Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations

Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. Here, we study ATP hydrolysis mechanisms in the kinesin-5 protein Eg5 by using combined quantum mechanics/molecular mechanics metadynamics simulations. Approximately 200 atoms at the catalytic site are treated by a dispersion-corrected density functional and, in total, 13 metadynamics simulations are performed with their cumulative time reaching ∼0.7 ns. Using the converged runs, we compute free energy surfaces and obtain a few hydrolysis pathways. The pathway with the lowest free energy barrier involves a two-water chain and is initiated by the P_γ–O_β dissociation concerted with approach of the lytic water to P_γO₃^–. This immediately induces a proton transfer from the lytic water to another water, which then gives a proton to the conserved Glu270. Later, the proton is transferred back from Glu270 to HPO₄^2– via another hydrogen-bonded chain. We find that the reaction is favorable when the salt bridge between Glu270 in switch II and Arg234 in switch I is transiently broken, which facilitates the ability of Glu270 to accept a proton. When ATP is placed in the ADP-bound conformation of Eg5, the ATP-Mg moiety is surrounded by many water molecules and Thr107 blocks the water chain, which together make the hydrolysis reaction less favorable. The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F₁-ATPase, raising the possibility of a common mechanism

Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations

Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. Here, we study ATP hydrolysis mechanisms in the kinesin-5 protein Eg5 by using combined quantum mechanics/molecular mechanics metadynamics simulations. Approximately 200 atoms at the catalytic site are treated by a dispersion-corrected density functional and, in total, 13 metadynamics simulations are performed with their cumulative time reaching ∼0.7 ns. Using the converged runs, we compute free energy surfaces and obtain a few hydrolysis pathways. The pathway with the lowest free energy barrier involves a two-water chain and is initiated by the P_γ–O_β dissociation concerted with approach of the lytic water to P_γO₃^–. This immediately induces a proton transfer from the lytic water to another water, which then gives a proton to the conserved Glu270. Later, the proton is transferred back from Glu270 to HPO₄^2– via another hydrogen-bonded chain. We find that the reaction is favorable when the salt bridge between Glu270 in switch II and Arg234 in switch I is transiently broken, which facilitates the ability of Glu270 to accept a proton. When ATP is placed in the ADP-bound conformation of Eg5, the ATP-Mg moiety is surrounded by many water molecules and Thr107 blocks the water chain, which together make the hydrolysis reaction less favorable. The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F₁-ATPase, raising the possibility of a common mechanism

Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations

Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. Here, we study ATP hydrolysis mechanisms in the kinesin-5 protein Eg5 by using combined quantum mechanics/molecular mechanics metadynamics simulations. Approximately 200 atoms at the catalytic site are treated by a dispersion-corrected density functional and, in total, 13 metadynamics simulations are performed with their cumulative time reaching ∼0.7 ns. Using the converged runs, we compute free energy surfaces and obtain a few hydrolysis pathways. The pathway with the lowest free energy barrier involves a two-water chain and is initiated by the P_γ–O_β dissociation concerted with approach of the lytic water to P_γO₃^–. This immediately induces a proton transfer from the lytic water to another water, which then gives a proton to the conserved Glu270. Later, the proton is transferred back from Glu270 to HPO₄^2– via another hydrogen-bonded chain. We find that the reaction is favorable when the salt bridge between Glu270 in switch II and Arg234 in switch I is transiently broken, which facilitates the ability of Glu270 to accept a proton. When ATP is placed in the ADP-bound conformation of Eg5, the ATP-Mg moiety is surrounded by many water molecules and Thr107 blocks the water chain, which together make the hydrolysis reaction less favorable. The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F₁-ATPase, raising the possibility of a common mechanism

Structural Rearrangements and Magic Numbers in Reactions between Pyridine-Containing Water Clusters and Ammonia

Molecular cluster ions H⁺(H₂O)_<i>n</i>, H⁺(pyridine)­(H₂O)_<i>n</i>, H⁺(pyridine)₂(H₂O)_<i>n</i>, and H⁺(NH₃)­(pyridine)­(H₂O)_<i>n</i> (<i>n</i> = 16–27) and their reactions with ammonia have been studied experimentally using a quadrupole-time-of-flight mass spectrometer. Abundance spectra, evaporation spectra, and reaction branching ratios display magic numbers for H⁺(NH₃)­(pyridine)­(H₂O)_<i>n</i> and H⁺(NH₃)­(pyridine)₂(H₂O)_<i>n</i> at <i>n</i> = 18, 20, and 27. The reactions between H⁺(pyridine)_<i>m</i>(H₂O)_<i>n</i> and ammonia all seem to involve intracluster proton transfer to ammonia, thus giving clusters of high stability as evident from the loss of several water molecules from the reacting cluster. The pattern of the observed magic numbers suggest that H⁺(NH₃)­(pyridine)­(H₂O)_<i>n</i> have structures consisting of a NH₄⁺(H₂O)_<i>n</i> core with the pyridine molecule hydrogen-bonded to the surface of the core. This is consistent with the results of high-level ab initio calculations of small protonated pyridine/ammonia/water clusters