Polarizable models for the simulation of protein-water systems in dissipative particle dynamics.
Dr. Emanuel Peter (Institute of Computational Science, Università della Svizzera italiana, Lugano, CH)

Polarization effects play a major role in many biological processes ranging from effects at lipid bilayers to protein folding. In this talk I present a new method for the simulation of polarizability effects in dissipative particle dynamics (DPD). Based on the Drude oscillator model, we implemented a new coarse-grained water model and applied this model to simulations of water-membrane systems [1]. At a later stage, we developed a new model for simulations of proteins. Both models significantly enhance sampling of biologically relevant processes, i.e. in simulations of protein folding, or the dynamics of membrane embedded proteins.

For the polarizable water model, we employ long-range electrostatics and Drude oscillators, and calibrate the model using the compressibility and dielectric constant of water. We validate the model by sampling the dielectric properties of solutions of sodium chloride at various concentrations. Additionally, we apply our model in equilibrium and electroporation simulations of lipid bilayer systems.

The protein model is based on the polarization of the protein backbone and a simplified representation of the sidechains in combination with the polarizable water model. We define our model parameters using the experimental structures of 2 proteins : TrpZip2 and TrpCage [2].
We validate the model on folding of the B1 fragment of protein G (GB1), demonstrating that it successfully predicts folding of this protein into its native conformation.
As a perspective of this model I will give a short outlook on simulations of protein aggregation, a relevant process in several Amyloid diseases, e.g. Alzheimer’s and Diabetes II.

[ 1 ] E. K. Peter, I. V. Pivkin, J. Chem. Phys. 141(16), 164506 (2014).
[ 2 ] E. K. Peter, I. V. Pivkin, submitted (2015).