User Project Details

GCS-MDhNPC

Atomistic Molecular Dynamics Simulations of the Human Nuclear Pore Complex

Chemistry

Max-Planck Gesellschaft

Max-Planck-Institut für Biophysik

The nuclear pore complex (NPC) is the largest protein assembly found in eukaryotic cells. It functions as a gateway for the transport of molecules in and out of the nucleus and is located in the nuclear envelope. NPCs are involved in key biological processes such as gene expression, chromatin organization, and DNA repair, and their malfunction is associated with aging and neurodegenerative diseases, as well as different types of cancer. Advanced experimental techniques in combination with molecular dynamics (MD) simulations are starting to shed light on the NPC structure. All-atom MD simulations of the NPC scaffold, the GP210 ring, and the full NPC will allow us to study the NPC conformational dynamics, its response to mechanical stress, and the properties of the permeability barrier. The large size of the NPC poses a simulation challenge: a simulation box for this system contains around 200 million atoms, a size much larger than can be achieved currently with atomistic MD simulations.