T. Oyama

发表

The 2.8-Å Crystal Structure of the Dynein Motor Domain

K. Sutoh, T. Kon, T. Oyama, 2012 .

Crystal structure of human lectin-like, oxidized low-density lipoprotein receptor 1 ligand binding domain and its ligand recognition mode to OxLDL.

I. Ohki, M. Ohnishi-Kameyama, D. Tsuchiya, 2005, Structure.

Improvement of the transactivation activity of phenylpropanoic acid-type peroxisome proliferator-activated receptor pan agonists: effect of introduction of fluorine at the linker part.

M. Makishima, Y. Hashimoto, K. Morikawa, 2008, Bioorganic & medicinal chemistry letters.

Bidirectional fluorescence properties of pyrene-based peroxisome proliferator-activated receptor (PPAR) α/δ dual agonist.

Y. Hashimoto, K. Morikawa, H. Miyachi, 2012, Bioorganic & medicinal chemistry.

Crystal Structures of the Human Peroxisome Proliferator-Activated Receptor (PPAR)α Ligand-Binding Domain in Complexes with a Series of Phenylpropanoic Acid Derivatives Generated by a Ligand-Exchange Soaking Method.

H. Miyachi, T. Oyama, I. Ishii, 2021, Biological & pharmaceutical bulletin.

PPARα Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates

M. Suematsu, Yasuo Watanabe, T. Itoh, 2020, iScience.

Electric Conductivity of Nanoparticle Composites Coated with Oxidized Aminothiophenol and Adhered on Resin Plates

K. Kuwabara, T. Oyama, T. Muraki, 2014 .

Functional and Structural Insights into Human PPARα/δ/γ Subtype Selectivity of Bezafibrate, Fenofibric Acid, and Pemafibrate

Yui Machida, T. Oyama, I. Ishii, 2022, International journal of molecular sciences.

Structural Basis for Anti-non-alcoholic Fatty Liver Disease and Diabetic Dyslipidemia Drug Saroglitazar as a PPAR α/γ Dual Agonist.

Yui Machida, T. Oyama, I. Ishii, 2021, Biological & pharmaceutical bulletin.

Structure-based design and synthesis of fluorescent PPARalpha/delta co-agonist and its application as a probe for fluorescent polarization assay of PPARdelta ligands.

M. Makishima, Y. Hashimoto, K. Morikawa, 2008, Chemical & pharmaceutical bulletin.

[Design and synthesis of peroxisome proliferator-activated receptor (PPAR) delta agonists and its implication to the driving force to elicit PPAR delta selectivity].

M. Makishima, S. Hirono, I. Nakagome, 2009, Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan.

Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor δ in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative

H. Miyachi, T. Oyama, Kazuki Takiguchi, 2022, Acta crystallographica. Section F, Structural biology communications.

Molecular dynamics study-guided identification of cyclic amine structures as novel hydrophobic tail components of hPPARγ agonists.

K. Matsuno, N. Matsuura, Yuta Tanaka, 2014, Bioorganic & medicinal chemistry letters.

The clamp-loading complex for processive DNA replication

Y. Ishino, K. Morikawa, S. Ishino, 2004, Nature Structural &Molecular Biology.

A crystallization and preliminary X-ray diffraction study of the Arabidopsis thaliana proliferating cell nuclear antigen (PCNA2) alone and in a complex with a PIP-box peptide from Flap endonuclease 1.

T. Oyama, W. Strzałka, E. Kowalska, 2020, Acta biochimica Polonica.

Preparation of co-crystals of human PPARα-LBD and ligand for high-resolution X-ray crystallography

T. Oyama, I. Ishii, S. Kamata, 2021, STAR protocols.

Crystal Structures of Copper-depleted and Copper-bound Fungal Pro-tyrosinase

T. Oyama, G. Kurisu, N. Fujieda, 2013, The Journal of Biological Chemistry.

Peroxisome proliferator-activated receptor gamma (PPARγ) has multiple binding points that accommodate ligands in various conformations: Structurally similar PPARγ partial agonists bind to PPARγ LBD in different conformations.

H. Miyachi, T. Oyama, M. Ohashi, 2015, Bioorganic & medicinal chemistry letters.

Different structures of the two peroxisome proliferator-activated receptor gamma (PPARγ) ligand-binding domains in homodimeric complex with partial agonist, but not full agonist.

