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Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments

submitted on 19.06.2019, 11:30 and posted on 19.06.2019, 17:01 by Peter Reinholdt, Erik Kjellgren, Casper Steinmann, Jógvan Magnus Haugaard Olsen
The fragment-based polarizable embedding model combined with an appropriate electronic-structure method constitutes a highly efficient and accurate multiscale approach for computing spectroscopic properties of a central moiety including effects from its molecular environment through an embedding potential. There is, however, a comparatively high computational overhead associated with the computation of the embedding potential which is derived from first principles calculations on individual fragments of the environment. To reduce the computational cost associated with the calculation of embedding-potential parameters, we developed a set of amino-acid-specific transferable parameters tailored for large-scale polarizable embedding calculations that include proteins. The amino-acid-based parameters are obtained by simultaneously fitting to a set of reference electric potentials based on structures derived from a backbone-dependent rotamer library. The developed cost-effective polarizable protein potential (CP3) consists of atom-centered charges and isotropic dipole-dipole polarizabilities of the standard amino acids. In terms of reproduction of electric potentials, the CP3 is shown to perform consistently and with acceptable accuracy across both small tripeptide test systems and larger proteins. We show, through applications on realistic protein systems, that acceptable accuracy can be obtained by using a pure CP3 representation of the protein environment, thus altogether omitting the cost associated with the calculation of embedding-potential parameters. High accuracy comparable to the full fragment-based approach can be achieved through a mixed description where the CP3 is used only to describe amino acids beyond a threshold distance from the central quantum part.


Carlsberg Foundation (Grant ID: CF15-0823)

Hylleraas Center

The Research Council of Norway

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UiT The Arctic University of Norway



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No conflict of interest



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in Journal of Chemical Theory and Computation