Makoto Nakakido 研究室

主宰者：Makoto Nakakido

東京大学

AI 要約（直近 5 年の研究成果）

この研究室は、タンパク質の構造と機能、および分子間相互作用の仕組みを解明することを主な研究課題としています。特に感染症の原因菌が持つ栄養獲得タンパク質、神経細胞の接着や可塑性に関わる分子、ならびに細胞内小器官間の相互作用を対象として研究を進めています。研究の手法としては、クライオ電子顕微鏡法による高分解能構造解析、表面プラズモン共鳴などの生物物理学的測定、質量分析、分子動力学シミュレーション、遺伝子解析など、複数の実験技術を組み合わせています。また、単一領域抗体（ナノボディ）や改変抗体の設計・開発を通じて、生物学的プロセスの制御手段を創出することも重要な活動です。主要な発見としては、タンパク質の結合様式や凝集挙動が表面電荷やプローブ設計に大きく影響されること、細菌の金属獲得システムが治療標的として機能すること、細胞膜間の接着複合体が微細な構造変化で機能を調節されることなど、分子レベルでの相互作用メカニズムの詳細が示されています。これらの知見は、感染症治療や神経疾患の理解、さらには新規医薬品開発への応用へと向かっています。

※ AI（Claude）が、公開されている論文要旨から研究の問い・手法・主要な発見を事実情報として抽出・再構成して自動生成しています。誤りを含む可能性があるため、正確性は研究室公式情報でご確認ください。

外部リンク

研究成果（96 件）

[2026] Fluorescent protein-based probe architecture modulates rotational and translational diffusion readouts in polarization-dependent fluorescence correlation spectroscopy
DOI: https://doi.org/10.1093/jmicro/dfag021
[2026] Mass photometry analysis revealed monomer-dimer equilibrium of the synaptic adhesion molecule neuroligin
DOI: https://doi.org/10.1016/j.bbrc.2026.153830
[2026] Structural analysis of <scp>Cu/Zn‐superoxide dismutase</scp> linked to neurodegenerative disease by antibody‐guided cryo‐ <scp>EM</scp>
DOI: https://doi.org/10.1002/pro.70615
[2026] Structural basis for the intestinal protocadherin-based intermicrovillar adhesion complex
DOI: https://doi.org/10.64898/2026.05.11.724279
[2026] Development of an inhibitory monoclonal nanobody targeting Streptococcus pyogenes siderophore binding protein FtsB
DOI: https://doi.org/10.1016/j.jbc.2026.111224
[2025] Development of a VHH that inhibits the binding of neuronal pentraxin 2 to a postsynaptic glutamate receptor, AMPAR
DOI: https://doi.org/10.1016/j.jbc.2025.110975
[2025] Structural basis for heme binding by the Shr protein from Streptococcus pyogenes
DOI: https://doi.org/10.1016/j.jbc.2025.111012
[2025] Development of a VHH that inhibits the binding of neuronal pentraxin 2 to a postsynaptic glutamate receptor, AMPAR
DOI: https://doi.org/10.1016/j.jbc.2025.110975
[2025] PRELP functions via multiple interactions with intrinsically weak affinity relying on ECM anchoring and remodeling
DOI: https://doi.org/10.1038/s41598-025-09018-7
[2025] Improving the solubility of single domain antibodies using <scp>VH</scp>‐like hallmark residues
DOI: https://doi.org/10.1002/pro.70189

