iMOS Master: Correlation of solvent fluctuations with dynamics of…

Correlation of solvent fluctuations with dynamics of simple ligand binding to biomolecular surfaces

Christopher Päslack

Image1_ChristopherWe   used   classical   atomistic   molecular   dynamics   (MD) simulations  to investigate how and to what extend collective protein-water motions affect the dynamics of ligand binding to a biomolecular surface. Therefore, the free energy surface (i.e. potential  of mean  force,  PMF)  along  the  reaction  coordinate was determined via Umbrella Sampling and based on that we obtained static one-body friction/diffusion profiles of the ligand along  the  reaction  coordinate.  The  reaction  coordinate  was defined  as  the distance  between  the  hydrophobic  patch  of ubiquitin and the ligand (LJ-spere).

We could show that dynamics of the ligand are affected both by the binding affinity in terms of the PMF as well as by internal motions  of  the  protein.  Furthermore,  the  ligand couples  to solvent  fluctuations  in  the  vicinity  of  the  hydrophobic  binding patch of ubiquitin.

Folie_Christ.1024_768After finishing his iMOS Master’s thesis Christopher Päslack started his PhD research in the group of Prof. Lars Schäfer.

Link to  Master course in Molecular Sciences and Simulation (iMOS) at Ruhr-University Bochum