H. Miyachi, T. Oyama, M. Ohashi, 2015, Bioorganic & medicinal chemistry letters.

Structural design and synthesis of arylalkynyl amide-type peroxisome proliferator-activated receptor γ (PPARγ)-selective antagonists based on the helix12-folding inhibition hypothesis.

M. Makishima, K. Matsuno, N. Matsuura, 2015, European journal of medicinal chemistry.

Design and synthesis of a series of α-benzyl phenylpropanoic acid-type peroxisome proliferator-activated receptor (PPAR) gamma partial agonists with improved aqueous solubility.

Kenji Matsuno, Masao Ohashi, K. Matsuno, 2013, Bioorganic & medicinal chemistry.

The nuclear receptor PPARγ individually responds to serotonin‐ and fatty acid‐metabolites

K. Morikawa, Tsuyoshi Waku, R. Nakamori, 2010, The EMBO journal.

Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids.

K. Morikawa, N. Kamiya, H. Jingami, 2009, Journal of molecular biology.

Integrated molecular mechanism directing nucleosome reorganization by human FACT

K. Morikawa, T. Oyama, Y. Tsunaka, 2016, Genes & development.

The 2.8 Å crystal structure of the dynein motor domain

K. Sutoh, T. Kon, T. Shima, 2012, Nature.

Crystal structure of beta-amylase from Bacillus cereus var. mycoides at 2.2 A resolution.

M. Kusunoki, T. Oyama, Y. Nitta, 1999, Journal of biochemistry.

Crystal structures of beta-amylase from Bacillus cereus var mycoides in complexes with substrate analogs and affinity-labeling reagents.

H. Miyake, M. Kusunoki, T. Oyama, 2003, Journal of Biochemistry (Tokyo).

Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm

Y. Ishino, K. Morikawa, T. Shirai, 2009, BMC Structural Biology.

Crystal structures of autoinhibitory PDZ domain of Tamalin: implications for metabotropic glutamate receptor trafficking regulation

S. Nakanishi, K. Morikawa, H. Jingami, 2007, The EMBO journal.

Architectures of archaeal GINS complexes, essential DNA replication initiation factors

Y. Ishino, K. Morikawa, T. Shirai, 2011, BMC Biology.

CENP-T-W-S-X Forms a Unique Centromeric Chromatin Structure with a Histone-like Fold

Karen E Gascoigne, T. Hori, Aussie Suzuki, 2012, Cell.

Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery.

H. Shinagawa, K. Morikawa, D. Tsuchiya, 2002, Molecular cell.

Atomic structure of the clamp loader small subunit from Pyrococcus furiosus.

Y. Ishino, K. Morikawa, I. Cann, 2001, Molecular cell.

Three-dimensional electron microscopy of the clamp loader small subunit from Pyrococcus furiosus.

Y. Ishino, K. Morikawa, T. Oyama, 2001, Journal of structural biology.

Disordered interdomain region of Gins is important for functional tetramer formation to stimulate MCM helicase in Thermoplasma acidophilum

D. Kohda, Y. Ishino, S. Ishino, 2015, Bioscience, biotechnology, and biochemistry.

Mutational analysis of Pyrococcus furiosus replication factor C based on the three-dimensional structure

Y. Ishino, K. Morikawa, S. Ishino, 2003, Extremophiles.

Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication

Y. Ishino, T. Shirai, M. Kusunoki, 2016, Nucleic acids research.

Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome

Y. Ishino, S. Ishino, T. Oyama, 2021, Nucleic acids research.

Structural and functional studies of MinD ATPase: implications for the molecular recognition of the bacterial cell division apparatus

K. Morikawa, T. Oyama, I. Hayashi, 2001, The EMBO journal.

Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis.

Hirofumi Suzuki, Y. Ishino, K. Morikawa, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Detection of subunit interfacial modifications by tracing the evolution of clamp-loader complex.

T. Shirai, T. Oyama, M. Saito, 2005, Protein engineering, design & selection : PEDS.

Crystal structures of the Arabidopsis thaliana proliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C‐terminal segment

K. Morikawa, T. Oyama, W. Strzałka, 2009, Protein science : a publication of the Protein Society.

Investigation of the clamp loading mechanism from biochemical and 3D structural perspectives

Hirofumi Suzuki, Y. Ishino, K. Morikawa, 2007 .

Mechanism to Load the Clamp onto DNA: Seeing Vivid Structures by Single Particle Analysis

Hirofumi Suzuki, Y. Ishino, K. Morikawa, 2006 .