続きを表示（残り 86 件）

[2025] Development of a small compound that regulates the function of a maltodextrin-binding protein of Streptococcus pyogenes by multifaceted screenings
DOI: https://doi.org/10.1038/s41598-025-02175-9
[2025] Antiviral potential of proton-type zeolite
DOI: https://doi.org/10.1371/journal.pone.0324484
[2025] PRELP functions via multiple interactions with intrinsically weak affinity relying on ECM anchoring and remodeling
DOI: https://doi.org/10.1038/s41598-025-09018-7
[2025] Improving the solubility of single domain antibodies using <scp>VH</scp>‐like hallmark residues
DOI: https://doi.org/10.1002/pro.70189
[2025] Development of a small compound that regulates the function of a maltodextrin-binding protein of Streptococcus pyogenes by multifaceted screenings
DOI: https://doi.org/10.1038/s41598-025-02175-9
[2025] Supercharging design of an anti-lysozyme Fab antibody to regulate ligand-dependent reversible aggregation
DOI: https://doi.org/10.1038/s41428-025-01046-4
[2025] Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering
DOI: https://doi.org/10.1038/s41467-025-58538-3
[2025] Supercharging design of an anti-lysozyme Fab antibody to regulate ligand-dependent reversible aggregation
DOI: https://doi.org/10.1038/s41428-025-01046-4
[2025] Affinity‐stability trade‐off mechanism of residue 35 in framework region 2 of <scp>VHH</scp> antibodies with β‐hairpin <scp>CDR3</scp>
DOI: https://doi.org/10.1002/pro.70095
[2025] Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering
DOI: https://doi.org/10.1038/s41467-025-58538-3
[2025] Specific recognition mechanism of an antibody to sulfated tyrosine and its potential use in biological research
DOI: https://doi.org/10.1016/j.jbc.2025.108176
[2025] Specific recognition mechanism of an antibody to sulfated tyrosine and its potential use in biological research
DOI: https://doi.org/10.1016/j.jbc.2025.108176
[2025] myCRP, Cysteine-Rich Protein in the Yesso Scallop Mizuhopecten yessoensis, Is a Novel High-Molecular Weight Cd-Binding Protein
DOI: https://doi.org/10.1007/s10126-025-10553-7
[2025] Structural basis for heme binding by the Shr protein from Streptococcus pyogenes
DOI: https://doi.org/10.1016/j.jbc.2025.111012
[2024] Triphenylphosphonium-modified catiomers enhance in vivo mRNA delivery through stabilized polyion complexation
DOI: https://doi.org/10.1039/d4mh00325j
[2024] Structural basis for the recognition of human hemoglobin by the heme-acquisition protein Shr from Streptococcus pyogenes
DOI: https://doi.org/10.1038/s41598-024-55734-x
[2024] Generation of antibodies to an extracellular region of the transporters Glut1/Glut4 by immunization with a designed antigen
DOI: https://doi.org/10.1016/j.jbc.2024.105640
[2024] Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies
DOI: https://doi.org/10.1016/j.jbc.2024.107989
[2024] Development of an Antibody-Drug Conjugate Targeting CADM1 in Adult T-Cell Leukemia/Lymphoma
DOI: https://doi.org/10.1182/blood-2024-198569
[2024] Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies
DOI: https://doi.org/10.1016/j.jbc.2024.107989
[2024] Structural basis for the ligand promiscuity of the hydroxamate siderophore binding protein FtsB from Streptococcus pyogenes
DOI: https://doi.org/10.1016/j.str.2024.09.018
[2024] Development of novel humanized VHH synthetic libraries based on physicochemical analyses
DOI: https://doi.org/10.1038/s41598-024-70513-4
[2024] High‐throughput system for the thermostability analysis of proteins
DOI: https://doi.org/10.1002/pro.5029
[2024] Functional insights of Tyr37 in framework region 2 directly contributing to the binding affinities and dissociation kinetics in single-domain VHH antibodies
DOI: https://doi.org/10.1016/j.bbrc.2024.149839
[2024] Structural basis for the ligand promiscuity of the hydroxamate siderophore binding protein FtsB from Streptococcus pyogenes
DOI: https://doi.org/10.1016/j.str.2024.09.018
[2024] Development of novel humanized VHH synthetic libraries based on physicochemical analyses
DOI: https://doi.org/10.1038/s41598-024-70513-4
[2024] High‐throughput system for the thermostability analysis of proteins
DOI: https://doi.org/10.1002/pro.5029
[2024] Characterization of a novel format <scp>scFv</scp>×<scp>VHH</scp> single‐chain biparatopic antibody against metal binding protein <scp>MtsA</scp>
DOI: https://doi.org/10.1002/pro.5017
[2024] Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab
DOI: https://doi.org/10.1016/j.bbrc.2024.149969
[2024] Functional insights of Tyr37 in framework region 2 directly contributing to the binding affinities and dissociation kinetics in single-domain VHH antibodies
