Faculty and research guide

Laboratory of functional biomolecules

Akihiko Nakamura

Enzymes keep the living organisms "alive". Our laboratory try to reveal the relationship between functions and structures of enzymes using the combination of single-molecule observation, crystallography and biochemical assay.

Our main targets are extracellular enzymes, e.g. cellulase, chitinase, hyaluronidase and polyethylene terephthalate (PET) hydrolase.
Former two enzymes hydrolyze the cellulose or chitin, which are the main component of plant cell-wall or outer shell of crustacean respectively. These polysaccharides are the abundant biomass on the earth, but too much stable for utilization due to the crystal packings. The enzymes, efficiently hydrolyze the crystals, catch the molecular chain end on the surface and move along with the chain with continuous hydrolysis of glycoside bonds. After some reactions, enzymes release the chain and desorb from the crystal.
The analysis of this cycle of reaction needs the single molecule observation, because not all of the bound enzyme is productive. Single molecule technique enable us to separate the productive and non-productive enzymes and analyze the elementary steps of movements. Additionally, the crystallographic analysis teach us the interaction between enzymes and molecular chains in atomic scale. From these results, we revealed the catalytic reaction and moving mechanism of enzymes.
Hyaluronidase hydrolyze the hyaluronan displayed on the surface of animal cells and play important role in the fertilization and infection of pathogen. We applied our methods for the analysis of hyaluronidase to reveal the moving mechanism and degradation mechanism of hyaluronan.
PET hydrolase have some possibility to clean up the PET released into the environment. We are trying to produce the mutants with higher degradation activity according to the knowledge about the efficient degradation of solid substrates by cellulases and chitinases.

Fig. 1 Single molecule observation with a total internal reflection fluorescence microscopy

Fig. 2 Results of X-ray crystallography carved in crystals