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List of works by Yoshifumi Nishimura

A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations

scientific article published on 16 June 2011

A mimetic of the mSin3-binding helix of NRSF/REST ameliorates abnormal pain behavior in chronic pain models.

scientific article published on 7 September 2017

A possible correlation between DNA conformation and the mode of action of restriction enzymes

scientific article published on 01 December 1984

A protein recycling system for nuclear magnetic resonance-based screening of drug candidates

scientific article

Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome

scientific article published on 03 August 2020

An A-form poly(dG).poly(dC) in H2O solution

scientific article published in 1985

Anomalous temperature dependence of the phosphorus-31 nuclear magnetic resonance chemical shift in d(CCGG) and d(CCTAGG) at the junction of the pyrimidine stack followed by the purine stack

scientific article published on 01 October 1986

Application of 13C nuclear magnetic resonance spectroscopy to molecular structural analyses of antibody molecules

scientific article published on 01 June 1989

C-terminal acidic domain of histone chaperone human NAP1 is an efficient binding assistant for histone H2A-H2B, but not H3-H4.

scientific article published on 4 February 2016

Characteristic H3 N-tail dynamics in the nucleosome core particle, nucleosome, and chromatosome

scientific article published on 17 February 2022

Charge-neutralization effect of the tail regions on the histone H2A/H2B dimer structure.

scientific article published on 3 April 2015

Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways.

scientific article published on 24 October 2017

Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities.

scientific article published on January 2005

Conclusive evidence of the reconstituted hexasome proven by native mass spectrometry

scientific article

Correction: Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly.

scientific article published on 6 September 2017

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome.

scientific article published in April 2017

Crystallization and preliminary X-ray diffraction studies on the DNA-binding domain of the transcriptional activator protein PhoB from Escherichia coli.

scientific article published on 28 September 2002

Cytochrome d axial ligand of the bd-type terminal quinol oxidase from Escherichia coli

scientific article published on 01 November 1993

Dataset for the NMR structure of the intrinsically disordered acidic region of XPC bound to the PH domain of TFIIH p62.

scientific article

Deimination stabilizes histone H2A/H2B dimers as revealed by electrospray ionization mass spectrometry

scientific article published on August 2010

Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-binding domain

scientific article published on 01 November 1995

Dynamics of DNA in chromatin and DNA binding mode to core protein

scientific article published on 01 February 1983

Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH

scientific article

Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site

scientific article

Evaluation of binding affinity of protein-mutant DNA complexes in solution by laser spray mass spectrometry

scientific article

Extended string binding mode of the phosphorylated transactivation domain of tumor suppressor p53

scientific article

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

scientific article published on 03 March 2016

Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing.

scientific article published on August 1992

Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2 and NPM3 during sperm chromatin remodeling.

scientific article

Gas-phase structure of the histone multimers characterized by ion mobility mass spectrometry and molecular dynamics simulation.

scientific article published on 29 March 2013

Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly

scientific article published on August 2017

Internal motion of deoxyribonucleic acid in chromatin. Nanosecond fluorescence studies of intercalated ethidium.

scientific article published in December 1983

Intrinsic nucleic acid-binding activity of Chp1 chromodomain is required for heterochromatic gene silencing

scientific article

Investigation of molecular size of transcription factor TFIIE in solution.

scientific article published in November 2005

Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence

scientific article published on 01 July 1997

Lifetime of tyrosine fluorescence in nucleosome core particles

scientific article published on 01 June 1982

Local and overall conformations of DNA double helices with the A - T base pairs

scientific article published on 01 August 1986

Location of phosphorylation site and DNA-binding site of a positive regulator, OmpR, involved in activation of the osmoregulatory genes of Escherichia coli

scientific article published on 01 June 1989

Mass spectrometric approach for characterizing the disordered tail regions of the histone H2A/H2B dimer

scientific article published on 29 January 2015

N-terminal phosphorylation of HP1α increases its nucleosome-binding specificity

scientific article

NMR dynamics distinguish between hard and soft hydrophobic cores in the DNA-binding domain of PhoB and demonstrate different roles of the cores in binding to DNA

scientific article published on 24 January 2007

NMR structure of the hRap1 Myb motif reveals a canonical three-helix bundle lacking the positive surface charge typical of Myb DNA-binding domains

scientific article

Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain

scientific article

Nuclear magnetic resonance study on the interaction of aclacinomycin-A with a deoxyribo-hexanucleotide pentaphosphate d(CCTAGG)2 in aqueous solution

scientific article published on 01 November 1986

Nucleosome organization and chromatin dynamics in telomeres

scientific article published on March 2015

On the base-stacking in the 5'-terminal cap structure of mRNA: a fluorescence study.

