N. Kamiya

Molecular dynamics unveils multiple-site binding of inhibitors with reduced activity on the surface of dihydrofolate reductase

This study uses molecular dynamics to analyze inhibitor binding to DHFR, showing that reduced activity correlates with multiple-bound states on the protein surface.

Exploring the molecular structure of lipids in the design of artificial lipidated antifungal proteins

This study explores lipid modifications of a chitin-binding domain to enhance antifungal activity, finding that specific lipid lengths improve efficacy against Trichoderma viride without significant cytotoxicity.

Engineered Active Zymogen of Microbial Transglutaminase

This paper designs an engineered active zymogen of microbial transglutaminase (EzMTG) that exhibits cross-linking activity without requiring proteolysis, and identifies mutations that balance binding affinity and catalytic activity.

Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics

This study uses molecular dynamics to compare binding free-energy landscapes of two structurally similar ligands to an FMN riboswitch, revealing distinct binding pathways and orientation effects.

Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism

The paper improves the thermostability and activity of the PET-degrading enzyme Cut190 through mutagenesis and structural analysis, revealing the role of Ca2+ ions and a novel ejecting form in the reaction mechanism.

Fly-casting with ligand-sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule

This paper uses a computational method to simulate the binding mechanism of bosentan to hETB, identifying key steps like fly-casting and ligand-sliding.

Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome

The paper reports cryo-EM structures of a thermophilic cyanobacterial phycobilisome, revealing protein subunit arrangements and energy transfer pathways.

Clomipramine suppresses ACE2-mediated SARS-CoV-2 entry

This study shows clomipramine inhibits SARS-CoV-2 entry into cardiomyocytes and synergizes with remdesivir to suppress infection.

Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling

This paper uses enhanced conformational sampling to study the binding mechanism of a phosphorylated peptide to a 14-3-3 protein, identifying stable clusters and a phosphorylation-dependent binding process.

Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

This study accelerates molecular dynamics simulations using ultrasound to study ligand binding pathways on proteins, revealing previously undetectable kinetic features and binding pathways.

Recombinant production of active microbial transglutaminase in E. coli using self-cleavable zymogen with mutated propeptide

This paper describes the production of active microbial transglutaminase in E. coli using a modified zymogen with mutations in the propeptide to achieve pure, active enzyme.

A new lipid force field (FUJI)

The paper develops a new lipid force field (FUJI) to accurately simulate lipid bilayers using the LJ-PME method without experimental data fitting.