Biophysics and Physicobiology

The Biophysical Society of Japan.

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8th Biophysics and Physicobiology Editors' Choice Award (2021)

“Crystalline chitin hydrolase is a burnt-bridge Brownian motor”
Akihiko Nakamura, Kei-ichi Okazaki, Tadaomi Furuta, Minoru Sakurai, Jun Ando, Ryota Iino
Biophysics and Physicobiology, Vol.17, pp.51-58 (2020)

Reason for the award by Tamiki Komatsuzaki

 The single-molecule experiments on the molecular motor Chitinase A from bacterium Serratia marcescens (SmChiA) were overviewed. The TIRDF microscopy accomplished a high temporal-spatial resolution, whose spatial resolution was 0.3 nm, the step size of SmChiA could be measured to be 1 nm in detail. While SmChiA exhibits back and forward stepping motion with a similar free energy level to each other, as a whole it moves directionally on crystalline chitin by hydrolysis of a single polymer chain to soluble chitobiose. From the measured rate constants on the back and forward steps in addition to the structure analysis and their molecular dynamics simulation of SmChiA, it was shown that SmChiA slides forward and backward under thermal fluctuation without large conformational changes of the protein, but shortening of the chain by a chitobiose unit stabilizes the backward state. Their results demonstrate that SmChiA is a burnt-bridge Brownian ratchet motor. Because Chitinase is a new topic in the field of single-molecule experiments on molecular motors such as myosin, kinesin, dynein and F1-ATPase, and two reviewers in this area have also evaluated this as a timely review paper that should attract and interest readers in BPPB, the Editor-in-Charge recommends this article for the award.


“Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH”
Ryuma Sato, Yoshiharu Mori, Risa Matsui, Noriaki Okimoto, Junpei Yamamoto, Makoto Taiji
Biophysics and Physicobiology, Vol.17, pp.113-124 (2020)

Reason for the award by Haruki Nakamura

 In this article, the authors studied why cryptochrome-DASH (CRYD) cannot repair CPD in double-stranded DNA (dsDNA), despite CRYD is highly homologous to dsDNA repair enzyme photolyase (PL). In order to understand the reason, the authors applied theoretical calculations of Quantum Mechanics (QM)/Molecular Mechanics (MM) and Molecular Dynamics (MD), to compute the electron transfer reaction and DNA binding. Based upon their results, the authors prepared a mutant protein and tested the enzyme activity of DNA repair by both computations and experiments. The authors found that CRYD and PL have the similar electron transfer reactivities by QM/MM computations. They also confirmed the DNA repair activity of CRYD for UV-damaged single-stranded DNA (ssDNA) but not that for dsDNA by DNA repair assay experiment. Finally, from MD simulations, the authors concluded that a transient salt bridge is formed between CRYD and dsDNA, in contrast to PL where it is formed stably. The instability of the salt bridge between CRYD and dsDNA is suggested to reduce the dsDNA binding affinity for CRYD. The authors tackled to solve a complicated issue by various biophysical approaches, computations and experiments, both of which are at high level.



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