title: Stochastic ensembles, conformationally adaptive teamwork, and enzymatic detoxification.
abstract: It has been appreciated for a long time that enzymes exist as conformational ensembles throughout multiple stages of the reactions they catalyze, but there is renewed interest in the functional implications. The energy landscape that results from conformationlly diverse poteins is a complex surface with an energetic topography in multiple dimensions, even at the transition state(s) leading to product formation, and this represents a new paradigm. At the same time there has been renewed interest in conformational ensembles, a new paradigm concerning enzyme function has emerged, wherein catalytic promiscuity has clear biological advantages in some cases. "Useful", or biologically functional, promiscuity or the related behavior of "multifunctionality" can be found in the immune system, enzymatic detoxification, signal transduction, and the evolution of new function from an existing pool of folded protein scaffolds. Experimental evidence supports the widely held assumption that conformational heterogeneity promotes functional promiscuity. The common link between these coevolving paradigms is the inherent structural plasticity and conformational dynamics of proteins that, on one hand, lead to complex but evolutionarily selected energy landscapes and, on the other hand, promote functional promiscuity. Here we consider a logical extension of the overlap between these two nascent paradigms: functionally promiscuous and multifunctional enzymes such as detoxification enzymes are expected to have an ensemble landscape with more states accessible on multiple time scales than substrate specific enzymes. Two attributes of detoxification enzymes become important in the context of conformational ensembles: these enzymes metabolize multiple substrates, often in substrate mixtures, and they can form multiple products from a single substrate. These properties, combined with complex conformational landscapes, lead to the possibility of interesting time-dependent, or emergent, properties. Here we demonstrate these properties with kinetic simulations of nonequilibrium steady state (NESS) behavior resulting from energy landscapes expected for detoxification enzymes. Analogous scenarios with other promiscuous enzymes may be worthy of consideration.
authors.affiliation: Department of Medicinal Chemistry and Department of Applied Mathematics, University of Washington, Seattle, Washington 98190, United States. winky@uw.edu
authors.forename: William M
authors.initials: WM
authors.lastname: Atkins
authors.forename: Hong
authors.initials: H
authors.lastname: Qian
mesh_terms: D020168:ATP Binding Cassette Transporter, Subfamily B, Member 1 / Q000737:chemistry* / Q000493:pharmacokinetics; D001693:Biological Transport, Active; D002384:Catalysis; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry* / Q000378:metabolism / Q000493:pharmacokinetics; D014453:Glucuronosyltransferase / Q000737:chemistry* / Q000493:pharmacokinetics; D008658:Inactivation, Metabolic; D008024:Ligands; D008956:Models, Chemical; D011487:Protein Conformation; D013269:Stochastic Processes; D013379:Substrate Specificity
chemical_list: D020168:ATP Binding Cassette Transporter, Subfamily B, Member 1; D008024:Ligands; D003577:Cytochrome P-450 Enzyme System; D014453:Glucuronosyltransferase