Modeling of enzyme-catalyzed P–O bond cleavage in the adenosine triphosphate molecule

Khrenova, Maria G.; Mulashkina, Tatiana I.; Stepanyuk, Roman A.; Nemukhin, Alexander V.

doi:10.1016/j.mencom.2024.01.001

Cited by 2 publications

(1 citation statement)

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“…Ab initio molecular dynamics simulations have indicated that, during ATP hydrolysis in actin, a new hydroxyl bond formed in the orthophosphate molecule during hydrolysis may be vibrationally excited [ 27 ], and, if this happens in myosin, then the phosphate release state might help to facilitate the transfer of vibrational energy from orthophosphate to the relay helix. Indeed, the catalytic mechanism of ATP hydrolysis in myosin is believed to be similar to that in actin; in both proteins, the reaction is dissociative, involves two water molecules in proton transfers, and results in the creation of the double-protonated phosphate H 2 PO 4 − [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy

Freedman,

Tuszynski

2024

IJMS

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The Davydov model was conjectured to describe how an amide I excitation created during ATP hydrolysis in myosin might be significant in providing energy to drive myosin’s chemomechanical cycle. The free energy surfaces of the myosin relay helix peptide dissolved in 2,2,2-trifluoroethanol (TFE), determined by metadynamics simulations, demonstrate local minima differing in free energy by only ~2 kT, corresponding to broken and stabilized hydrogen bonds, respectively. Experimental pump-probe and 2D infrared spectroscopy were performed on the peptide dissolved in TFE. The relative heights of two peaks seen in the pump-probe data and the corresponding relative volumes of diagonal peaks seen in the 2D-IR spectra at time delays between 0.5 ps and 1 ps differ noticeably from what is seen at earlier or later time delays or in the linear spectrum, indicating that a vibrational excitation may influence the conformational state of this helix. Thus, it is possible that the presence of an amide I excitation may be a direct factor in the conformational state taken on by the myosin relay helix following ATP hydrolysis in myosin.

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Section: Introductionmentioning

confidence: 99%