Research Project
Grant-in-Aid for Young Scientists (B)
Enzymes catalyze important chemical reactions in living systems. The enzyme reactions for material formations and energy conversions are highly efficient. Simple reactions are clarified by theoretical analyses, however, complicated reactions in many important enzymes are still unclear. Therefore, reactions of threonine synthase (ThrS), nitrite reductase (NiR), nitric oxide reductase (NOR) and DNA topoisomerase (Topo) are investigated by a mixed quantum mechanical and molecular mechanical (QM/MM) method. We utilized supercomputers and massive parallel simulations were performed. We elucidated the reaction mechanism by investigations for the protonation states, hydrogen-bonding network, existence of waters and possible reaction pathways.
All 2014 2013 2012 Other
All Journal Article (9 results) (of which Peer Reviewed: 6 results) Presentation (95 results) (of which Invited: 14 results) Remarks (6 results)
Journal of the American Chemical Society
Volume: 136(12) Pages: 4525-4533
J. Am. Chem. Soc.
Volume: 136 Issue: 12 Pages: 4525-4533
10.1021/ja408780c
Journal of Biomolecular Structure and Dynamics
Volume: - Issue: 11 Pages: 1759-1765
10.1080/07391102.2013.834848
Molecular Physics
Volume: 112, 3-4 Pages: 393-397
情報処理学会論文誌コンピューティングシステム(ACS)
Volume: 6, 4 Pages: 26-37
Volume: 6 Pages: 26-37
International Journal of Quantum Chemistry
Volume: 113 Issue: 3 Pages: 342-347
10.1002/qua.24074
Volume: 113 Issue: 4 Pages: 525-541
10.1002/qua.24117
Internat. J. Quantum Chem
Volume: 113 Issue: 4 Pages: 453-473
10.1002/qua.24280
http://www2.ccs.tsukuba.ac.jp/people/mshoji/index.html
https://www.ccs.tsukuba.ac.jp/pr/media/threonine_140314
http://www.ccs.tsukuba.ac.jp/wordpress/uploads/2014/03/press_140314.pdf
http://www.ccs.tsukuba.ac.jp/pr/media/threonine_140314