Explaining Biological Phenomena through the Laws of Physics and Chemistry
Biological phenomena are governed by biomacromolecules such as proteins. While people often speak of the “mystery of life,” in principle, every biological process should be explainable by the laws of physics and chemistry. What appears mysterious is simply the result of complexity: biomacromolecules consist of vast numbers of atoms, making them difficult for humans to fully comprehend. Our laboratory uses the power of computers to uncover the mechanisms by which proteins and other biomacromolecules function.
Molecular simulation is the core methodology of our research. By calculating the forces acting on the atoms that constitute biomacromolecules, solvents, and biological membranes, and solving Newton’s equations of motion, molecular simulation allows us to reproduce the dynamic behavior of entire systems that include biomacromolecules.
For example, we study a transporter from Escherichia coli that contributes to multidrug resistance by expelling a variety of drugs from the cell. This transporter uses the proton gradient across the cell membrane as an energy source to drive drug efflux. Through molecular simulations, we identified the binding sites of protons within the transporter. Beyond this, we collaborate with many life science researchers to analyze the functions of diverse biomacromolecules. For more details, please visit our laboratory website.
Educational approach
Fostering Experts in Bioinformatics and Molecular Simulation
At Komaba, I teach a "Life Sciences" course for second-year students in the Natural Sciences I stream. My lectures aim to help students understand biological phenomena through the lenses of physics, chemistry, and mathematics.
I teach "Bioinformatics I" and "Bioinformatics II" for undergraduate students in the Faculty of Agriculture. "Bioinformatics I" covers the fundamentals of bioinformatics, including public databases and sequence similarity. "Bioinformatics II" focuses on the basics of molecular simulation, such as quantum chemical calculations and molecular dynamics methods.
For graduate students, I am in charge of two courses within the Agricultural Bioinformatics Educational Program: "Introduction to Structural Bioinformatics" and "Molecular Modeling and Molecular Simulation." In the introductory course, I explain how to use structural databases and viewers. In "Molecular Modeling and Molecular Simulation," I provide practical instruction, including hands-on exercises in molecular dynamics simulation and complex modeling, in addition to explaining the fundamentals of molecular mechanics and dynamics.
Ultimately, my goal in the lab is to train individuals who can skillfully use bioinformatics and molecular simulation to conduct a multi-faceted analysis of complex phenomena involving biological macromolecules.
Vision for industry-academia collaboration
We Welcome Collaborations in Molecular Simulation
We actively welcome opportunities for education and collaborative research in molecular simulation. Our laboratory has experience in training researchers from private companies who had no prior background in molecular simulation, covering a range of methodologies from basic molecular dynamics (MD) to advanced approaches such as replica exchange methods, tailored to specific research goals.
Potential areas for collaboration include: Protein structure prediction, Prediction of protein–small molecule complex structures, Refinement of predicted structures using molecular dynamics simulations, Interaction analysis, Binding affinity prediction.
