Author

K. Fujishima

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· 2 Biochemistry· 1 Evolutionary Biology· 1 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 5 Research Focus:chromatin & epigenetic regulation· 2 Research Focus:protein folding & dynamics· 2 Research Focus:cell type annotation· 1 Assay:protein structure· 1 Assay:proteomics· 1

Frequent Co-Authors

K. Hlouchova· 3 shared M. Makarov· 2 shared V. G. Giacobelli· 2 shared A. C. S. Rocha· 1 shared A. C. Sanchez Rocha· 1 shared A. J. Maheshwari· 1 shared A. M. Faustino· 1 shared A. Narita· 1 shared

Activity by Year

2015-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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3 shared papersBiophysics

K. Hlouchova

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability

S. Codispoti, T. Yamaguchi, M. Makarov, V. G. Giacobelli, M. Masek, M. H. Kolar, A. C. Sanchez Rocha, K. Fujishima, G. Zanchetta, K. Hlouchova

This paper investigates the role of ribosomal peptides in protoribosome compartmentalization and stability, showing that RNA-protein interactions protect RNA from degradation and influence structural flexibility.

bioRxiv · Jan 29, 2024Biophysics

Early selection of the amino acid alphabet was adaptively shaped by biophysical constraints of foldability

M. Makarov, A. C. S. Rocha, R. Krystufek, I. Cherepashuk, V. Dzmitruk, T. Charnavets, A. M. Faustino, M. Lebl, K. Fujishima, S. D. Fried, K. Hlouchova

This study investigates why the modern amino acid alphabet evolved to include 20 canonical amino acids by showing that foldability constraints shaped the selection of early amino acids.

bioRxiv · Jun 14, 2022Biophysics

Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution

C. Akil, S. Ali, L. T. Tran, J. Gaillard, W. Li, K. Hayashida, M. Hirose, T. Kato, A. Oshima, K. Fujishima, L. Blanchoin, A. Narita, R. C. Robinson

This study presents the structure of Odinarchaeota tubulin and shows it forms tubules similar to FtsZ, suggesting it is an evolutionary intermediate between prokaryotic and eukaryotic microtubule-forming proteins.

bioRxiv · Oct 22, 2021Evolutionary Biology

In vitro evolution reveals primordial RNA-protein interaction mediated by metal cations

V. G. Giacobelli, K. Fujishima, M. Lepsik, V. Tretyachenko, T. Kadava, L. Bednarova, P. Novak, K. Hlouchova

This study uses in vitro evolution to show that RNA-protein interactions in early life could be mediated by metal cations and acidic residues instead of aromatic/basic amino acids.

bioRxiv · Aug 1, 2021 · PreprintBiochemistry

CRISPR/Cas9-Assisted Transformation-Efficient Reaction (CRATER), a novel method for selective transformation

L. J. Rothschild, D. T. Greenberg, J. R. Takahashi, K. A. Thompson, A. J. Maheshwari, R. E. Kent, G. McCutcheon, J. D. Shih, C. Calvet, T. D. Devlin, T. Ju, D. Kunin, E. Lieberman, T. Nguyen, F. G. Tran, , K. Fujishima

The paper introduces CRATER, a CRISPR/Cas9-based method that improves plasmid transformation efficiency by selectively cleaving unwanted byproducts, increasing efficiency from 20% to 97%.

bioRxiv · Sep 27, 2015 · PreprintSynthetic Biology