title: Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme.
abstract: β-Lactamases are produced by many modern bacteria as a mechanism of resistance toward β-lactam antibiotics, the most common antibiotics in use. β-Lactamases, however, are ancient enzymes that originated billions of years ago. Recently, proteins corresponding to 2- to 3-Gy-old Precambrian nodes in the evolution of Class A β-lactamases have been prepared and shown to be moderately efficient promiscuous catalysts, able to degrade a variety of antibiotics with catalytic efficiency levels similar to those of an average modern enzyme. Remarkably, there are few structural differences (in particular at the active-site regions) between the resurrected enzymes and a penicillin-specialist modern β-lactamase. Here, we propose that the ancestral promiscuity originates from conformational dynamics. We investigate the differences in conformational dynamics of the ancient and extant β-lactamases through MD simulations and quantify the contribution of each position to functionally related dynamics through Dynamic Flexibility Index. The modern TEM-1 lactamase shows a comparatively rigid active-site region, likely reflecting adaptation for efficient degradation of a specific substrate (penicillin), whereas enhanced deformability at the active-site neighborhood in the ancestral resurrected proteins likely accounts for the binding and subsequent degradation of antibiotic molecules of different size and shape. Clustering of the conformational dynamics on the basis of Principal Component Analysis is in agreement with the functional divergence, as the ancient β-lactamases cluster together, separated from their modern descendant. Finally, our analysis leads to testable predictions, as sites of potential relevance for the evolution of dynamics are identified and mutations at those sites are expected to alter substrate-specificity.
authors.affiliation: Center for Biological Physics, Department of Physics, Arizona State University.
authors.forename: Taisong
authors.initials: T
authors.lastname: Zou
authors.affiliation: Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
authors.forename: Valeria A
authors.initials: VA
authors.lastname: Risso
authors.affiliation: Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-Universidad de Granada), Granada, Spain.
authors.forename: Jose A
authors.initials: JA
authors.lastname: Gavira
authors.affiliation: Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada, Spain sanchezr@ugr.es banu.ozkan@asu.edu.
authors.forename: Jose M
authors.initials: JM
authors.lastname: Sanchez-Ruiz
authors.affiliation: Center for Biological Physics, Department of Physics, Arizona State University sanchezr@ugr.es banu.ozkan@asu.edu.
authors.forename: S Banu
authors.initials: SB
authors.lastname: Ozkan
mesh_terms: D000900:Anti-Bacterial Agents / Q000378:metabolism; D001419:Bacteria / Q000201:enzymology*; D020134:Catalytic Domain; D019143:Evolution, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation; D025341:Principal Component Analysis; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity; D001618:beta-Lactamases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D001618:beta-Lactamases
keywords: ancestral enzyme; molecular dynamics; protein dynamics and structure