List of works - Naoki Kunishima

A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI.

scientific article published on September 2005

An electrospray-ionization mass spectrometry analysis of the pH-dependent dissociation and denaturation processes of a heterodimeric protein

scientific article published on 01 January 2000

Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser

scientific article

Atomic structure of the GCSF-receptor complex showing a new cytokine-receptor recognition scheme

scientific article

Availability of NHS-biotin labeling to identify free protein lysine revealed by experiment and MD simulation

scientific article published on 17 July 2018

Biochemical and structural characterization of a short-chain dehydrogenase/reductase of Thermus thermophilus HB8: a hyperthermostable aldose-1-dehydrogenase with broad substrate specificity.

scientific article

Characterization and N-terminal sequence of a 5 kDa polypeptide in the photosystem I core complex from spinach

scientific article published on 01 December 1989

Circular dichroism analysis of the interaction between the alpha and beta subunits in a killer toxin produced by a halotolerant yeast, Pichia farinosa

scientific article published on 01 February 1997

Cloning, sequencing, and heterologous expression of a gene coding for Arthromyces ramosus peroxidase.

scientific article published on July 1995

Crystal Structural and Functional Analysis of the Putative Dipeptidase from Pyrococcus horikoshii OT3

scientific article

Crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus

scientific article

Crystal structure of SAM-dependent methyltransferase from Pyrococcus horikoshii.

scientific article published on 24 November 2017

Crystal structure of a component of glycine cleavage system: T-protein from Pyrococcus horikoshii OT3 at 1.5 A resolution.

scientific article published in February 2005

Crystal structure of dehydroquinate synthase from Thermus thermophilus HB8 showing functional importance of the dimeric state

scientific article published on 01 January 2005

Crystal structure of novel NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8.

scientific article published on September 2005

Crystal structure of product-bound complex of UDP-N-acetyl-d-mannosamine dehydrogenase from Pyrococcus horikoshii OT3

scientific article published on 08 October 2014

Crystal structure of rat Bcl-xL. Implications for the function of the Bcl-2 protein family

scientific article

Crystal structure studies of NADP+ dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain.

scientific article published on 14 May 2014

Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation.

scientific article published in October 2005

Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis

scientific article

Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism

scientific article

Crystal structures of type IIIH NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles

scientific article published on 24 July 2014

Crystallization and preliminary X-ray diffraction studies of a novel killer toxin from a halotolerant yeast Pichia farinosa.

scientific article published in January 1997

Crystallization and preliminary X-ray diffraction studies of peroxidase from a fungus Arthromyces ramosus

scientific article published on 01 February 1993

Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids.

scientific article published on 15 August 2017

Dimeric core structure of modular stator subunit E of archaeal H+ -ATPase

scientific article published on 09 December 2006

Dimeric crystal structure of rabbit L-gulonate 3-dehydrogenase/lambda-crystallin: insights into the catalytic mechanism.

scientific article published on 8 July 2010

Further thermo-stabilization of thermophilic rhodopsin from Thermus thermophilus JL-18 through engineering in extramembrane regions

scientific article published on 16 October 2020

Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions

scientific article published on 16 August 2005

High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center.

scientific article published on 2 August 2008

Imaging Fully Hydrated Whole Cells by Coherent X-Ray Diffraction Microscopy ⬇️

scientific article published on February 28, 2013

Integrated database of information from structural genomics experiments

scientific article published on 19 April 2013

Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

scientific article

Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation.

scientific article published on 30 June 2015

Novel versatile cryoprotectants for heavy-atom derivatization of protein crystals

scientific article published on 19 April 2006

Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 A resolution crystallographic study at pH 4.5

scientific article

Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate

scientific article

Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation

scientific article published on 31 July 2017

Purification, crystallization and preliminary X-ray analysis of a complex between granulocyte colony-stimulating factor and its soluble receptor

scientific article published on 01 June 2000

Purification, crystallization and preliminary X-ray analysis of the fumarylacetoacetase family member TTHA0809 from Thermus thermophilus HB8

scientific article published on 31 August 2007

Purification, crystallization and preliminary X-ray diffraction studies of a putative UDP-N-acetyl-D-mannosamine dehydrogenase from Pyrococcus horikoshii OT3.

