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Items: 1 to 20 of 24

1.

Dynamic recognition and linkage specificity in K63 di-ubiquitin and TAB2 NZF domain complex.

Moritsugu K, Nishi H, Inariyama K, Kobayashi M, Kidera A.

Sci Rep. 2018 Nov 7;8(1):16478. doi: 10.1038/s41598-018-34605-2.

2.
3.

Conformational change of a biomolecule studied by the weighted ensemble method: Use of the diffusion map method to extract reaction coordinates.

Fujisaki H, Moritsugu K, Mitsutake A, Suetani H.

J Chem Phys. 2018 Oct 7;149(13):134112. doi: 10.1063/1.5049420.

PMID:
30292230
4.

Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion.

Moritsugu K, Terada T, Kokubo H, Endo S, Tanaka T, Kidera A.

J Chem Phys. 2018 Aug 21;149(7):072314. doi: 10.1063/1.5027444.

PMID:
30134720
5.

Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB.

Matsunaga Y, Yamane T, Terada T, Moritsugu K, Fujisaki H, Murakami S, Ikeguchi M, Kidera A.

Elife. 2018 Mar 6;7. pii: e31715. doi: 10.7554/eLife.31715.

6.

Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance.

Ishiyama S, Nishiyama A, Saeki Y, Moritsugu K, Morimoto D, Yamaguchi L, Arai N, Matsumura R, Kawakami T, Mishima Y, Hojo H, Shimamura S, Ishikawa F, Tajima S, Tanaka K, Ariyoshi M, Shirakawa M, Ikeguchi M, Kidera A, Suetake I, Arita K, Nakanishi M.

Mol Cell. 2017 Oct 19;68(2):350-360.e7. doi: 10.1016/j.molcel.2017.09.037.

7.

Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes.

Moritsugu K, Terada T, Kidera A.

J Phys Chem B. 2017 Feb 2;121(4):731-740. doi: 10.1021/acs.jpcb.6b11696. Epub 2017 Jan 18.

PMID:
28052666
8.

Coupled Nosé-Hoover equations of motion to implement a fluctuating heat-bath temperature.

Fukuda I, Moritsugu K.

Phys Rev E. 2016 Mar;93(3):033306. doi: 10.1103/PhysRevE.93.033306. Epub 2016 Mar 15.

PMID:
27078483
9.

Extended string-like binding of the phosphorylated HP1α N-terminal tail to the lysine 9-methylated histone H3 tail.

Shimojo H, Kawaguchi A, Oda T, Hashiguchi N, Omori S, Moritsugu K, Kidera A, Hiragami-Hamada K, Nakayama J, Sato M, Nishimura Y.

Sci Rep. 2016 Mar 3;6:22527. doi: 10.1038/srep22527.

10.

Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

Fujisaki H, Moritsugu K, Matsunaga Y, Morishita T, Maragliano L.

Front Bioeng Biotechnol. 2015 Sep 3;3:125. doi: 10.3389/fbioe.2015.00125. eCollection 2015. Review.

11.

Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.

Moritsugu K, Koike R, Yamada K, Kato H, Kidera A.

PLoS One. 2015 Jul 6;10(7):e0131583. doi: 10.1371/journal.pone.0131583. eCollection 2015.

12.

Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

Moritsugu K, Terada T, Kidera A.

PLoS Comput Biol. 2014 Oct 23;10(10):e1003901. doi: 10.1371/journal.pcbi.1003901. eCollection 2014 Oct.

13.

Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes.

Moritsugu K, Kidera A, Smith JC.

J Phys Chem B. 2014 Jul 24;118(29):8559-65. doi: 10.1021/jp503956m. Epub 2014 Jul 7.

PMID:
24999844
14.

Multiscale enhanced path sampling based on the Onsager-Machlup action: application to a model polymer.

Fujisaki H, Shiga M, Moritsugu K, Kidera A.

J Chem Phys. 2013 Aug 7;139(5):054117. doi: 10.1063/1.4817209.

PMID:
23927253
15.

REACH coarse-grained simulation of a cellulose fiber.

Glass DC, Moritsugu K, Cheng X, Smith JC.

Biomacromolecules. 2012 Sep 10;13(9):2634-44. doi: 10.1021/bm300460f. Epub 2012 Aug 31.

PMID:
22937726
16.

Minimum free energy path of ligand-induced transition in adenylate kinase.

Matsunaga Y, Fujisaki H, Terada T, Furuta T, Moritsugu K, Kidera A.

PLoS Comput Biol. 2012;8(6):e1002555. doi: 10.1371/journal.pcbi.1002555. Epub 2012 Jun 7.

17.

Disorder-to-order transition of an intrinsically disordered region of sortase revealed by multiscale enhanced sampling.

Moritsugu K, Terada T, Kidera A.

J Am Chem Soc. 2012 Apr 25;134(16):7094-101. doi: 10.1021/ja3008402. Epub 2012 Apr 11.

PMID:
22468560
18.

Scalable free energy calculation of proteins via multiscale essential sampling.

Moritsugu K, Terada T, Kidera A.

J Chem Phys. 2010 Dec 14;133(22):224105. doi: 10.1063/1.3510519.

PMID:
21171681
19.

Theory and normal-mode analysis of change in protein vibrational dynamics on ligand binding.

Moritsugu K, Njunda BM, Smith JC.

J Phys Chem B. 2010 Jan 28;114(3):1479-85. doi: 10.1021/jp909677p.

PMID:
20043649
20.

REACH coarse-grained normal mode analysis of protein dimer interaction dynamics.

Moritsugu K, Kurkal-Siebert V, Smith JC.

Biophys J. 2009 Aug 19;97(4):1158-67. doi: 10.1016/j.bpj.2009.05.015.

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