Author

S. Wakatsuki

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

Biology Disciplines

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Biophysics· 8 Biochemistry· 3 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 11 Research Focus:protein structure prediction· 5 Assay:structural biology· 5 Research Focus:protein folding & dynamics· 4 Organism:bacteria (other)· 3 Assay:protein structure· 3 Organism:C. elegans· 2 Research Focus:cell signaling & trafficking· 2

Frequent Co-Authors

H. DeMirci· 7 shared R. G. Sierra· 4 shared Y. Yoshikuni· 4 shared B. Hayes· 3 shared C. A. Francis· 3 shared E. H. Dao· 3 shared F. Poitevin· 3 shared H. I. Ciftci· 3 shared

Activity by Year

2017-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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7 shared papersBiophysics

H. DeMirci

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Author profile →

12 papers

Recent·Most cited

4D Crystallography Captures Transient IF1-Ribosome Dynamics in Translation Initiation

I. Yapici, E. H. Dao, S. Yokoi, E. Destan, E. Ayan, A. Shafiei Kamel, F. B. Ertem, C. Kulakman, M. Yilmaz, B. Tosun, H. Ciftci, A. Kepceoglu, J. A. Johnson, O. Guven, A. Ergul, , H. DeMirci

This study uses 4D crystallography to capture transient dynamics of IF1 binding to the 30S ribosomal subunit, revealing allostery and interactions during translation initiation.

bioRxiv · Oct 27, 2023 · PreprintBiophysics

Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter

M. Currie, J. Davies, M. Scalise, A. Gulati, J. Wright, M. Newton-Vesty, G. Abeysekera, R. Subramanian, W. Wahlgren, R. Friemann, J. Allison, P. Mace, M. Griffin, B. Demeler, S. Wakatsuki, , R. North

This study reports the cryo-EM structure of a TRAP transporter from Haemophilus influenzae, revealing its dimeric architecture, Na+ sites, and substrate binding site, supported by mutagenic and functional data.

bioRxiv · Aug 28, 2023 · PreprintBiochemistry

Crystal Structure of the 4-Hydroxybutyryl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus

J. A. Johnson, B. B. Tolar, B. Tosun, Y. Yoshikuni, C. A. Francis, S. Wakatsuki, H. Demirci

The paper presents the crystal structure of Nmar_0206 from Nitrosopumilus maritimus, revealing a conserved interdomain linker loop that influences homodimer stability and contributes to the enzyme's energy efficiency in the 3HP/4HB cycle.

bioRxiv · Jul 14, 2023Biophysics

Inter-subunit coupling enables fast CO2-fixation by reductive carboxylases

H. Demirci, Y. Rao, G. M. Stoffel, B. Vögeli, K. Schell, A. Gomez, A. Batyuk, C. Gati, R. G. Sierra, M. S. Hunter, E. H. Dao, H. I. Ciftci, B. Hayes, F. Poitevin, P. Li, , S. Wakatsuki

This paper investigates the structural and dynamic mechanisms of CO2 fixation by ECRs, revealing inter-subunit coupling that enables fast catalytic activity.

bioRxiv · Feb 23, 2022 · PreprintBiophysics

Structural Insights into Bifunctional Thaumarchaeal Crotonyl-CoA Hydratase and 3-Hydroxypropionyl-CoA Dehydratase from Nitrosopumilus maritimus

E. Destan, B. Yuksel, B. B. Tolar, E. Ayan, S. Deutsch, Y. Yoshikuni, S. Wakatsuki, C. A. Francis, H. DeMirci

This study presents the first high-resolution crystal structure of a bifunctional enzyme involved in the 3HP/4HB cycle in Nitrosopumilus maritimus, revealing its dual catalytic activities.

bioRxiv · Sep 22, 2021 · PreprintBiochemistry

Structural adaptation of oxygen tolerance in 4-hydroxybutyrl-CoA dehydratase, a key enzyme of archaeal carbon fixation