scientific article published on 14 April 2007

Purification, crystallization and preliminary X-ray diffraction studies of the ATP-binding subunit of an ABC transporter fromGeobacillus kaustophilus ⬇️

scientific article published on October 30, 2012

Purification, crystallization and preliminary crystallographic analysis of RecA superfamily ATPase PH0284 from Pyrococcus horikoshii OT3.

scientific article

Purification, crystallization and preliminary crystallographic analysis of archaeal 6-pyruvoyl tetrahydrobiopterin synthase homologue PH0634 from Pyrococcus horikoshii OT3

scientific article published on 16 December 2006

Purification, crystallization and preliminary crystallographic analysis of the glycine-cleavage system component T-protein from Pyrococcus horikoshii OT3.

scientific article

Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3

scientific article

Purification, crystallization and preliminary crystallographic analysis of the vacuole-type ATPase subunit E from Pyrococcus horikoshii OT3

scientific article

Purification, crystallization and preliminary crystallographic study of the putative enolase MJ0232 from the hyperthermophilic archaeon Methanococcus jannaschii

scientific article published on 31 October 2008

Remarkable improvement in the heat stability of CutA1 from Escherichia coli by rational protein design

scientific article

Role of charged residues in stabilization of Pyrococcus horikoshii CutA1, which has a denaturation temperature of nearly 150 °C

scientific article published on 14 November 2011

Stabilization due to dimer formation of phosphoribosyl anthranilate isomerase from Thermus thermophilus HB8: X-ray Analysis and DSC experiments

scientific article published in May 2005

Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry

scientific article published on 01 October 2005

Strategy for Stabilization of CutA1 Proteins Due to Ion-Ion Interactions at Temperatures of over 100 °C.

scientific article published on 12 April 2018

Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5'-monophospate analogues

scientific article published on 03 January 2019

Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+.

scientific article

Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.

scientific article published on 19 October 2005

Structure of a haloacid dehalogenase superfamily phosphatase PH1421 from Pyrococcus horikoshii OT3: oligomeric state and thermoadaptation mechanism

scientific article

Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability

scientific article

Structure of putative CutA1 fromHomo sapiensdetermined at 2.05 Å resolution

scientific article

Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes

scientific article

Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2

scientific article

Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality

scientific article

The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8

scientific article

The novel acidophilic structure of the killer toxin from halotolerant yeast demonstrates remarkable folding similarity with a fungal killer toxin

scientific article

Thermodynamic analysis of unusually thermostable CutA1 protein from human brain and its protease susceptibility.

scientific article

Thermodynamics of protein denaturation at temperatures over 100 °C: CutA1 mutant proteins substituted with hydrophobic and charged residues.

scientific article published on 26 October 2015

Visualization of internal 3D structure of small live seed on germination by laboratory-based X-ray microscopy with phase contrast computed tomography

scientific article published on 01 February 2020

[A new cytokine-receptor recognition scheme revealed by the complex structure of G-CSF and its receptor]

scientific article published on 01 July 2000

List of works by Naoki Kunishima

A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI.

An electrospray-ionization mass spectrometry analysis of the pH-dependent dissociation and denaturation processes of a heterodimeric protein

Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser

Atomic structure of the GCSF-receptor complex showing a new cytokine-receptor recognition scheme

Availability of NHS-biotin labeling to identify free protein lysine revealed by experiment and MD simulation

Biochemical and structural characterization of a short-chain dehydrogenase/reductase of Thermus thermophilus HB8: a hyperthermostable aldose-1-dehydrogenase with broad substrate specificity.

Characterization and N-terminal sequence of a 5 kDa polypeptide in the photosystem I core complex from spinach

Circular dichroism analysis of the interaction between the alpha and beta subunits in a killer toxin produced by a halotolerant yeast, Pichia farinosa

Cloning, sequencing, and heterologous expression of a gene coding for Arthromyces ramosus peroxidase.

Crystal Structural and Functional Analysis of the Putative Dipeptidase from Pyrococcus horikoshii OT3

Crystal structure of ATP-binding subunit of an ABC transporter from Geobacillus kaustophilus

Crystal structure of SAM-dependent methyltransferase from Pyrococcus horikoshii.

Crystal structure of a component of glycine cleavage system: T-protein from Pyrococcus horikoshii OT3 at 1.5 A resolution.

