A polarizable coarse-grained protein model for dissipative particle dynamics.
We present a new coarse-grained polarizable protein model for dissipative particle dynamics (DPD) method. This method allows large timesteps in particle-based systems and speeds up sampling by many orders of magnitude. Our new model is based on the electrostatic polarization of the protein backbone and a detailed representation of the sidechains in combination with a polarizable water model. We define our model parameters using the experimental structures of two proteins, TrpZip2 and TrpCage. Backmapping and subsequent short replica-exchange molecular dynamics runs verify our approach and show convergence to the experimental structures on the atomistic level. We validate our model on five different proteins: GB1, the WW-domain, the B-domain of Protein A, the peripheral binding subunit and villin headpiece.
Institute of Computational Science, Faculty of Informatics, University of Lugano, Lugano, Switzerland. igor.pivkin@usi.ch.
Emanuel K
EK
Peter
Kirill
K
Lykov
Igor V
IV
Pivkin
D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010316:Particle Size; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties; D014867:Water / Q000737:chemistry
D011506:Proteins; D014867:Water