Dresden 2003 – scientific programme

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SYSE: Simulation and experiment

SYSE 2: Poster (gemeinsam mit SYCN und CPP)

SYSE 2.19: Poster

Tuesday, March 25, 2003, 19:00–21:00, ZEU/250

Determination of the binding energy of a receptor–ligand pair using Steered Molecular Dynamics — •Daniel Pflugfelder, Andrew Aird, Carsten Tietz, and Jörg Wrachtrup — 3. Physikalisches Institut, Universität Stuttgart

In signaling cascades of cells the binding–unbinding kinetics of first and second messenger proteins play a crucial role in signal transduction. We determined the binding energy and the binding type on atomistic level of a ligand to its receptor by molecular dynamics simulation. As a model system we choose the Tumor Necrosis Factor (TNF) and its receptor (TNF-R1). Starting from the known ligand-receptor complex structure (1TNR.pdb) we set up the TNF-trimer bond to one receptor. To unravel the detailed unbinding kinetics we use Steered Molecular Dynamics (SMD) to separate the ligand from its receptor. Using the force–distance curve it is possible to determine the free enthalpy along the reaction coordinate. The results are compared with Δ G values obtained by the MMPBSA-method.