Berlin 2024 – scientific programme
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BP: Fachverband Biologische Physik
BP 21: Poster IIIb
BP 21.16: Poster
Wednesday, March 20, 2024, 11:00–14:30, Poster C
Using molecular dynamics simulation as a microscope of the peptide's translocation process through an aerolysin nanopore — •Michel Mom1, Kumar Sarthak2, Aleksei Aksimentiev2, and Christian Holm1 — 1Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany — 2Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana- Champaign, Urbana, United-States
In recent years, a cost-effective method was developed to sequence DNA and RNA with high precision at the single-molecule level. This research project aims to extend this sequencing method to proteins and peptides which is still in the early stages. The method involves placing the analyte in an electrolyte solution separated by a lipid membrane which contains an implemented biological nanopore. An applied electrical voltage drives ion and analyte transport through the nanopore. The presence of the analyte in the nanopore results in a temporary reduction of the open-pore current, from which one can draw valuable conclusions about the structure of the investigated protein. To understand the effects of the analyte transport on the ionic flow at the atomic level, we conduct molecular dynamics simulations. Our results offer valuable insights into the translocation process of the peptide, revealing regions of resistance and predicting the residual ionic current. This poster demonstrates our application of molecular dynamics simulations to translocate peptides through a novel aerolysin nanopore variant, showcasing a proof of concept for future studies.
Keywords: Protein sequencing; Nanopore sensing; Computational biophysics; Molecular dynamics