Research
Chemical reaction plays an essential role in various complex systems, e.g. materials and proteins. Yet, how reaction occurs, and how it interacts with the environment, are often not clear. I am interested in the hierarchical events that occur around chemical reactions, and have been developing and applying theoretical tools to study these systems.
My recent focus has been on the dynamics of protein itself, and how it affects the reaction in enzymes. I hope to pursue these research to understand the molecular mechanism of enzyme catalysis and protein function regulation by chemical reactions.
Conformational dynamics of enzyme and ligand during enzyme catalysis
J. Phys. Chem. Lett. 10, 474-480 (2019) Suppl. Cover
J. Chem. Theory Comput. 16, 3396-3407 (2020)
We studied the transition dynamics during Pin1-catalyzed isomerization reaction using transition path sampling simulations. The results show that, in contrast to the coupled protein-ligand dynamics indicated by minimum free energy path, protein-ligand interactions necessary for catalysis are set up prior to the isomerization event, i.e. as a conformational excited state. Conformational flexibility of protein thus helps access the excited state during catalysis.
Molecular details behind protein's heterogeneous dynamics
J. Phys. Chem. B 120, 11683-11691 (2016)
J. Chem. Phys. 142, 135101 (2015)
We proposed an approach to analyze the slow dynamics in MD trajectories. By studying the folding mechanisms of Pin1 WW domain and Villin headpiece, we found that folding/unfolding transitions happen in various time scales. Multiple transition pathways are found in both proteins, indicating that folding occurs in a heterogeneous manner, even in proteins as small as 35 residues.
Molecular origin of slow ATP hydrolysis in KaiC
Science 349, 312-316 (2015)
In collaboration with the experimental group lead by Prof. Akiyama at IMS, we have been studying the clock protein KaiC to understand the molecular mechanism of circadian rhythm in cyanobacteria. So far, we found that the slow ATP hydrolysis in the N-terminal domain of KaiC determines the circadian oscillation period, and revealed the molecular origin of this slowness.
Ligand binding at the water-material interface
J. Phys. Chem. B 118, 8210-8220 (2014)
J. Chem. Theory Comput. 9, 5059-5069 (2013)
We studied the mechanism of peptide binding onto a titanium dioxide surface. The result shows that the water molecule on the surface needs to be accounted for to understand the binding mechanism. Furthermore, peptides on the surface were shown to sample conformations different from those in solution.
Simulating photochemical reaction dynamics
J. Phys. Chem. A 116, 2808-2818 (2012)
We developed a method to perform ab initio molecular dynamics simulations of photoreaction dynamics involving multiple electronic excited states. The method was applied to photoisomerizations of multiple molecules involving ethylene, and time-resolved photoelectron spectrum of ethylene was predicted.
Gallery of some of other researches
