A polarizable coarse-grained protein model for dissipative particle dynamics

Physical Chemistry Chemical Physics : PCCP
Emanuel K PeterIgor V Pivkin

Abstract

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.

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Citations

Jun 23, 2016·Chemical Reviews·Sebastian KmiecikAndrzej Kolinski
Dec 12, 2012·PloS One·Shee-Mei LokScott F Michael
Sep 19, 2017·PLoS Computational Biology·Kirill LykovIgor V Pivkin
Apr 24, 2017·The Journal of Chemical Physics·Pep Español, Patrick B Warren
Dec 4, 2020·The Journal of Physical Chemistry. B·Chandan Kumar Choudhury, Olga Kuksenok

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