Detecting structural similarity of ligand interactions in the lipid metabolic system including enzymes, lipid-binding proteins and nuclear receptors.

K. Morikawa, T. Shirai, Tsuyoshi Waku, 2011, Protein engineering, design & selection : PEDS.

Domain Architectures and Characterization of an RNA-binding Protein, TLS*

T. Takumi, K. Morikawa, N. Kasai, 2004, Journal of Biological Chemistry.

Structural basis for channelling mechanism of a fatty acid β‐oxidation multienzyme complex

Daisuke Tsuchiya, Yasuo Tsunaka, K. Morikawa, 2004, The EMBO journal.

Peroxisome proliferator-activated receptors (PPARs) have multiple binding points that accommodate ligands in various conformations: phenylpropanoic acid-type PPAR ligands bind to PPAR in different conformations, depending on the subtype.

Naoyuki Kuwabara, Toshiyuki Shimizu, Masao Ohashi, 2012, Journal of medicinal chemistry.

Structure of the entire stalk region of the Dynein motor domain.

Genji Kurisu, Haruki Nakamura, Narutoshi Kamiya, 2014, Journal of molecular biology.

Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures

Y. Hashimoto, K. Morikawa, Tsuyoshi Waku, 2009, Acta crystallographica. Section D, Biological crystallography.

Atomic structure of mutant PPARγ LBD complexed with 15d‐PGJ2: Novel modulation mechanism of PPARγ/RXRα function by covalently bound ligands

K. Morikawa, Tsuyoshi Waku, T. Oyama, 2009, FEBS letters.

Mutational and Structural Analyses of Caldanaerobius polysaccharolyticus Man5B Reveal Novel Active Site Residues for Family 5 Glycoside Hydrolases

Haruki Nakamura, R. Mackie, K. Morikawa, 2013, PloS one.

Determination of the Critical Amino Acids Involved in the Peroxisome Proliferator‐Activated Receptor (PPAR) δ Selectivity of Phenylpropanoic Acid‐Derived Agonists

M. Makishima, S. Hirono, I. Nakagome, 2008, ChemMedChem.

Functional and Structural Insights into the Human PPARα/δ/γ Targeting Preferences of Anti-NASH Investigational Drugs, Lanifibranor, Seladelpar, and Elafibranor

Yui Machida, T. Oyama, I. Ishii, 2023, Antioxidants.

Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex

Y. Ishino, K. Morikawa, T. Oyama, 2009, Proceedings of the National Academy of Sciences.

Direct visualization of DNA baton pass between replication factors bound to PCNA

D. Kohda, Y. Ishino, K. Morikawa, 2018, Scientific Reports.

Structural insights into the PIP2 recognition by syntenin-1 PDZ domain.

K. Morikawa, H. Jingami, T. Sugi, 2008, Biochemical and biophysical research communications.

Purification, crystallization and preliminary X-ray analysis of the ligand-binding domain of human lectin-like oxidized low-density lipoprotein receptor 1 (LOX-1).

I. Ohki, T. Oyama, S. Machida, 2005, Acta crystallographica. Section F, Structural biology and crystallization communications.

Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm

Y. Ishino, K. Morikawa, T. Shirai, 2009, BMC Structural Biology.

Structure of the entire stalk region of the Dynein motor domain.

Haruki Nakamura, Y. Toyoshima, N. Kamiya, 2014, Journal of molecular biology.

Different structures of the two peroxisome proliferator-activated receptor gamma (PPARγ) ligand-binding domains in homodimeric complex with partial agonist, but not full agonist.

H. Miyachi, T. Oyama, M. Ohashi, 2015, Bioorganic & medicinal chemistry letters.

Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids.

H. Jingami, Tsuyoshi Waku, T. Oyama, 2009 .

Crystallization and preliminary X-ray analysis of the Pax6 paired domain bound to the Pax6 gene enhancer.

K. Okazaki, K. Morikawa, Makoto Ito, 2005, Acta crystallographica. Section F, Structural biology and crystallization communications.

[Toward High-throughput Crystal Structure Determination of PPAR Ligand-binding Domains in Complexes with Less Soluble Ligands].

T. Oyama, 2022, Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan.

Determination of the Critical Amino Acids Involved in the Peroxisome Proliferator‐Activated Receptor (PPAR) δ Selectivity of Phenylpropanoic Acid‐Derived Agonists

M. Makishima, S. Hirono, I. Nakagome, 2008, ChemMedChem.