Regensburg 2022 – scientific programme

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BP: Fachverband Biologische Physik

BP 7: Poster 1

BP 7.25: Poster

Monday, September 5, 2022, 18:00–20:00, P1

Protein folding as described by different internal coordinates — •Sofia Sartore — Albert-Ludwigs-Universität Freiburg

Proteins reach their final structure (native state) through a process named folding. A powerful tool to investigate such process are molecular dynamics simulations, that can simulate the folding of a protein, giving as output a folding trajectory up to hundreds of microseconds long. This trajectory however needs to be further interpreted and analyzed in order to obtain an understandable model of the process, consisting of states that correspond to metastable conformation of the protein during the folding. To build such states, identifying the main features that are responsible for the folding of the protein is of utmost importance, as well as choosing appropriate coordinates to describe the dynamics under study. Using internal coordinates such as dihedral angles or interatomic distances proves to be convenient, since they disregard the overall motion of the system. In this poster we analyse what influence the choice of different input coordinates has on the resulting picture of the process: we compare an analysis of the fast folding protein HP35 based on dihedral angles as internal coordinates with one based on contacts, a particular set of interatomic distances that satisfy specific requirements. We find that using different input coordinates highlights different dynamics of the system, resulting in different descriptions of the same physical process.