Kinesin's Nucleotide-Binding Pocket And Its Conformational

Kinesin uses the energy of ATP in two ways.First,the specific binding of kinesin's motor head,ATP molecule and magnesium can lower the total energy of the complex structure,induce a series of conformational changes of the nucleotide-binding pocket(NBP)and initiate kinesin's force-generation process.Second,kinesin can catalyze the ATP hydrolysis and release the products.This process will induce a series of reverse conformational changes to recover the kinesin to the initial conformation before ATP binding.Kinesin's force-generation process is induced by ATP's binding to the nucleotide-binding pocket of motor domain with the stimulation of microtubule.Therefore,the detailed conformational changes of motor domain induced by ATP binding are keys to understand the mechanism of kinesin's motility.Based on the newly obtained crystal structures of apo-state(4LNU)and ATP-state(4HNA)kinesin-microtubule complexes,we investigate the structural characteristics of kinesin's nucleotide-binding pocket and its conformational changes in the ATP-binding process using molecular dynamics simulations.We find that:(1)kinesin's nucleotide-binding pocket has direct and indirect contacts with microtubule.These contacts are realized through hydrogen bonds and salt bridges among ser235 and lys237 of kinesin's L11 loop and a series of negatively charged residues(glu414,glu417 and glu420)of MT's ?-tubulin.The hydrogen bond between glu236 of N-3(L11 loop)and thr255 of ?4 is indirect interaction between NBP and MT.We also find that ser235 is the center of this rotation process.(2)Mg2+ has a key function in kinesin's motor-domain rotation.In this process,N-2(switch-?)is stable and N-1(P-loop)will rotate around the center under the strong force.Therefore,the central ?-sheet will rotate accordingly.(3)An aromatic residue of P-loop,together with other four residues of ?1,provides a hydrophobic pocket for nucleotide's adenosine ring to stabilize the nucleotide molecule.Though this residue is not quite conservative,the aromatic ring is highly conservative in kinesin super family.(4)A complete mechanical pathway from ATP binding to neck linker docking is proposed.