2026-143-8

The toxins of the Destroying Angel: computational investigation

Vedoucí práce: M. Sc. Wim Dehaen, Ph.D.

Konzultant: -

Podstata a cíl práce

Amanita Virosa, also known as the European Destroying Angel, is a highly toxic mushroom, and is a major contributor to lethal poisonings after accidental ingestion. This mushroom contains amatoxins, phallotoxins and virotoxins, all of which belong to the class of modified small cyclic peptides. Despite their chemical similarity, amatoxins target RNA polymerase II, whereas phallotoxins and virotoxins bind to actin. Using computational methods, the molecular basis of this distinction and factors contributing to the binding, stability and surprising polyvalency of these toxic agents will be explored.

Náplň činnosti studenta

The student will learn to work with the protein data bank (PDB), and retrieve and evaluate relevant protein structures. The students will assess the binding interactions of the toxins with their target using structure based methods such as docking (using Vina, PLANTS, …) and molecular dynamics (using OpenMM), including preparing the molecular system properly for such simulations. Cheminformatic and molecular modelling methods will be used to explain the thermostability, shape constraints and conformational behavior of cyclic peptides, mainly using the RDKit cheminformatics package. Communication during the project will be conducted in English.

Doplňující informace

Místo řešení: Ústav informatiky a chemie (143)

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