Purification of Cyclin-Dependent Kinase Fusion Complexes for In Vitroh Analysis

Protein kinases are common elements in multiple signaling networks, influencing numerous downstream processes by directly phosphorylating specific target proteins. During the cell cycle, multiple complexes, each comprising one cyclin and one cyclin-dependent kinase (Cdk), function to regulate the orderly progression of cell cycle events. The mechanisms of cyclin-Cdk mediated control have, in part, been established through biochemical experiments involving the purification of cyclin and Cdk proteins to evaluate the activity of a given complex toward its target substrate proteins.Here I present a detailed procedure to simplify the preparation of cyclin-Cdk complexes by purifying them as a single fusion molecule with a 1:1 molar ratio and a detailed protocol for performing reconstituted kinases assays with the purified complexes.This methodology has allowed us to measure the activity and specificity of all budding yeast cyclin-Cdk1 complexes toward the model substrate histone H1. In addition, it has allowed us to perform kinase assays with a panel of purified human cyclin-Cdk complexes to analyze their specificity toward the retinoblastoma protein (Rb) and map the substrate cyclin-Cdk kinase docking interactions between Rb and human G1-Cdk complex.This chapter is focused on purification of cell cycle cyclin-Cdk complexes, but also affords a generalizable framework that can be adapted to other cyclin-dependent kinases like transcriptional cyclin-Cdks or any other multisubunit enzyme complexes. Taken together, the described workflow is a powerful and flexible biochemical platform for solving long-standing biological questions and has potential value in synthetic biology and in therapeutic discovery.