List of works - Takuji Oyama

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

scientific article published on 01 March 2020

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

scientific article

Architectures of archaeal GINS complexes, essential DNA replication initiation factors ⬇️

scientific article published on April 28, 2011

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

scientific article

Atomic structure of mutant PPARgamma LBD complexed with 15d-PGJ2: novel modulation mechanism of PPARgamma/RXRalpha function by covalently bound ligands

scientific article

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

scientific article

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

scientific article published on February 3, 2012

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article (publication date: April 2003)

Crystal structures of copper-depleted and copper-bound fungal pro-tyrosinase: insights into endogenous cysteine-dependent copper incorporation.

scientific article published on 7 June 2013

Crystal structures of theArabidopsis thalianaproliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C-terminal segment

scientific article

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

scientific article published on 25 October 2005

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

scientific article published on February 14, 2013

Design, synthesis, and structural analysis of phenylpropanoic acid-type PPARγ-selective agonists: discovery of reversed stereochemistry-activity relationship

scientific article

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

scientific article published on 06 January 2011

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

scientific article published in March 2005

Determination of the critical amino acids involved in the peroxisome proliferator-activated receptor (PPAR) delta selectivity of phenylpropanoic acid-derived agonists

scientific article published on 01 November 2008

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

scientific article published on 01 May 2015

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

scientific article published in Scientific Reports

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

scientific article published on 24 November 2014

Domain architectures and characterization of an RNA-binding protein, TLS

scientific article

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

scientific article published on 25 April 2022

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

scientific article

Integrated molecular mechanism directing nucleosome reorganization by human FACT

scientific article published on 10 March 2016

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

scientific article published on 24 June 2014

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

scientific article published on 4 February 2003

Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases

scientific article

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

scientific article

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

scientific article

Pivotal role of a conserved histidine in <i>Escherichia coli</i> ribonuclease HI as proposed by X-ray crystallography

scientific article published in 2022

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

scientific article

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

scientific article

Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex

scientific article

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

scientific article

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

scientific article published on 4 December 2007

Structure of the entire stalk region of the Dynein motor domain

scientific article

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

scientific article published in September 2008

The 2.8 Å crystal structure of the dynein motor domain ⬇️

scientific article published on March 7, 2012

The clamp-loading complex for processive DNA replication

scientific article

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

scientific article published on 01 April 2001

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

scientific article published in June 2009

List of works by Takuji Oyama

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

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

Architectures of archaeal GINS complexes, essential DNA replication initiation factors ⬇️

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

Atomic structure of mutant PPARgamma LBD complexed with 15d-PGJ2: novel modulation mechanism of PPARgamma/RXRalpha function by covalently bound ligands

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

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

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

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

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

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

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

Crystal structures of copper-depleted and copper-bound fungal pro-tyrosinase: insights into endogenous cysteine-dependent copper incorporation.

Crystal structures of theArabidopsis thalianaproliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C-terminal segment

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

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

Design, synthesis, and structural analysis of phenylpropanoic acid-type PPARγ-selective agonists: discovery of reversed stereochemistry-activity relationship

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

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

Determination of the critical amino acids involved in the peroxisome proliferator-activated receptor (PPAR) delta selectivity of phenylpropanoic acid-derived agonists

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

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

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

Domain architectures and characterization of an RNA-binding protein, TLS

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

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

Integrated molecular mechanism directing nucleosome reorganization by human FACT

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

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

Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases

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

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

Pivotal role of a conserved histidine in <i>Escherichia coli</i> ribonuclease HI as proposed by X-ray crystallography

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

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

Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex

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

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

Structure of the entire stalk region of the Dynein motor domain

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

The 2.8 Å crystal structure of the dynein motor domain ⬇️

The clamp-loading complex for processive DNA replication

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

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