Decrypting the Structural, Dynamic, and Energetic
Basis of a Monomeric Kinesin Interacting with a Tubulin Dimer in Three
ATPase States by All-Atom Molecular Dynamics Simulation
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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
monomer in complex with a tubulin dimer. Starting from a recently
solved crystal structure of ATP-like kinesin–tubulin complex
by the Knossow lab, we have used flexible fitting of cryo-electron-microscopy
maps to construct new structural models of the kinesin–tubulin
complex in APO and ATP state, and then conducted extensive MD simulations
(total 400 ns for each state), followed by flexibility analysis, principal
component analysis, hydrogen bond analysis, and binding free energy
analysis. Our modeling and simulation have revealed key nucleotide-dependent
changes in the structure and flexibility of the nucleotide-binding
pocket (featuring a highly flexible and open switch I in APO state)
and the tubulin-binding site, and allosterically coupled motions driving
the APO to ATP transition. In addition, our binding free energy analysis
has identified a set of key residues involved in kinesin–tubulin
binding. On the basis of our simulation, we have attempted to address
several outstanding issues in kinesin study, including the possible
roles of β-sheet twist and neck linker docking in regulating
nucleotide release and binding, the structural mechanism of ADP release,
and possible extension and shortening of α4 helix during the
ATPase cycle. This study has provided a 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