Nobuhiko Tokuriki

The paper maps the global distribution of β-lactamases across environments and microbes, revealing their abundance and potential origins in plant and wastewater ecosystems.

This study maps substrate-dependent epistasis in phosphotriesterase by analyzing 64 mutation combinations across nine substrates, revealing how intramolecular wiring changes to support promiscuity and functional trade-offs.

This study investigates how functional and conformational substates change during enzyme evolution using single-molecule kinetic assays and simulations, showing coordinated shifts in substate equilibria that optimize catalytic efficiency.

This paper shows enzyme kinetic parameters exhibit non-specific epistasis due to multi-state catalytic cycles, and provides tools to correct for this effect in mechanistic inference.

This paper shows how evolution improves enzyme function by shifting the rate-limiting step from substrate binding to sub-state interconversion in β-lactamase OXA-48.

This study shows that ecological matching between metabolic roles and nutrient strategies stabilizes multi-species consortia during microbial metabolic evolution.

The paper introduces a sequence analysis pipeline that improves exploration of protein sequence space through hierarchical clustering and alternative homology metrics, demonstrating scalability and utility in analyzing large datasets.

The paper identifies alkaline phosphatase (AP) as a widespread promiscuous enzyme capable of oxidizing phosphite, contributing to microbial phosphorus cycling.

The paper examines how thermodynamic binding strategies in proteins evolved in response to temperature changes, showing a shift from entropy-driven to enthalpy-driven binding over time.

This paper introduces LASE, a method using ancestral sequence reconstruction to train protein language models with higher accuracy and faster computation than large models.

The paper uses coevolutionary analysis and deep mutational scanning to study epistatic networks in B1-lactamases, revealing both conserved and specific interactions across homologs.

The paper describes how two distinct enzymes evolved from a common ancestor through different mutational paths, leading to divergent molecular and phenotypic outcomes.

This study shows that β-lactamases from different Ambler classes confer cefiderocol resistance and can evolve to increase resistance through mutations.

This study identifies five mutations that enable the evolution of a xenobiotic-degrading enzyme and shows that higher-order epistasis shapes its adaptive landscape and substrate specificity.

The paper revises the biosynthetic pathway for the cofactor F420 in bacteria by identifying the correct substrate for guanylyltransferases and elucidating the role of the C-terminal domain of FbiB.

This study shows how an enzyme evolved from a solute-binding protein through structural and catalytic changes, highlighting mechanisms of de novo enzyme emergence.