Atsushi Suenaga

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The ion permeation process, driven by a membrane potential through an outer membrane protein, OmpF porin of Escherichia coli, was simulated by molecular dynamics. A Na+ ion, initially placed in the solvent region at the outer side of the porin channel, moved along the electric field passing through the porin channel in a 1.3 nsec simulation; the permeation(More)
1 We have achieved a sustained performance of 55 TFLOPS for molecular dynamics simulations of the amyloid fibril formation of peptides from the yeast Sup35 in an aqueous solution. For performing the calculations, we used the MDGRAPE-3 system—a special-purpose computer system for molecular dynamics simulations. Its nominal peak performance was 415 TFLOPS for(More)
We are developing the 'Protein Explorer' system, a petaflops special-purpose computer system for molecular dynamics simulations. The Protein Explorer is a PC cluster equipped with special-purpose engines that calculate nonbonded interactions between atoms, which is the most time-consuming part of the simulations. A dedicated LSI 'MDGRAPE-3 chip' performs(More)
We report here on the characterization of a mutation in the ceruloplasmin gene in a 45 year old woman with insulin-dependent diabetes mellitus who presented with the recent onset of gait disturbance and dysarthria. Physical examination revealed an ataxic gait, scanning speech and retinal degeneration. Magnetic resonance imaging of the brain was consistent(More)
Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, this method is not completely reliable and therefore unsatisfactory. In this study, we used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular docking in order to improve the enrichment(More)
An immunoprecipitation assay was used to measure omega-conotoxin MVIIC (P/Q-type) binding and blocking calcium channel antibodies in 67 patients with Lambert-Eaton myasthenic syndrome (LEMS) and in a large control population. We first showed the presence of omega-conotoxin MVIIC-blocking antibody in LEMS patients. Binding antibodies were detected in 55 of(More)
The ClC chloride channels control the ionic composition of the cytoplasm and the volume of cells, and regulate electrical excitability. Recently, it has been proposed that prokaryotic ClC channels are H+-Cl- exchange transporter. Although X-ray and molecular dynamics (MD) studies of bacterial ClC channels have investigated the filter open-close and ion(More)
We investigated the conformational change in the human prion protein owing to an Ala 117 → → → →Val mutation by using molecular dynamics simulations. This mutation is related to Gerstmann-Sträussler-Sheinker disease, one of the familial prion diseases. Five prion protein structures were simulated in the periodic or non-periodic system. The results of(More)