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Academic OrganizationAcademic Assembly School of Science and Technology Institute of AgricultureTEL
Education and Research OrganizationInterdisciplinary Cluster for Cutting Edge Research Institute for Biomedical SciencesFAX
PositionAssistant ProfessorMail Address
Address8304, Minamiminowa-Village, Kamiina-County 399-4598Web site


Assigned Class
Graduate School of Science and Technology Department of Biomedical Engineering Biotechnology Division
Research Field
Keywords:Theoretical biology, Bioinformatics
Current Subject
Molecular simulation

Computational structural biology

Intrinsically disordered protein


Books, Articles, etc.
Free-Energy Landscape of Intrinsically Disordered Proteins Investigated by All-Atom Multicanonical Molecular Dynamics, Protein Conformational Dynamics: Advances in Experimental Medicine and Biology 805 , 331-351
Springer 2013(Dec. 16)
Author:Junichi Higo, Koji Umezawa

Identification of a novel osteogenetic oligodeoxynucleotide (osteoDN) that promotes osteoblast differentiation in a TLR9-independent manner.
Nanomaterials,12(10):1680 2022(May 14)
Author:Nihashi Y, Miyoshi M, Umezawa K, Shimosato T, Takaya T.

Myogenetic oligodeoxynucleotide complexed with berberine promotes differentiation of chicken myoblasts.
Animal Science Journal,92(1):e13597 2021(Jul. 25)
Author:Nihashi Y, Shinji S, Umezawa K, Shimosato T, Ono T, Kagami H, Takaya T

Identification of the Myogenetic Oligodeoxynucleotides (myoDNs) That Promote Differentiation of Skeletal Muscle Myoblasts by Targeting Nucleolin
Frontiers in Cell and Developmental Biology,8:616706 2021(Jan.)
Author:Shinji S, Umezawa K, Nihashi Y, Nakamura S, Shimosato T, Takaya T.

Hyperstable De Novo Protein with a Dimeric Bisecting Topology
ACS SYNTHETIC BIOLOGY,9(2):254-259 2020(Jan. 17)
Author:Kimura N., Mochizuki K., Umezawa K., Hecht MH., Arai R.

Berberine and palmatine inhibit the growth of human rhabdomyosarcoma cells.
Biosci Biotechnol Biochem,84(1):63-75 2020
Author:Shinji, S; Nakamura, S; Nihashi, Y; Umezawa, K; Takaya, T

Distinct cell proliferation, myogenic differentiation, and gene expression in skeletal muscle myoblasts of layer and broiler chickens
Scientific Reports,9:16527 2019(Nov. 11)
Author:Nihashi Y, Umezawa K, Shinji S, Hamaguchi Y, Kobayashi H, Kono T, Ono T, Kagami H, Takaya T

Synthesis of epigallocatechin trimer, (epigallocatechin)2-epicatechin, and (epigallocatechin)2-catechin via a Lewis acid mediated one-pot condensation and their antitumor activities in prostate cancer cells.
Tetrahedron,74(27):3534-3542 2018(Jul. 05)
Author:Ichikawa M, Yamamoto S, Ishihara C, Nonobe S, Hattori Y, Umezawa K, Fujii H, Makabe H

Structural and dynamical characteristics of tropomyosin epitopes as the major allergens in shrimp.
Biochemical and Biophysical Research Communications,498(1) 2018(Mar. 25)
Author:Ozawa H, Umezawa K, Takano M, Ishizaki S, Watabe S, Ochiai Y

Epicatechin oligomers longer than trimers have anti-cancer activities, but not the catechin counterparts
Scientific Reports,7(1):7791 2017(Aug. 10)
Author:Takanashi K, Suda M, Matsumoto K, Ishihara C, Toda K, Kawaguchi K, Senga S, Kobayashi N, Ichikawa M, Katoh M, Hattori Y, Kawahara S, Umezawa K, Fujii H, and Makabe H

Over-Destabilization of Protein-Protein Interaction in Generalized Born Model and Utility of Energy Density Integration Cutoff
Journal of Physical Chemistry B,121:4669-4677 2017(Apr. 20)
Author:Mizuhara Y, Parkin D, Umezawa K, Ohnuki J, Takano M

信州大学農学部紀要,53:34-43 2017(Mar. 21)

Intrinsic disorder accelerates dissociation rather than association
Proteins: Structure, Function, and Bioinformatics,-(-) 2016(May 18)
Author:Koji Umezawa, Jun Ohnuki, Junichi Higo, Mitsunori Takano

Enhanced sampling simulations to construct free-energy landscape of protein–partner substrate interaction
Biophysical Reviews,8(1):45-62 2016(Jan. 11)
Author:Jinzen Ikebe, Koji Umezawa, Junichi Higo

virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent
The Journal of Chemical Physics,138:184106 2013(May 10)
Author:Junichi Higo, Koji Umezawa, Haruki Nakamura

Conformational ensembles of an intrinsically disordered protein pKID with and without a KIX domain in explicit solvent investigated by all-atom multicanonical molecular dynamics
Biomolecules,2(1):104-121 2012(Feb. 22)
Author:Koji Umezawa, Jinzen Ikebe, Mitsunori Takano, Haruki Nakamura, Junichi Higo

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water
Journal of Computational Chemistry,32(7):1286-1297 2010(Dec. 15)
Author:Jinzen Ikebe, Koji Umezawa, Narutoshi Kamiya, Takanori Sugihara, Yasushige Yonezawa, Yu Takano, Haruki Nakamura, Junichi Higo

Solvent flow patterns fluctuating largely around a protein and correlation with solvent density fluctuations: A molecular dynamics study
The Journal of Chemical Physics,132:155103 2010(Apr. 16)
Author:Koji Umezawa, Ryota Morikawa, Haruki Nakamura, Junichi Higo

Conformational requirement on peptides to exert laminin's activities and search for protein segments with laminin's activities
Biopolymers,92(2):124-131 2009(Jan. 29)
Author:Koji Umezawa, Jinzen Ikebe, Motoyoshi Nomizu, Haruki Nakamura, Junichi Higo

Solvent Site-Dipole Field Accompanying Protein-Ligand Approach Process
Chem-Bio Informatics Journal,8(1):14-24 2008(Apr. 29)
Author:Norikazu Takano, Koji Umezawa, et al.

Structure dependency of a 24-residue peptide humanin on solvent and preferential solvation by trifluoroethanol studied by multicanonical sampling
Chemical Physics Letters,455(4-6):293-296 2008(Apr. 10)
Author:Ryosuke Yagisawa, Narutoshi Kamiya, Jinzen Ikebe, Koji Umezawa, Junichi Higo

Collective solvent flows around a protein investigated by molecular dynamics simulation
The Journal of Chemical Physics,127(4):045101 2007(Jul. 26)
Author:Koji Umezawa, Junichi Higo, Sakurako Shimotakahara, Heisaburo Shindo

Cyclic Peptide Analysis of the Biologically Active Loop Region in the Laminin α3 Chain LG4 Module Demonstrates the Importance of Peptide Conformation on Biological Activity
Biochemistry,46(7):1952-1960 2007(Jan. 30)
Author:Kozue Kato-Takagaki, Nobuharu Suzuki, Fumiharu Yokoyama, Shu Takaki, Koji Umezawa, Junichi Higo, Marumi Mochizuki, Yamato Kikkawa, Shinya Oishi, Atsushi Utani, Motoyoshi Nomizu