Author

K.-i. Okazaki

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Biophysics· 3 Biochemistry· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:deep learning· 3 Organism:bacteria (other)· 2 Research Focus:protein structure prediction· 2 Approach:statistical model· 2 Assay:structural biology· 2 Research Focus:cell type annotation· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

A. Yamashita· 2 shared T. Jaunet-Lahary· 2 shared A. Nakamura· 1 shared D. Woehlert· 1 shared G. Hummer· 1 shared H. Iwanari· 1 shared H. Jung· 1 shared J. Ohnuki· 1 shared

Activity by Year

2019-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersBiophysics

A. Yamashita

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Accelerated Molecular Dynamics and AlphaFold Uncover a Missing Conformational State of Transporter Protein OxlT

J. Ohnuki, T. Jaunet-Lahary, A. Yamashita, K.-i. Okazaki

The paper uses accelerated molecular dynamics and AlphaFold2 to identify a missing inward-open conformation of the OxlT transporter protein.

bioRxiv · Oct 26, 2023Biophysics

Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

T. Jaunet-Lahary, T. Shimamura, M. Hayashi, N. Nomura, K. Hirasawa, T. Shimizu, M. Yamashita, K. Kojima, Y. Sudo, T. Tamura, H. Iwanari, T. Hamakubo, S. Iwata, K.-i. Okazaki, T. Hirai, A. Yamashita

This study determines the crystal structures of OxlT, an oxalate transporter, and reveals its mechanism for selective oxalate uptake and exclusion of other carboxylates.

bioRxiv · Nov 15, 2021Biochemistry

Chemical-state-dependent free energy profile from single-molecule trajectories of biomolecular motor: Application to processive chitinase

K.-i. Okazaki, A. Nakamura, R. Iino

This study uses single-molecule trajectories to estimate a chemical-state-dependent free energy profile for processive chitinase, revealing how chemical state changes drive unidirectional motion.

bioRxiv · Mar 26, 2020Biophysics

Mechanism of electroneutral sodium/proton antiporter from transition-path shooting

K.-i. Okazaki, D. Woehlert, J. Warnau, H. Jung, O. Yildiz, W. Kuehlbrandt, G. Hummer

This study uses transition-path shooting to simulate the Na+/H+ antiporter PaNhaP, revealing its transport mechanism and identifying key conformational changes.

bioRxiv · Feb 3, 2019Biophysics