A Systems Approach to Understanding the Allosteric Mechanism of Pyruvate Kinase M2

Abstract

Allostery is a crucial phenomenon in biology, which enables cells to tune metabolic and signaling pathways in response to subtle chemical cues. Despite its importance we are unable to ascribe a quantifiable structural description to allosteric regulation in many cases, leaving it somewhat of a biophysical enigma. While allosteric sites hold great promise as therapeutic targets in recently described cases, little is known about how proteins propagate allosteric information between distal sites. To better understand the structural mechanisms behind protein allostery, we combine molecular dynamics (MD) simulations with experimental biophysical tools to identify allosteric pathways within key metabolic enzymes.Initially, we investigated the allosteric mechanism of pyruvate kinase M2 (PKM2). A number of studies have revealed that PKM2 expression may be enriched in proliferating cells and that allosteric control of its activity is crucial for their growth and survival. Although PKM2 has been well characterised, the structural basis of how its activity is regulated remains poorly understood. To address this apparent gap in the literature, we use PKM2 as a proof-of-principle to demonstrate that an integrated systems approach can uncover dynamic and energetic events associated with the allosteric mechanism of enzymes. Using atomistic molecular dynamics simulations we find that a network of cooperative residues communicate structural information to the active site, upon binding of allosteric ligands, to stabilize either the active or the inactive conformation of the enzyme.1. Anastasiou D, et al. Nature chemical biology. 2012;8(10):839-47.2. Anastasiou D, et al. Science. 2011;334(6060):1278-83.3. Pandini A, et al. FASEB. 2012;26(2):868-81.4. Pandini A, et al. Bioinformatics, 2013. 29(16): p. 2053-5.