Scientific results using RCCS

Nervous activity is subjected to complex regulation by ion channels. In this study, we reproduced the divalent cations block in molecular dynamics simulation and elucidated the blocking mechanism. It was observed that introducing a hydrophilic environment into the channel lumen allows the stable existence of divalent cations. This retention of divalent cations makes it difficult for ions to permeate the ion channel. This result also provides new knowledge about the reproduction of polyvalent ions in molecular dynamics simulations.

K. Irie, Y. Oda, T. Sumikama, A. Oshima, Y. Fujiyoshi, Nat. Commun., 14, 4236 (2023).

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. Ozawa, 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

2023-06-13 June 19 0:00-6:00: network access to RCCS will be unavailable due to SINET maintenance

Network access to RCCS will be unavailable for about 15 minutes at most twice during 0:00-6:00 AM on June 19 due to the SINET maintenance. Access to login servers and this website will not be available during the period. Submitted jobs are not affected by this maintenance. Thank you for your understanding and cooperation.

2023-05-08 May 11 (Thu) 9:00-17:00 NOUS maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, May 11 due to the scheduled maintenance. Thank you for your understanding.

2023-03-31 Apr 4 (Mon) 10:50-12:15 Website temporarily suspended for maintenance

(Apr 3 13:07) Due to the delay of the maintenance work, the website was resumed at 13:03. Sorry for the inconvenience.
This website will be temporarily unavailable from 10:50 to 12:15 on Monday, April 3 due to the server maintenance.

2023-03-01 Mar 9 (Thu) 9:00-17:00 NOUS maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, Mar 9 due to the scheduled maintenance. Thank you for your understanding.

2023-01-31 New system will be available from 10:00 on Feb. 1

We will start operation with the new system on February 1 (Wed) at 10:00.
The period from Feb 1 to the scheduled maintenance on Mar 6 (Mon) is a testing phase.
CPU points won't be consumed by submitted jobs.

2022-12-15 NOUS system failure (Dec 15) and maintenance (Dec 19-20, Dec 22)

The application system NOUS has been out of service since around noon on 12/15 (Thu).
NOUS will be unavailable twice next week on the following dates.

  • Dec 19 (Mon) 21:00 - Dec 20 (Tue) 3:00 (temporary maintenance)
  • Dec 22 (Thu) 12:00-13:00 (scheduled maintenance)

We apologize for the inconvenience and appreciate your understanding and cooperation.
(Dec 16 update) NOUS system failure occurred around the noon on Dec 15 was finally solved around 20:00 on Dec 15.

2022-10-25 Nov 10 (Thu) 9:00-17:00 NOUS maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, Nov 10 due to the scheduled maintenance. Thank you for your understanding.

2022-10-25 Operation start date of the new system is postponed to January 2023 or later

We sincerely apologize for the inconvenience. Due to delays in securing materials, we can't start operation of the new system from December 1st. The new system is scheduled to be launched on January 2023 or later. We will report further details on this website as soon as they are finalized.

2022-10-11 Oct 13 (Thu) 12:00-13:00 NOUS maintenance

Application submission system NOUS will be unavailable from 12:00 to 13:00 on Thursday, Oct. 13 due to the maintenance. Thank you for your understanding.

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