Lectures and seminars Extra MTC Infection and Immunology Seminar: "Addressing microbiology by bioinformatic and biochemical approaches"

Host
 

Please contact  Ute Römling or Daniel Sorobetea if you want to meet Professor Tokuriki.

Meeting: 
meeting-ID: 682 9755 9409
Code: 961730

Selected references

1: Sakuma M, Konno N, Gholipour S, Chen JZ, Tokuriki N. Widespread promiscuous alkaline phosphatases underscore ancient microbial phosphite utilization. Proc Natl Acad Sci U S A. 2025 Dec 9;122(49):e2513042122. doi: 10.1073/pnas.2513042122. Epub 2025 Dec 4. PMID: 41343678; PMCID: PMC12704751.

2: Sakuma M, Buda K, Bunzel HA, Frøhlich C, Tokuriki N. Functional sub-states link conformational landscapes and protein evolution. Curr Opin Struct Biol. 2025 Oct;94:103134. doi: 10.1016/j.sbi.2025.103134. Epub 2025 Aug 16. PMID: 40819485.

3: Kehila D, Tafreshi AG, Tokuriki N. Stability of multi-species consortia during microbial metabolic evolution. Evolution. 2025 Oct 17;79(10):2156-2166 doi: 10.1093/evolut/qpaf141. PMID: 40622976.

4: Gholipour S, Lee D, Tokuriki N. Molecular Evolution and Origins of Antibiotic Resistance Genes. Biochemistry. 2025 Jun 17;64(12):2516-2528. doi: 10.1021/acs.biochem.5c00044. Epub 2025 Jun 2. PMID: 40457171.

5: Erdoğan AN, Dasmeh P, Socha RD, Chen JZ, Life BE, Jun R, Kiritchkov L, Kehila D, Serohijos AWR, Tokuriki N. Neutral drift upon threshold-like selection promotes variation in antibiotic resistance phenotype. Nat Commun. 2024 Dec 30;15(1):10813. doi: 10.1038/s41467-024-55012-4. PMID: 39737968; PMCID: PMC11685847.

6: Chen JZ, Bisardi M, Lee D, Cotogno S, Zamponi F, Weigt M, Tokuriki N. Understanding epistatic networks in the B1 β-lactamases through coevolutionary statistical modeling and deep mutational scanning. Nat Commun. 2024 Sep 30;15(1):8441. doi: 10.1038/s41467-024-52614-w. Erratum in: Nat Commun. 2024 Nov 27;15(1):10276. doi: 10.1038/s41467-024-54714-z. PMID: 39349467; PMCID: PMC11442494.

7: Fröhlich C, Bunzel HA, Buda K, Mulholland AJ, van der Kamp MW, Johnsen PJ, Leiros HS, Tokuriki N. Epistasis arises from shifting the rate-limiting step during enzyme evolution of a β-lactamase. Nat Catal. 2024;7(5):499-509. doi: 10.1038/s41929-024-01117-4. Epub 2024 Feb 23. PMID: 38828429; PMCID: PMC11136654.

8: Kehila D, Tokuriki N. Measuring differential fitness costs and interactions between genetic cassettes using fluorescent spectrophotometry. Appl Environ Microbiol. 2024 Feb 21;90(2):e0141923. doi: 10.1128/aem.01419-23. Epub 2024 Feb 1. PMID: 38299817; PMCID: PMC10880626.

9: Buda K, Miton CM, Fan XC, Tokuriki N. Molecular determinants of protein evolvability. Trends Biochem Sci. 2023 Sep;48(9):751-760. doi: 10.1016/j.tibs.2023.05.009. Epub 2023 Jun 15. PMID: 37330341.

10: Buda K, Miton CM, Tokuriki N. Pervasive epistasis exposes intramolecular networks in adaptive enzyme evolution. Nat Commun. 2023 Dec 21;14(1):8508. doi: 10.1038/s41467-023-44333-5. PMID: 38129396; PMCID: PMC10739712.

11: Miton CM, Tokuriki N. Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw. Biochemistry. 2023 Jan 17;62(2):148-157. doi: 10.1021/acs.biochem.2c00188. Epub 2022 Jul 13. PMID: 35830609

12: Chen JZ, Fowler DM, Tokuriki N. Environmental selection and epistasis in an empirical phenotype-environment-fitness landscape. Nat Ecol Evol. 2022 Apr;6(4):427-438. doi: 10.1038/s41559-022-01675-5. Epub 2022 Feb 24. PMID: 35210579.

13: Jackson C, Toth-Petroczy A, Kolodny R, Hollfelder F, Fuxreiter M, Kamerlin SCL, Tokuriki N. Adventures on the Routes of Protein Evolution-In Memoriam Dan Salah Tawfik (1955-2021). J Mol Biol. 2022 Apr 15;434(7):167462. doi:10.1016/j.jmb.-2022.167462. Epub 2022 Jan 29. PMID: 35104498

14: Laurino P, Tokuriki N. Dan Salah Tawfik (1955-2021). Nat Chem Biol. 2021 Sep;17(9):930. doi: 10.1038/s41589-021-00864-w. PMID: 34400838.

15: Anderson DW, Baier F, Yang G, Tokuriki N. The adaptive landscape of a metallo-enzyme is shaped by environment-dependent epistasis. Nat Commun. 202 Jun 23;12(1):3867. doi: 10.1038/s41467-021-23943-x. PMID: 34162839; PMCID: PMC8222346.

16: Fröhlich C, Chen JZ, Gholipour S, Erdogan AN, Tokuriki N. Evolution of β-lactamases and enzyme promiscuity. Protein Eng Des Sel. 2021 Feb 15;34:gzab013. doi: 10.1093/protein/gzab013. PMID: 34100551.

17: Miton CM, Buda K, Tokuriki N. Epistasis and intramolecular networks I protein evolution. Curr Opin Struct Biol. 2021 Aug;69:160-168. Doi 10.1016/j.sbi.2021.04.007. Epub 2021 May 30. PMID: 34077895.

18: Miton CM, Chen JZ, Ost K, Anderson DW, Tokuriki N. Statistical analysis of mutational epistasis to reveal intramolecular interaction networks in proteins. Methods Enzymol. 2020;643:243-280. doi: 10.1016/bs.mie.2020.07.012. Epub 2020 Aug 25. PMID: 32896284.

19: Yang G, Miton CM, Tokuriki N. A mechanistic view of enzyme evolution. Protein Sci. 2020 Aug;29(8):1724-1747. doi: 10.1002/pro.3901. PMID: 32557882; PMCID: PMC7380680.

20: Chen JZ, Fowler DM, Tokuriki N. Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase. Elife. 2020 Jun 8;9:e56707. doi: 10.7554/eLife.56707. PMID: 32510322; PMCID: PMC7308095.