DOI: https://doi.org/10.1016/j.bbrc.2024.149839
[2024] Generation of antibodies to an extracellular region of the transporters Glut1/Glut4 by immunization with a designed antigen
DOI: https://doi.org/10.1016/j.jbc.2024.105640
[2024] Structural basis for the recognition of human hemoglobin by the heme-acquisition protein Shr from Streptococcus pyogenes
DOI: https://doi.org/10.1038/s41598-024-55734-x
[2023] Dispersion Function of a Protein, DP‐1, Identified inCollimonas sp. D‐25, for the Synthesis of Gold Nanoparticles
DOI: https://doi.org/10.1002/cbic.202300221
[2023] Enhancing thermal stability in the <scp>CH2</scp> domain to suppress aggregation through the introduction of simultaneous disulfide bonds in Pichia pastoris
DOI: https://doi.org/10.1002/pro.4831
[2023] Conformational features and interaction mechanisms of <scp>VHH</scp> antibodies with β‐hairpin <scp>CDR3</scp>: A case of <scp>Nb8‐HigB2</scp> interaction
DOI: https://doi.org/10.1002/pro.4827
[2023] PRELP secreted from mural cells protects the function of blood brain barrier through regulation of endothelial cell-cell integrity
DOI: https://doi.org/10.3389/fcell.2023.1147625
[2023] Arginine cluster introduction on framework region in anti‐lysozyme antibody improved association rate constant by changing conformational diversity of <scp>CDR</scp> loops
DOI: https://doi.org/10.1002/pro.4745
[2023] Group A Streptococcus cation diffusion facilitator proteins contribute to immune evasion by regulating intracellular metal concentrations
DOI: https://doi.org/10.1016/j.bbrc.2023.07.052
[2023] Enhancing thermal stability in the <scp>CH2</scp> domain to suppress aggregation through the introduction of simultaneous disulfide bonds in Pichia pastoris
DOI: https://doi.org/10.1002/pro.4831
[2023] Conformational features and interaction mechanisms of <scp>VHH</scp> antibodies with β‐hairpin <scp>CDR3</scp>: A case of <scp>Nb8‐HigB2</scp> interaction
DOI: https://doi.org/10.1002/pro.4827
[2023] Biophysical insight into protein-protein interactions in the Interleukin-11/Interleukin-11Rα/glycoprotein 130 signaling complex
DOI: https://doi.org/10.1016/j.bbrc.2023.10.010
[2023] Specific peptide conjugation to a therapeutic antibody leads to enhanced therapeutic potency and thermal stability by reduced Fc dynamics
DOI: https://doi.org/10.1038/s41598-023-43431-0
[2023] Peripheral administration of nanomicelle-encapsulated anti-Aβ oligomer fragment antibody reduces various toxic Aβ species in the brain
DOI: https://doi.org/10.1186/s12951-023-01772-y
[2023] Biophysical insight into protein-protein interactions in the Interleukin-11/Interleukin-11Rα/glycoprotein 130 signaling complex
DOI: https://doi.org/10.1016/j.bbrc.2023.10.010
[2023] Specific peptide conjugation to a therapeutic antibody leads to enhanced therapeutic potency and thermal stability by reduced Fc dynamics
DOI: https://doi.org/10.1038/s41598-023-43431-0
[2023] Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes
DOI: https://doi.org/10.1016/j.jbc.2023.105254
[2023] Arginine cluster introduction on framework region in anti‐lysozyme antibody improved association rate constant by changing conformational diversity of <scp>CDR</scp> loops
DOI: https://doi.org/10.1002/pro.4745
[2023] Group A Streptococcus cation diffusion facilitator proteins contribute to immune evasion by regulating intracellular metal concentrations
DOI: https://doi.org/10.1016/j.bbrc.2023.07.052
[2023] Investigating the Antiviral Properties of Copper- and Silver-containing Polyoxometalates Using a High-throughput Screening Method
DOI: https://doi.org/10.1246/cl.230264
[2023] Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth
DOI: https://doi.org/10.1016/j.jbc.2023.104927
[2023] Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene
DOI: https://doi.org/10.1038/s41598-023-32444-4
[2023] Design of single-domain VHH antibodies to increase the binding activity in SPR amine coupling
DOI: https://doi.org/10.1016/j.bbrc.2023.04.048
[2023] Ligand Installation to Polymeric Micelles for Pediatric Brain Tumor Targeting
DOI: https://doi.org/10.3390/polym15071808
[2023] Inactivation and spike protein denaturation of novel coronavirus variants by CuxO/TiO2 nano-photocatalysts
DOI: https://doi.org/10.1038/s41598-023-30690-0
[2023] Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth
DOI: https://doi.org/10.1016/j.jbc.2023.104927
[2023] Dispersion Function of a Protein, DP‐1, Identified inCollimonas sp. D‐25, for the Synthesis of Gold Nanoparticles
DOI: https://doi.org/10.1002/cbic.202300221
[2023] Design of single-domain VHH antibodies to increase the binding activity in SPR amine coupling
DOI: https://doi.org/10.1016/j.bbrc.2023.04.048
