相関から眺める生体分子運動の解析

要旨あり生体高分子の揺らぎとダイナミクス－シミュレーションと実験の統計解析－研究詳

Donepezil reverses buprenorphine-induced central respiratory depression in anesthetized rabbits

Buprenorphine is a mixed opioid receptor agonist-antagonist used in acute and chronic pain management. Although this agent's analgesic effect increases in a dose-dependent manner, buprenorphine-induced respiratory depression shows a marked ceiling effect at higher doses, which is considered to be an indicator of safety. Nevertheless, cases of overdose mortality or severe respiratory depression associated with buprenorphine use have been reported. Naloxone can reverse buprenorphine-induced respiratory depression, but is slow-acting and unstable, meaning that new drug candidates able to specifically antagonize buprenorphine-induced respiratory depression are needed in order to enable maximal analgesic effect without respiratory depression. Acetylcholine is an excitatory neurotransmitter in central respiratory control. We previously showed that a long-acting acetylcholinesterase inhibitor, donepezil, antagonizes morphine-induced respiratory depression. We have now investigated how donepezil affects buprenorphine-induced respiratory depression in anesthetized, paralyzed, and artificially ventilated rabbits. We measured phrenic nerve discharge as an Índex of respiratory rate and amplitude, and compared discharges following the injection of buprenorphine with discharges following the injection of donepezil. Buprenorphine-induced suppression of the respiratory rate and respiratory amplitude was antagonized by donepezil (78.4 ± 4.8 %, 92.3% ± 22.8 % of control, respectively). These findings indicate that systemically administered donepezil restores buprenorphine-induced respiratory depression in anesthetized rabbits

Distribution-function approach to free energy computation.

Connections are explored between the free energy difference of two systems and the microscopic distribution functions of the energy difference. On the basis of a rigorous relationship between the energy distribution functions and the free energy, the scheme of error minimization is introduced to derive accurate and simple methods of free energy computation. A set of distribution-function approaches are then examined against model systems, and the newly derived methods exhibit state-of-art performance. It is shown that the notion of error minimization is powerful to improve the free energy calculation using distribution functions

A COMPUTATIONAL STUDY OF FREE-ENERGY CHANGES UPON PROTEIN MUTATIONS

The free-energy difference of two physicochemical states is an essential value describing the stability of the molecules. In the context of protein engineering, the free-energy changes upon mutations can answer whether the protein is stabilized or destabilized upon mutations.Developments in molecular dynamics simulation, combined with the growth of the computational power in the recent computer hardware,provides us a way to predict the free-energy difference of proteins upon mutations at a cost of moderate computational requirements.We reimplemented a state-of-the-art free-energy estimation method for protein mutations, FEP/REST (free energy perturbation /replica exchange with solute tempering) and its improvements on a molecular dynamics software GROMACS. We evaluated its prediction capability by comparing it with experimental measurements. Accuracies, parameter choices and extensions will be discussed.2020 Biophysical Society Annual Meetin

Interaction of naphthalene derivatives with lipids in membranes studied by the 1H-nuclear Overhauser effect and molecular dynamics simulation.

The location, orientation, and dynamics of hydrophobic small molecules in lipid membranes are studied through combined use of solution-state (1)H-NMR and MD simulation. 1-Naphthol and 1-methylnaphthalene were adopted as the small molecules with or without hydrophilic groups. The nuclear Overhauser effect (NOE) measurement was performed for large unilamellar vesicles (100 nm in diameter) composed of dimyristoylphosphatidylcholine (DMPC) and the naphthalene derivative. The transient NOE-SE (spin-echo) scheme previously reported (J. Phys. Chem. B, 2011, 115, 9106-9115) was employed to quantitatively determine the NOE cross relaxation rate constant between DMPC and the naphthalene derivative. The observed NOE shows that both the naphthalene derivatives distribute over a wide domain across the normal of the essentially planar membrane ranging from the hydrophobic core to the hydrophilic headgroup. The experimental NOE information was further refined in combination with the analysis of time correlation functions in MD simulation. It was found that 1-naphthol exhibits a slight preference for pointing its OH group toward the hydrophilic domain of the membrane and that no definite preference can be concluded for the orientation of 1-methylnaphthalene. When 1-naphthol and 1-methylnaphthalene are compared, the NOE is stronger for 1-naphthol due to the restricted motion of the OH group. The slowdown of the 1-naphthol motion is also evidenced by the (1)H spectral line width

Prediction of Ciclesonide Binding Site on Middle-East Respiratory Syndrome Coronavirus Nsp15 Multimer by Molecular Dynamics Simulations

Ciclesonide, a corticosteroid, was known to inhibit the growth of Middle-east respiratory syndrome (MERS) coronavirus. However, its molecular mechanism was unknown. We tried to uncover the molecular mechanism from the molecular dynamics simulation.SARS_CoV_2_nsp15.pdf: The preprint document.nsp15-mers-supp.zip: Supplemental data including binding poses and parameter files for the simulation.</div