martinez-Rodriguez, Sergio, Gavira, Jose A., Mebrat, Mubark D., Van Horn, Wade D., Sanchez-Ruiz, Jose M., Banu Ozkan, S.
• Format: Article
• Language: English
• Subjects: 101/6; 119/118; 631/114/469; 631/57/2266; 639/766/747; 82/80; Allosteric properties; Amides; Amino Acid Sequence - genetics; Amino acids; Antibiotics; beta-Lactamases - genetics; beta-Lactamases - metabolism; Catalytic Domain - genetics; Computational Biology; Computer applications; Degradation; Dynamics; Enzymes; Escherichia coli - drug effects; Escherichia coli - enzymology; Evolution; Evolution, Molecular; Flexibility; Humanities and Social Sciences; Molds; Molecular Dynamics Simulation; multidisciplinary; Penicillins - metabolism; Precambrian; Protein Conformation; Protein structure; Proteins; Science; Science (multidisciplinary); Substrate Specificity; Substrates; β Lactamase; β-Lactam antibiotics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-22089-0

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. TEM-1 β-lactamase evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency and degrades β-lactam antibiotics with a strong preference for penicillins. Here authors developed a computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism and show a putative Precambrian β-lactamase that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements.