N. Kobayashi

发表

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists

Toshimichi Fujiwara, Naohiro Kobayashi, T. Fujiwara, 2017, Computational and structural biotechnology journal.

Structural insight into the zinc finger CW domain as a histone modification reader.

T. Umehara, P. Güntert, T. Kigawa, 2010, Structure.

Solution structure of the GUCT domain from human RNA helicase II/Guβ reveals the RRM fold, but implausible RNA interactions

Peter Güntert, Satoru Watanabe, Naoya Tochio, 2009, Proteins.

Robust folding of a de novo designed ideal protein even with most of the core mutated to valine

N. Koga, T. Fujiwara, T. Sugiki, 2020, Proceedings of the National Academy of Sciences.

Structural basis for the dual RNA-recognition modes of human Tra2-β RRM

Sumio Sugano, Peter Güntert, Satoru Watanabe, 2010, Nucleic acids research.

A robust method for quantitative identification of ordered cores in an ensemble of biomolecular structures by non-linear multi-dimensional scaling using inter-atomic distance variance matrix

N. Kobayashi, 2014, Journal of biomolecular NMR.

Structures of the first and second double‐stranded RNA‐binding domains of human TAR RNA‐binding protein

P. Güntert, T. Kigawa, S. Yokoyama, 2011, Protein science : a publication of the Protein Society.

Solution structure of Gaussia Luciferase with five disulfide bonds and identification of a putative coelenterazine binding cavity by heteronuclear NMR

N. Kobayashi, N. Wu, S. Unzai, 2020, Scientific Reports.

Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints

T. Ikegami, Yoshikazu Hattori, Kyoko Furuita, 2014, Journal of Biomolecular NMR.

Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study.

F. Tama, O. Miyashita, A. Shimada, 2020, Biochimica et biophysica acta. General subjects.

Structural Basis for Inhibition of the MDM2:p53 Interaction by an Optimized MDM2-Binding Peptide Selected with mRNA Display

N. Kobayashi, N. Tabata, N. Doi, 2014, PloS one.

1H, 13C, and 15N resonance assignments and solution structures of the KH domain of human ribosome binding factor A, mtRbfA, involved in mitochondrial ribosome biogenesis

P. Güntert, T. Kigawa, S. Yokoyama, 2022, Biomolecular NMR Assignments.

Solution structure of the splicing factor motif of the human Prp18 protein

P. Güntert, T. Kigawa, S. Yokoyama, 2012, Proteins.

The synthesis and biological activity of EGF-family related peptides

N. Kobayashi, S. Y. Shin, E. Munekata, 1994 .

An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

T. Kigawa, S. Yokoyama, E. Ulrich, 2012, Journal of Biomolecular NMR.

Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner

E. Obayashi, H. Yoshida, Sam-Yong Park, 2020, Biomedicines.

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

Hirofumi Suzuki, K. Kinoshita, T. Kawabata, 2017, Protein science : a publication of the Protein Society.

Validation of Structures in the Protein Data Bank

Naohiro Kobayashi, Haruki Nakamura, Zukang Feng, 2017, Structure.

Structure of Musashi1 in a complex with target RNA: the role of aromatic stacking interactions

H. Okano, N. Kobayashi, Takao Imai, 2011, Nucleic acids research.

Protein Data Bank: the single global archive for 3D macromolecular structure data

Cole H. Christie, Jose M. Duarte, Rachel Kramer Green, 2018, Nucleic acids research.

Solution structure of Vanabin2, a vanadium(IV)-binding protein from the vanadium-rich ascidian Ascidia sydneiensis samea.

S. Yokoyama, H. Hirota, N. Kobayashi, 2005, Journal of the American Chemical Society.

Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization

K. Ikeda, Y. Kubo, I. Shimada, 2020, bioRxiv.

Structure, interaction and real‐time monitoring of the enzymatic reaction of wild‐type APOBEC3G

S. Yokoyama, N. Kobayashi, H. Takaku, 2009, The EMBO journal.

Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA

H. Okano, N. Kobayashi, Takao Imai, 2017, Molecules.

A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription

S. Yokoyama, J. Lausen, M. H. Werner, 2007, Nature Structural &Molecular Biology.

RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing

P. Güntert, M. Hagiwara, S. Yokoyama, 2014, Nature Structural &Molecular Biology.

Solution structure of the first RNA recognition motif domain of human spliceosomal protein SF3b49 and its mode of interaction with a SF3b145 fragment

P. Güntert, T. Kigawa, S. Yokoyama, 2016, Protein science : a publication of the Protein Society.

The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition

Y. Hayashizaki, P. Güntert, T. Kigawa, 2008, Nucleic acids research.

How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2?

Naohiro Kobayashi, Masahiro Kinoshita, Mitsunori Ikeguchi, 2019, J. Chem. Inf. Model..

Solution structure of the second RNA recognition motif (RRM) domain of murine T cell intracellular antigen-1 (TIA-1) and its RNA recognition mode.

Y. Hayashizaki, P. Güntert, T. Kigawa, 2008, Biochemistry.

Sensitivity-Enhanced Solid-State NMR Detection of Structural Differences and Unique Polymorphs in Pico- to Nanomolar Amounts of Brain-Derived and Synthetic 42-Residue Amyloid-β Fibrils.

Y. Ishii, N. Kobayashi, S. Meredith, 2021, Journal of the American Chemical Society.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Naohiro Kobayashi, Haruki Nakamura, Zukang Feng, 2017, Structure.

Structural insight into the interaction of ADP‐ribose with the PARP WWE domains

P. Güntert, T. Kigawa, S. Yokoyama, 2012, FEBS letters.

Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3

S. Sugano, P. Güntert, T. Kigawa, 2009, Nucleic acids research.

Exploration of novel αβ-protein folds through de novo design

N. Koga, G. Chikenji, T. Fujiwara, 2021, bioRxiv.

Plastic roles of phenylalanine and tyrosine residues of TLS/FUS in complex formation with the G-quadruplexes of telomeric DNA and TERRA

N. Kobayashi, R. Kurokawa, T. Nagata, 2018, Scientific Reports.

1H, 15N and 13C resonance assignments of the conserved region in the middle domain of S. pombe Sin1 protein

T. Ikegami, Yoshikazu Hattori, Kyoko Furuita, 2015, Biomolecular NMR assignments.

1H, 13C and 15N resonance assignments and solution structures of the two RRM domains of Matrin-3

P. Güntert, T. Kigawa, S. Yokoyama, 2021, Biomolecular NMR Assignments.

Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA.

N. Kobayashi, S. Tate, N. Tochio, 2013, Biochemical and biophysical research communications.

Conversion of two-state to multi-state folding kinetics on fusion of two protein foldons.

A. Fersht, K. Inaba, N. Kobayashi, 2000, Journal of molecular biology.

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

Christoph Steinbeck, Daniel Schober, Jie Hao, 2018, Analytical chemistry.

Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway.

O. Ohara, P. Güntert, T. Kigawa, 2009, Journal of molecular biology.

Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus.

S. Honda, N. Kobayashi, E Munekata, 2000, Journal of molecular biology.

KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies

Peter Güntert, Naoya Tochio, Seizo Koshiba, 2007, Journal of biomolecular NMR.

Solution structure of the kinase‐associated domain 1 of mouse microtubule‐associated protein/microtubule affinity‐regulating kinase 3

Y. Hayashizaki, T. Kigawa, S. Yokoyama, 2006, Protein science : a publication of the Protein Society.

Role of side-chains in the cooperative beta-hairpin folding of the short C-terminal fragment derived from streptococcal protein G.

S. Honda, N. Kobayashi, E. Munekata, 2000, Biochemistry.

NMR analysis of the binding of a rhodanese peptide to a minichaperone in solution.

A. Fersht, S. Freund, N. Kobayashi, 1999, Journal of molecular biology.

The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif.

N. Kobayashi, K. Igarashi, S. Tate, 2014, Biochemistry.

Solution structure of the cysteine‐rich domain in Fn14, a member of the tumor necrosis factor receptor superfamily

P. Güntert, T. Kigawa, S. Yokoyama, 2009, Protein science : a publication of the Protein Society.

Solution structure of the RWD domain of the mouse GCN2 protein

K. Kinoshita, J. Kawai, Piero Carninci, 2004, Protein science : a publication of the Protein Society.

Conjugation of two RNA aptamers improves binding affinity to AML1 Runt domain

Yoshikazu Nakamura, N. Kobayashi, Y. Haishima, 2017, Journal of biochemistry.

BioMagResBank (BMRB) as a Resource for Structural Biology.

Masashi Yokochi, Naohiro Kobayashi, Toshimichi Fujiwara, 2020, Methods in molecular biology.

Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA

H. Okano, N. Kobayashi, Takao Imai, 2017, Biomolecular NMR assignments.

Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3

P. Güntert, T. Kigawa, S. Yokoyama, 2014, Proteins.

1H, 13C, and 15N resonance assignments of the dsRBDs of mouse RNA helicase A

P. Güntert, S. Yokoyama, Y. Muto, 2013, Biomolecular NMR assignments.

Solution structures of the double‐stranded RNA‐binding domains from rna helicase A

P. Güntert, T. Kigawa, S. Yokoyama, 2012, Proteins.

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

Michael Nilges, Sameer Velankar, Torsten Herrmann, 2015, Nature Structural &Molecular Biology.

Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints

T. Ikegami, Yoshikazu Hattori, Kyoko Furuita, 2015, Journal of biomolecular NMR.

Complement assembly of two fragments of the streptococcal protein G B1 domain in aqueous solution

H. Uedaira, S. Honda, N. Kobayashi, 1995, FEBS letters.

Solution structure of immunoglobulin like domain of mouse nuclear lamin

T. Kigawa, S. Yokoyama, N. Kobayashi, 2004 .

Fragment reconstitution of a small protein: folding energetics of the reconstituted immunoglobulin binding domain B1 of streptococcal protein G.

H. Uedaira, S. Honda, N. Kobayashi, 1999, Biochemistry.

1H, 13C and 15N resonance assignment of the YTH domain of YTHDC2

P. Güntert, T. Kigawa, S. Yokoyama, 2020, Biomolecular NMR Assignments.

Comparative study on the conformation of phallotoxin and virotoxin in aqueous solution

N. Kobayashi, S. Endo, H. Faulstich, 1991 .

Comparative study on the conformation of phalloidin, viroisin, and related derivatives in aqueous solution.

N. Kobayashi, H. Kobayashi, S. Endo, 1995, European journal of biochemistry.

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

Akira R. Kinjo, Masashi Yokochi, Takeshi Iwata, 2016, Journal of Biomedical Semantics.

NMR study of xenotropic murine leukemia virus-related virus protease in a complex with amprenavir.

T. Ikegami, A. Ryo, N. Kobayashi, 2012, Biochemical and biophysical research communications.

1H NMR study on the conformation of bacitracin A in aqueous solution

N. Kobayashi, S. Endo, T. Takenouchi, 1992, FEBS letters.

The NMR structure of FliK, the trigger for the switch of substrate specificity in the flagellar type III secretion apparatus.

N. Kobayashi, S. Aizawa, S. Tate, 2011, Journal of molecular biology.

Conformational study on the IgG binding domain of protein G

N. Kobayashi, S. Endo, E. Munekata, 1993 .

The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif.

N. Kobayashi, K. Igarashi, S. Tate, 2014, Biochemistry.

Solution structure of the RNA binding domain in the human muscleblind‐like protein 2

P. Güntert, T. Kigawa, S. Yokoyama, 2009, Protein science : a publication of the Protein Society.

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

Joseph A. Cruz, D. Wishart, T. Ebbels, 2018, Analytical chemistry.