Decrypting the Structural, Dynamic and Energetic Basis of Kinesin Interacting with Tubulin Dimer in Three ATPase States by All-Atom Molecular Dynamics Simulation

Abstract

We have employed molecular dynamics (MD) simulation to investigate, with atomic details, the structural dynamics and energetics of three major ATPase states (ADP, APO and ATP state) of a human kinesin 1 complexed with a tubulin dimer. Starting from a recently solved crystal structure of ATP-like kinesin-tubulin complex by Knossow lab, we have performed flexible fitting of cryo-electron-microscopy maps of kinesin-decorated microtubules, followed with extensive MD simulation (400ns for each state), which is to our knowledge the longest MD simulation of kinesin-tubulin complex published to date. Our modeling and simulation have revealed extensive conformational changes at the tubulin-binding site and the nucleotide-binding pocket of kinesin between ADP, APO and ATP state, featuring a more twisted central β-sheet and a highly flexible and open switch I in APO state. We have found kinesin undergoing large structural fluctuations in APO state toward the direction of ATP state, which allosterically couple nucleotide-binding pocket with tubulin-binding site. We have identified a dynamic network of hydrogen bonds spanning the nucleotide-binding pocket and the kinesin-tubulin binding interface, which are predicted to control and couple nucleotide and tubulin binding during kinesin's ATPase cycle. In addition, we have employed binding free energy analysis to identify a set of key residues involved in kinesin-tubulin binding. Our simulation has also shed light on several outstanding issues in kinesin literature (such as the role of neck linker docking in regulating nucleotide binding, and possible extension/shortening of α4 helix during the ATPase cycle). This study has provided a most comprehensive structural and dynamic picture of kinesin's major ATPase states, and offered promising targets for future mutational and functional studies to investigate the molecular mechanism of kinesin motors.