Research Topic:
DNA recognition by DNA-processing proteins
Supervisor:
Prof. Petra Imhof, FAU
Thesis Abstract:
DNA repair is a fundamental process for the conservation of genetic information and prevention of diseases. It must be carried out in a very specific manner, so healthy DNA sequences are not damaged by the repair machinery. Hence, damage recognition is a crucial step, which is carried out by DNA Glycosylases. Using High Performance Computing, we calculate atom-level detailed simulations of DNA-Glycosylases to understand which interactions are important for damage recognition and specificity.
Publications:
•Jorge Amador-Balderas et al. “Mode of Metal Ligation Governs Inhibition of Carboxypeptidase A”. In: International Journal of Molecular Sciences 25 (Dec. 2024), p. 13725. doi: 10.3390/ijms252413725
Conference Presentations:
•2024: Poster presentation: “Insight into the active site conformation of DNA Repair Enzyme MBD4 from Molecular Simulations”; in BioExcel Summer School 2024, Sardegna Ricerche.
•2024: Poster presentation: “Insight into the active site conformation of DNA Repair Enzyme MBD4 from Molecular Simulations”; in NHR Conference 2024, Darmstadtium.
•2025: Poster presentation: “Computer-assisted Molecular Modelling and Dynamics can explain how Glu35 and Pro240 hSMUG1 mutants differently affect excision of Uracil and 5-hydroxymethyluracil from single-stranded DNA”; in World Association of Theoretical and Computational Chemists (WATOC) Triennial Congress 2025, Oslo congress Centre.
•2025: Oral presentation: “Computer-assisted Molecular Modelling and Dynamics can explain how Glu35 and Pro240 hSMUG1 mutants differently affect excision of Uracil and 5-hydroxymethyluracil from single-stranded DNA”; NHR Conference 2025, Georg-August Universitaet Goettingen.
•2026: Poster presentation: “Mutations in hSMUG1 and their effect in U/hmU excision: A computational study”; in Molecular Modelling Workshop 2026, Friedrich Alexander Universitaet Erlangen-Nuernberg.
•2026: Oral presentation: “Mutations in hSMUG1 and their effect in U/hmU excision: A computational study”; in Molecular Modelling Workshop 2026, Friedrich Alexander Universitaet Erlangen-Nuernberg.
Scientific Awards:
•Poster award at the Molecular Modelling Workshop 2026 for Poster: Mutations in hSMUG1 and their effect in U/hmU excision: A computational study