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Codispoti S, Yamaguchi T, Makarov M, Giacobelli VG, Mašek M, Kolář MH, Sanchez Rocha AC, Fujishima K*, Zanchetta G*, Hlouchová K.* (2024) The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability. Preprint at https://doi.org/10.1101/2024.01.29.577748
Aubel M, Buchel F, Heames B, Jones A, Honc O, Bornberg-Bauer E*, Hlouchova K.* (2024) High-throughput selection of human de novo-emerged sORFs with high folding potential. Preprint at https://doi.org/10.1101/2024.01.22.576604
Sanchez Rocha CA, Makarov M, Pravda L, Novotny M*, Hlouchova K.* (2023) Coenzyme-Protein Interactions since Early Life. eLife 2024, 13:RP94174. https://doi.org/10.7554/eLife.94174.1
Heames B, Buchel F, Aubel M, Tretyachenko V, Loginov D, Novak P, Lange A, Bornberg- Bauer E*, Hlouchova K.* (2023) Experimental characterization of de novo proteins and their unevolved random-sequence counterparts. Nature Ecology & Evolution https://doi.org/10.1038/s41559-023-02010-2
Makarov M, Sanchez Rocha AC, Krystufek R, Cherepashuk I, Dzmitruk V, Charnavets T, Faustino AM, Lebl M, Fujishima K, Fried SD*, Hlouchova K.* (2023) Early selection of the amino acid alphabet was adaptively shaped by biophysical constraints of foldability. J Am Chem Soc. 145(9):5320-5329. https://doi.org/10.1021/jacs.2c12987
Tretyachenko V, Vymetal J, Neuwirthova T, Vondrasek J, Fujishima K, Hlouchova K. (2022) Modern and prebiotic amino acids support distinct structural profiles in proteins. Open Biology 12: 220040.
https://doi.org/10.1098/rsob.220040
Giacobelli VG, Fujishima K, Lepsik M, Tretyachenko V, Kadava T, Makarov M, Bednarova L, Novak P, Hlouchova K. (2022) In vitro evolution reveals non-cationic protein – RNA interaction mediated by metal ions. Molecular Biology and Evolution, msac032. https://doi.org/10.1093/molbev/msac032.
Fried SD*, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K*. (2022) Peptides before and during the nucleotide world: and origins story emphasizing cooperation between proteins and nucleic acids. Journal of Royal Society Interface 19: 20210641. https://doi.org/10.1098/rsif.2021.0641
Makarov M, Meng J, Tretyachenko V, Srb P, Březinová A, Giacobelli VG, Bednárová L, Vondrášek J, Dunker AK* and Hlouchová K.* (2021) Enzyme catalysis prior to aromatic residues: reverse engineering of a dephosphoCoA kinase. Protein Science DOI10.1002/pro.4068
Bornberg-Bauer E, Hlouchova K, Lange A. (2020) Structure and function of naturally evolved de novo proteins. Current Opinions in Structural Biology. 68, 175-183. DOI: 10.1016/j.sbi.2020.11.010
Tretyachenko V, Voráček V, Souček R, FujishimaK, and Hlouchová K. (2020) CoLiDe: Combinatorial Library Design tool for probing protein sequence space. Bioinformatics DOI: 10.1093/bioinformatics/btaa804
Vymětal J, Vondrášek J, and Hlouchová, K. (2019). Sequence Versus Composition: What Prescribes IDP Biophysical Properties? Entropy, 21(7), 654. https://doi.org/10.3390/e21070654
Tretyachenko V, Vymětal J, Bednárová L, Kopecký V, Hofbauerová K, Jindrová H, Hubálek M, Souček R, Konvalinka J, Vondrášek J, and Hlouchová K. (2017) Random protein sequences can form defined secondary structure and are well-tolerated in vivo. SciRep 7, 15449. https://doi.org/10.1038/s41598-017-15635-8