Information about the FY2022 new system can be found here.

Scientific results using RCCS

Luminescent metal nanoclusters are expected to exhibit unique physical properties in the cluster structure depending on the ligand structure, metal type, number of nuclei and arrangement. In this study, carbon-centered gold-silver (CAu6Ag2) clusters with N-heterocyclic carbene (NHC) ligands were designed and synthesized, and it was found that these clusters emit strong phosphorescence in solution, and the contribution of NHC ligands to phosphorescence emission was revealed by theoretical calculation. The luminescence rate constant was calculated by an analysis including spin-orbit interactions, and the quantum yield was discussed in terms of the energy barrier to the minimum energy crossing point. Furthermore, the phosphorescent gold-silver clusters with long luminescence lifetime were used for cellular imaging, which revealed the pathway of uptake into the cell and selective localization to specific organelles, confirming their superior functionality, which is different from the non-selective uptake of conventional phosphine ligands.
Z. Lei, M. Endo, H. Ube, T. Shiraogawa, P. Zhao, K. Nagata, X.-L. Pei, T. Eguchi, T. Kamachi, M. Ehara, T. Ogawa, M. Shionoya Nature Commun. 13, 4288-1-9 (2022).

 The process of remdesivir uptake into the protein (RNA-dependent RNA polymerase) that replicates the gene of SARS-CoV-2 was revealed by molecular dynamics simulations. Remdesivir has a phosphate group with a negative charge, and the binding site of RNA polymerase has Mg2+ ions. In addition, RNA polymerase has lysine residues, which are positively charged, in a line toward the binding site. It was found that the lysine residue attracts the phosphate group of remdesivir and passes it to the next lysine residue sequentially, transporting the drug to the binding site like a bucket brigade.

S. Tanimoto, S. G. Itoh, and H. Okumura: Biophys. J. (2021), DOI: 10.1016/j.bpj.2021.07.026, “Bucket brigade” using lysine residues in RNA-dependent RNA polymerase of SARS-CoV-2

Functional dynamics plays an important role when biomolecular machines fulfill their functions. For example, transporter proteins transport their substrates across the membrane by changing their conformation between inward-open and outward-open conformations. Although it is difficult to directly simulate millisecond functional time of these biomolecular machines whose total atoms amount to several hundred thousand, we use techniques such as metadynamics or transition path sampling to uncover molecular mechanism of the functioning moments.

K. Okazaki, D. Wöhlert, J. Warnau, H. Jung, Ö. Yildiz, W. Kühlbrandt and G. Hummer, Nat. Commun. 10, 1742 (2019)

Analyses of ab initio MD trajectories for gold cluster structural transformation based on the global reaction route map clarify the dynamic reaction route going beyond the IRC pathways, leading to a new concept of "reaction path-jumping."

T. Tsutsumi, Y. Harabuchi, Y. Ono, S. Maeda, and T. Taketsugu, Phys. Chem. Chem. Phys., 20, 1364 (2018).

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Update Information

2022-04-04 Apr 24(Sun) 10:00-11:00 Network connection to RCCS unavailable (spare date: Apr 26)

Due to the network replacement work, network connection to RCCS will be temporarily unavailable on Apr 24 (Sun) 10:00-11:00. Submitted/running jobs won't be affected by this replacement work. However, access to this website and frontend nodes (ccfep) will be unavailable. The detailed schedule will be posted on this web site as soon as it is confirmed.
(Apr 26) replacement work on Apr 24 was successfully completed.


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