Berlin 2024 – scientific programme
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BP: Fachverband Biologische Physik
BP 21: Poster IIIb
BP 21.28: Poster
Wednesday, March 20, 2024, 11:00–14:30, Poster C
Coarse-grained simulations of peptide Lge1(1-80) — •Agaya Johnson1, Anton Polyansky2, Sofia Kantorovich1, and Bojan Zagrovic2 — 1Computational and Soft Matter Physics, University of Vienna, Kolingasse 14-16, 1090 Vienna, Austria — 2Department of Structural and Computational Biology, Campus-Vienna-Biocenter 5, 1030 Vienna
Biomolecular condensates in cells such as p-bodies, nucleoli and stress granules play an important role in regulating biological processes like transcription, ribonucleic acid(RNA) metabolism and ribosome biogenesis. Studying of such biomolecular condensates will give insight into the molecular basis of diseases, like neurodegenerative diseases, cancer and diabetes. The main purpose of this study is to understand the main phenomenon, which leads to the formation of these bimolecular condensates such that we get a conclusion, whether is it phase separation, self assemble or an aggregation. We use Lge1(1-80) peptide as a model for study because Lge1(1-80) is mostly disordered, prone to form many cation-pi and pi-pi interaction(R, G and R rich sequence) and because of its alternating net charge which are the prerequisites for the phase separation. Due to the limitation of high-resolution experimental techniques, we are using molecular dynamics simulation with coarse-grained approaches, with the help of software ESPResSo. Our goal is to develop a coarse-grained model for the proteins that exhibit structural transitions and to understand the fundamental mechanisms under those transitions.
Keywords: biomolecular condensates; coarse grained model for structural transitions; molecular dynamics simulations