How does evolution design functional free energy landscapes of proteins? A case study on the emergence of regulation in the Cyclin Dependent Kinase family

Evolution has altered the free energy landscapes of protein kinases to introduce different regulatory switches and modify their catalytic functions. In this work, we demonstrate how cyclin dependency has emerged in cyclin-dependent kinases (CDKs) by reconstructing their closest experimentally characterized cyclin-independent ancestor, CMGI, using molecular dynamics simulations. Four hypotheses are formulated to describe why CDKs require an additional regulatory switch, i.e. cyclin binding to adopt an active state. Each hypothesis is tested using all-atom molecular dynamics simulations of CDK2 and the ancestor. In both systems, the K33-E51 hydrogen bond and the alignment of regulatory-spine residues have similar stabilities. However, auto-inhibition due to a helical turn in the A-loop is observed to be less favorable in the ancestor. Unlike the ancestor, the aspartate of the DFG motif does not form a bidentate bond with a Mg²⁺ ion in CDK2. These results explain the experimental observation of cyclin independency of the ancestor. Our findings provide a mechanistic rationale for how evolution has added a new regulatory switch to CDKs to tightly regulate the signalling pathways. This approach is directly applicable to other proteins to study the emergence of different types of regulatory mechanisms.