scientific article published on March 1980

Protein 3000 project "Transcription and translation"

scientific article published in April 2008

Proton nuclear magnetic resonance study of a selectively deuterated mouse monoclonal antibody: use of two-dimensional homonuclear Hartmann-Hahn spectroscopy

scientific article published on 01 September 1989

Raman diagnosis of nucleic acid structure: sugar-puckering and glycosidic conformation in the guanosine moiety.

scientific article

Real-time and simultaneous monitoring of the phosphorylation and enhanced interaction of p53 and XPC acidic domains with the TFIIH p62 subunit.

scientific article published on June 2015

Selective dissociation of non-covalent bonds in biological molecules by laser spray.

scientific article published in September 2004

Sertraline, chlorprothixene, and chlorpromazine characteristically interact with the REST-binding site of the corepressor mSin3, showing medulloblastoma cell growth inhibitory activities

scientific article published in Scientific Reports

Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices

scientific article

Solution structure of a telomeric DNA complex of human TRF1

scientific article

Solution structure of the DNA-binding domain of human telomeric protein, hTRF1 ⬇️

scientific article published on August 15, 1998

Solution structure of the isolated histone H2A-H2B heterodimer.

scientific article

Stability analysis for double-stranded DNA oligomers and their noncovalent complexes with drugs by laser spray

scientific article

Structural Diversity of Nucleosomes Characterized by Native Mass Spectrometry

scientific article published on 12 June 2018

Structural Insight into the Mechanism of TFIIH Recognition by the Acidic String of the Nucleotide Excision Repair Factor XPC

scientific article

Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene

scientific article

Structural characterization of human general transcription factor TFIIF in solution

scientific article

Structural comparison of the PhoB and OmpR DNA-binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box

scientific article

Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH

scientific article

Structural polymorphism of chromodomains in Chd1.

scientific article

Structural visualization of key steps in nucleosome reorganization by human FACT

scientific article published on 15 July 2019

Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface

scientific article

Structure-spectrum correlations in nucleic acids. I. Raman lines in the 600-700 cm-1 range of guanosine residue.

scientific article published on September 1984

Substitutions of conserved aromatic amino acid residues in subunit I perturb the metal centers of the Escherichia coli bo-type ubiquinol oxidase

scientific article published on 01 February 1998

Telomeric repeats act as nucleosome-disfavouring sequences in vivo

scientific article published on 29 October 2013

The Eaf3 chromodomain acts as a pH sensor for gene expression by altering its binding affinity for histone methylated-lysine residues

scientific article published on 01 February 2020

The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH.

scientific article published on 4 November 2016

The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation

scientific article published on 01 February 1996

The neural repressor NRSF/REST binds the PAH1 domain of the Sin3 corepressor by using its distinct short hydrophobic helix

scientific article published on 26 October 2005

Thermal unfolding of proteins probed by laser spray mass spectrometry

scientific article

Three human RNA polymerases interact with TFIIH via a common RPB6 subunit

scientific article published on 01 January 2022

Top-down analysis of basic proteins by microchip capillary electrophoresis mass spectrometry

scientific article published on 01 January 2006

Two metal-binding sites in a lead ribozyme bound to competitively by Pb2+ and Mg2+--induced structural changes as revealed by NMR.

scientific article

Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment

scientific article

[A historical view of the double helix: its discovery, proof and prospects]

scientific article published on 01 May 2003

[Neural repressor NRSF/REST binds to the mSin3 PAH1 domain by using its short hydrophobic helix]

scientific article published on 01 July 2006

[New paradigm on dynamic protein structure: Introduction].

scientific article

[Protein dynamics and naturally unfolded state]

scientific article published on 01 August 2007

[Role of NMR in structural proteomics]

scientific article published on 01 June 2005

[Structural biology of a general transcription factor, TFIIE and its interaction mode with TFIIH]

scientific article published on 01 June 2008

[Structural biology of transcription on eukaryotic chromatin]

scientific article published on 01 August 2005

[Structural biology on transcription]

scientific article published on 01 June 2002

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