Crystal structure of dehydroquinate synthase from Thermus thermophilus HB8 showing functional importance of the dimeric state

Crystal structure of novel NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8.

Crystal structure of product-bound complex of UDP-N-acetyl-d-mannosamine dehydrogenase from Pyrococcus horikoshii OT3

Crystal structure of rat Bcl-xL. Implications for the function of the Bcl-2 protein family

Crystal structure studies of NADP+ dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain.

Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation.

Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis

Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism

Crystal structures of type IIIH NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles

Crystallization and preliminary X-ray diffraction studies of a novel killer toxin from a halotolerant yeast Pichia farinosa.

Crystallization and preliminary X-ray diffraction studies of peroxidase from a fungus Arthromyces ramosus

Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids.

Dimeric core structure of modular stator subunit E of archaeal H+ -ATPase

Dimeric crystal structure of rabbit L-gulonate 3-dehydrogenase/lambda-crystallin: insights into the catalytic mechanism.

Further thermo-stabilization of thermophilic rhodopsin from Thermus thermophilus JL-18 through engineering in extramembrane regions

Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions

High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center.

Imaging Fully Hydrated Whole Cells by Coherent X-Ray Diffraction Microscopy ⬇️

Integrated database of information from structural genomics experiments

Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation.

Novel versatile cryoprotectants for heavy-atom derivatization of protein crystals

Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 A resolution crystallographic study at pH 4.5

Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate

Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation

Purification, crystallization and preliminary X-ray analysis of a complex between granulocyte colony-stimulating factor and its soluble receptor

Purification, crystallization and preliminary X-ray analysis of the fumarylacetoacetase family member TTHA0809 from Thermus thermophilus HB8

Purification, crystallization and preliminary X-ray diffraction studies of a putative UDP-N-acetyl-D-mannosamine dehydrogenase from Pyrococcus horikoshii OT3.

Purification, crystallization and preliminary X-ray diffraction studies of the ATP-binding subunit of an ABC transporter fromGeobacillus kaustophilus ⬇️

Purification, crystallization and preliminary crystallographic analysis of RecA superfamily ATPase PH0284 from Pyrococcus horikoshii OT3.

Purification, crystallization and preliminary crystallographic analysis of archaeal 6-pyruvoyl tetrahydrobiopterin synthase homologue PH0634 from Pyrococcus horikoshii OT3

Purification, crystallization and preliminary crystallographic analysis of the glycine-cleavage system component T-protein from Pyrococcus horikoshii OT3.

Purification, crystallization and preliminary crystallographic analysis of the putative thiamine-biosynthesis protein PH1313 from Pyrococcus horikoshii OT3

Purification, crystallization and preliminary crystallographic analysis of the vacuole-type ATPase subunit E from Pyrococcus horikoshii OT3

Purification, crystallization and preliminary crystallographic study of the putative enolase MJ0232 from the hyperthermophilic archaeon Methanococcus jannaschii

Remarkable improvement in the heat stability of CutA1 from Escherichia coli by rational protein design

Role of charged residues in stabilization of Pyrococcus horikoshii CutA1, which has a denaturation temperature of nearly 150 °C

Stabilization due to dimer formation of phosphoribosyl anthranilate isomerase from Thermus thermophilus HB8: X-ray Analysis and DSC experiments

Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry

Strategy for Stabilization of CutA1 Proteins Due to Ion-Ion Interactions at Temperatures of over 100 °C.

Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5'-monophospate analogues

Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+.

Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.

Structure of a haloacid dehalogenase superfamily phosphatase PH1421 from Pyrococcus horikoshii OT3: oligomeric state and thermoadaptation mechanism

Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability

Structure of putative CutA1 fromHomo sapiensdetermined at 2.05 Å resolution

Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes

Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2

Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality

The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8

The novel acidophilic structure of the killer toxin from halotolerant yeast demonstrates remarkable folding similarity with a fungal killer toxin

Thermodynamic analysis of unusually thermostable CutA1 protein from human brain and its protease susceptibility.

Thermodynamics of protein denaturation at temperatures over 100 °C: CutA1 mutant proteins substituted with hydrophobic and charged residues.

Visualization of internal 3D structure of small live seed on germination by laboratory-based X-ray microscopy with phase contrast computed tomography

[A new cytokine-receptor recognition scheme revealed by the complex structure of G-CSF and its receptor]