Kansai Institute for Photon Science 　|　Molecular Modelling and Simulation Group

Department of Quantum Beam Life Science

Molecular Modelling and Simulation Group

Group Leader　H. Kono

Aim & Scope

Modeling and Simulation Group has been studying protein-protein, protein-DNA and protein-RNA interactions through computer simulation and biochemical experiment to elucidate molecular mechanisms on gene regulation. These interactions play fundamental roles in transcription, translation, replication, recombination and repair. Studies on their structures and dynamics help us to understand how these fundamental processes are controlled. To these ends, we are also developing various computational methods that can incorporate experimental data obtained with quantum beams such as x-ray, neutron and electron microscopy.

Group member

Group Page

Group homepage: 生体分子シミュレーショングループ

Recent Publications

1. H3 histone tail conformation within the nucleosome and the impact of K14 acetylation studied using enhanced sampling simulation, J. Ikebe, S. Sakuraba and H. Kono, PLoS Computational Biology 12, e1004788 (2016).
2. Two Arginine Residues Suppress the Flexibility of Nucleosomal DNA in the Canonical Nucleosome Core, H. Kono, K. Shirayama, Y. Arimura, H. Tachiwana and H. Kurumizaka, H., PLoS ONE 10:e0120635 (2015).
3. Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules, J. Ikebe, S. Sakuraba and H. Kono, Journal of Computational Chemistry 35, 39-50 (2014).
4. Giant cadherins Fat and Dachsous self-bend to organize properly spaced intercellular junctions, Y. Tsukasaki, N. Miyazaki, A. Matsumoto, S. Nagae, S. Yonemura, T. Tanoue, K. Iwasaki and M. Takeichi, Proc Natl Acad Sci U S A 111, 16011-6 (2014).
5. Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations, H. Ishida, Proteins: Structure, Function, and Bioinformatics 82, 1985-1999 (2014).
6. Free-energy landscape of reverse tRNA translocation through ribosome analyzed by electron microscopy density maps molecular dynamics simulations, H. Ishida and A. Matsumoto, PLoS ONE, 9, 3101951,(2014).
7. Local Dynamics Coupled to Hydration Water Determines DNA-sequence Dependent Deformability, H. Nakagawa, Y. Yonetani, K. Nakajima, S. Ohira-kawamura, T. Kikuchi, Y. Inamura, M. Kataoka and H. Kono, Physical Reviews E. 90, 022723-11 (2014).
8. Intensity of diffracted X-rays from biomolecules with radiation damage caused by strong X-ray pulses, T. Kai, A. Tokuhisa, K. Moribayashi, Y. Fukuda, H. Kono and N. Go, Journal of the Physical Society of Japan 83, 094301 (2014).
9. Local Conformational Changes in the DNA Interfaces of Proteins, T. Sunami and H. Kono, PLoS ONE (Internet) 8, e56080 (2013).
10. Phase retrieval from single biomolecule diffraction pattern, S. Ikeda and H. Kono, Optics Express 20, 3375-3387 (2012).