H. DeMirci, B. Tolar, T. Doukov, A. Petriceks, A. Pal, Y. Yoshikuni, A. Gomez, D. A. Saez, E. Vohringer-Martinez, T. Schwander, T. J. Erb, C. A. Francis, S. Wakatsuki

The paper investigates how 4HBD, a key enzyme in archaeal carbon fixation, adapted structurally to become oxygen-tolerant, revealing evolutionary changes that enabled aerobic metabolism.

bioRxiv · Feb 5, 2020 · PreprintEvolutionary Biology

A Bacterial Surface Layer Protein Exploits Multi-step Crystallization for Rapid Self-assembly

J. Herrmann, P.-N. Li, F. Jabbarpour, A. C. K. Chan, I. Rajkovic, T. Matsui, L. Shapiro, J. Smit, T. Weiss, M. E. P. Murphy, S. Wakatsuki

This paper shows a bacterial surface layer protein uses a multi-step pathway with a nucleation domain to rapidly crystallize, enabling efficient 2D self-assembly on cell surfaces.

Proceedings of the National Academy of Sciences · Dec 17, 2019Peer-reviewedBiophysics

Serial femtosecond X-ray diffraction of HIV-1 Gag MA-IP6 microcrystals at ambient temperature

H. I. Ciftci, R. G. Sierra, C. H. Yoon, Z. Su, H. Tateishi, R. Koga, K. Kotaro, F. Yumoto, T. Senda, M. Liang, S. Wakatsuki, M. Otsuka, M. Fujita, H. Demirci

This study uses serial femtosecond X-ray crystallography to analyze HIV-1 Gag MA-IP6 microcrystals at ambient temperature, achieving high-resolution diffraction data.

bioRxiv · Mar 23, 2019Biophysics

Continuous, Topologically Guided Protein Crystallization Controls Bacterial Surface Layer Self-Assembly

C. J. Comerci, J. Herrmann, J. Yoon, F. Jabbarpour, X. Zhou, J. F. Nomellini, J. Smit, L. Shapiro, S. Wakatsuki, W. E. Moerner

This study shows that protein self-assembly alone can form and maintain bacterial surface layers, guided by surface topology without enzymatic assistance.

bioRxiv · Feb 1, 2019Biophysics

Molecular recognition of M1-linked ubiquitin chains by native and phosphorylated UBAN domains

L. Herhaus, H. van den Bedem, S. Tang, S. Wakatsuki, I. Dikic, S. Rahighi

This study investigates how phosphorylation affects UBAN domain binding to M1-linked ubiquitin chains, revealing structural and functional differences among related proteins.

bioRxiv · Jan 16, 2019Biophysics

Structure of the 30S ribosomal decoding complex at ambient temperature

E. H. Dao, F. Poitevin, R. G. Sierra, C. Gati, Y. Rao, H. I. Ciftci, F. Aksit, A. McGurk, T. Obrinski, P. Mgbam, B. Hayes, C. de Lichtenberg, F. Pardo-Avila, N. Corsepius, L. Zhang, , H. DeMirci

The paper reports an ambient-temperature X-ray crystal structure of the Thermus thermophilus 30S ribosomal decoding complex, showing consistency with cryogenic structures but with minor conformational variations.

bioRxiv · Mar 9, 2018Biophysics

Structural and Functional analysis of the GABARAP Interaction Motif (GIM).

V. V. Rogov, A. Stolz, A. C. Ravicahandran, A. Law, H. Suzuki, A. Kniss, D. O. Rios-Szwed, F. Loehr, S. Wakatsuki, V. Doetsch, I. Dikic, R. C. J. Dobson, D. McEwan

The paper identifies a GABARAP-specific interaction motif (GIM) and demonstrates its selectivity over LC3 using biophysical and structural analyses.

The EMBO Reports · Aug 1, 2017Peer-reviewedBiochemistry