[2023] Ligand Installation to Polymeric Micelles for Pediatric Brain Tumor Targeting
DOI: https://doi.org/10.3390/polym15071808
[2023] Peripheral administration of nanomicelle-encapsulated anti-Aβ oligomer fragment antibody reduces various toxic Aβ species in the brain
DOI: https://doi.org/10.1186/s12951-023-01772-y
[2022] Structure and role of the linker domain of the iron surface-determinant protein IsdH in heme transportation in Staphylococcus aureus
DOI: https://doi.org/10.1016/j.jbc.2022.101995
[2022] Antibody recognition of complement factor H reveals a flexible loop involved in atypical hemolytic uremic syndrome pathogenesis
DOI: https://doi.org/10.1016/j.jbc.2022.101962
[2022] Development of a high-throughput method to screen novel antiviral materials
DOI: https://doi.org/10.1371/journal.pone.0266474
[2022] Improvement of the affinity of an anti-rat P2X4 receptor antibody by introducing electrostatic interactions
DOI: https://doi.org/10.1038/s41598-021-03784-w
[2022] Repression of the PRELP gene is relieved by histone deacetylase inhibitors through acetylation of histone H2B lysine 5 in bladder cancer
DOI: https://doi.org/10.1186/s13148-022-01370-z
[2022] Repression of the PRELP gene is relieved by histone deacetylase inhibitors through acetylation of histone H2B lysine 5 in bladder cancer
DOI: https://doi.org/10.1186/s13148-022-01370-z
[2022] Antibody recognition of complement factor H reveals a flexible loop involved in atypical hemolytic uremic syndrome pathogenesis
DOI: https://doi.org/10.1016/j.jbc.2022.101962
[2022] Improvement of the affinity of an anti-rat P2X4 receptor antibody by introducing electrostatic interactions
DOI: https://doi.org/10.1038/s41598-021-03784-w
[2022] Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3
DOI: https://doi.org/10.1002/pro.4450
[2022] Nucleic acid–triggered tumoral immunity propagates <scp>pH</scp>‐selective therapeutic antibodies through tumor‐driven epitope spreading
DOI: https://doi.org/10.1111/cas.15596
[2022] Structure and role of the linker domain of the iron surface-determinant protein IsdH in heme transportation in Staphylococcus aureus
DOI: https://doi.org/10.1016/j.jbc.2022.101995
[2021] Development of functional inhibitors to MtsA, a metal ion transporter from Streptococcus pyogenes
[2021] Proteomic identification and validation of novel interactions of the putative tumor suppressor PRELP with membrane proteins including IGFI-R and p75NTR
DOI: https://doi.org/10.1016/j.jbc.2021.100278
[2021] A Novel Cell-Based Intracellular Protein–Protein Interaction Detection Platform (SOLIS) for Multimodality Screening
DOI: https://doi.org/10.1021/acssynbio.0c00483
[2021] Development of functional inhibitors to MtsA, a metal ion transporter from Streptococcus pyogenes
[2021] Symposium
DOI: https://doi.org/10.3412/jsb.76.23
[2021] Proteomic identification and validation of novel interactions of the putative tumor suppressor PRELP with membrane proteins including IGFI-R and p75NTR
DOI: https://doi.org/10.1016/j.jbc.2021.100278
[2021] Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies
DOI: https://doi.org/10.1038/s41598-021-98977-8
[2021] Author Correction: Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
DOI: https://doi.org/10.1038/s41598-021-97892-2
[2021] Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies
DOI: https://doi.org/10.1038/s41598-021-98977-8
[2021] Author Correction: Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
DOI: https://doi.org/10.1038/s41598-021-97892-2
[2021] Mechanism of dimerization and structural features of human LI-cadherin
DOI: https://doi.org/10.1016/j.jbc.2021.101054
[2021] Characterization of a putative maltodextrin-binding protein of Streptococcus pyogenes, SPs0871 and the development of a VHH inhibitor
DOI: https://doi.org/10.1016/j.bbrc.2021.05.056
[2021] Single-chain variable fragment (scFv) targeting streptolysin O controls group A Streptococcus infection
DOI: https://doi.org/10.1016/j.bbrc.2021.06.021
[2021] Mechanism of dimerization and structural features of human LI-cadherin
DOI: https://doi.org/10.1016/j.jbc.2021.101054
[2021] Characterization of a putative maltodextrin-binding protein of Streptococcus pyogenes, SPs0871 and the development of a VHH inhibitor
DOI: https://doi.org/10.1016/j.bbrc.2021.05.056
[2021] A Novel Cell-Based Intracellular Protein–Protein Interaction Detection Platform (SOLIS) for Multimodality Screening
DOI: https://doi.org/10.1021/acssynbio.0c00483

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AI 要約（直近 5 年の研究成果）

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研究成果（96 件）

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