David Gnandt

Abstract

Computer simulations are an important addition to structural biology methods like X-ray crystallography, cryo-transmission electron microscopy or fluorescence labeling to understand large protein complexes from a theoretical and atomistic point of view. Protein complexes like the NADH:Ubiquinone oxidureductase involved in redox-reactions coupled with transport of small molecules or Ions over cell membranes are of high interest in understanding cell metabolism pathways. On the time scale of electron transport, molecule dynamic simulations are still a challenge to calculate free energy landscapes for these multi domain protein complexes. Electrostatic potential and energy originating from the charge distribution within biomolecules greatly impact intramolecular and intermolecular interactions.[1]
In order to quantitatively correct a serious conceptual problem of molecular dynamic simulation we aim to post-process the results of MD simulation by numerical finite difference dielectric continuum computations. Using the same strategy we approach to show an alternative way to calculate key parameters of charge transfer within these large multi domain protein aggregates.

For more information: http://www.theochem.uni-freiburg.de/the-group/david-gnandt-1

Methods

• Dielectric continuum calculation
• Molecular Dynamic (MD) Simulation

References

[1] Ch. Li, M. Petukh, L. Li and E. Alexov: Continuous development of schemes for parallel computing of electrostatics in biological systems: Implementation in DelPhi. J. Comput. Chem. (2013) 34, 22, 1949-1960.