The main project during my PhD journey (2019-2022) at Tokyo Institute of Technology (Prof. A. Kitao Lab) was an investigation into the dissociation mechanisms of two large biomolecules (protein/DNA complex). This investigation utilized a combination of enhanced sampling techniques known as dissociation parallel cascade selection molecular dynamics (dPaCS-MD) and the Markov state model (MSM). Through this combination, I identified the key residues involved in complex binding and shed light on the two major dissociation pathways. Moreover, employing the MSM, I calculated the standard binding free energy from the free energy landscape for various complexes, which showed good agreement with experimental values.
My pursuit of knowledge extended beyond the confines of my own research on protein/DNA interactions. Together with my colleagues, we embarked on interdisciplinary research projects, where we benchmarked the dPaCS-MD/MSM combination for three protein/ligand complexes: trypsin/benzamine, FKBP/FK506, and adenosine A2A receptor/T4E.
In April 2022, following my graduation, I began working as a postdoctoral researcher under the supervision of Prof. H. Kono at QST in Chiba, Japan. My research focused on improving protein stability, with a particular emphasis on quantitatively expressing stability to accurately predict the effects of mutations. Specifically, I investigated addition/deletion mutations and salt bridge mutations aimed at enhancing protein engineering stability through alchemical transformations. To achieve this, I employed free-energy perturbation and replica exchange with solute tempering (FEP/REST) techniques to enhance the sampling of intermediates. The free energy difference (∆∆G) served as the stability indicator.
In April 2024, I joined Shinobu Lab at the WPI Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, as a specially appointed researcher. Currently, my primary focus is on developing an innovative computational protocol for designing therapeutic peptides derived from antibodies. Additionally, I am planning to extend the application of two-dimensional (2D) generalized replica exchange with solute tempering (gREST) and replica-exchange umbrella sampling (REUS) techniques (2D-gREST/REUS) to study protein-DNA biocomplexes.