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  Benchmarking polarizable and non-polarizable force fields for Ca2+–peptides against a comprehensive QM dataset

Amin, K. S., Hu, X., Salahub, D. R., Baldauf, C., Lim, C., & Noskov, S. (2020). Benchmarking polarizable and non-polarizable force fields for Ca2+–peptides against a comprehensive QM dataset. The Journal of Chemical Physics, 153(14): 144102. doi:10.1063/5.0020768.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-4ECF-A Version Permalink: http://hdl.handle.net/21.11116/0000-0007-63D2-C
Genre: Journal Article

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 Creators:
Amin, Kazi S.1, Author
Hu, Xiaojuan2, Author              
Salahub, Dennis R.3, Author
Baldauf, Carsten4, Author              
Lim, Carmay5, 6, Author
Noskov, Sergei1, Author
Affiliations:
1CMS – Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada, ou_persistent22              
2NOMAD, Fritz Haber Institute, Max Planck Society, ou_3253022              
3Department of Chemistry, CMS – Centre for Molecular Simulation, IQST – Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada, ou_persistent22              
4Molecular Physics, Fritz Haber Institute, Max Planck Society, ou_634545              
5Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ou_persistent22              
6Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan, ou_persistent22              

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 Abstract: Explicit description of atomic polarizability is critical for the accurate treatment of inter-molecular interactions by force fields (FFs) in molecular dynamics (MD) simulations aiming to investigate complex electrostatic environments such as metal-binding sites of metalloproteins. Several models exist to describe key monovalent and divalent cations interacting with proteins. Many of these models have been developed from ion–amino-acid interactions and/or aqueous-phase data on cation solvation. The transferability of these models to cation–protein interactions remains uncertain. Herein, we assess the accuracy of existing FFs by their abilities to reproduce hierarchies of thousands of Ca2+–dipeptide interaction energies based on density-functional theory calculations. We find that the Drude polarizable FF, prior to any parameterization, better approximates the QM interaction energies than any of the non-polarizable FFs. Nevertheless, it required improvement in order to address polarization catastrophes where, at short Ca2+–carboxylate distances, the Drude particle of oxygen overlaps with the divalent cation. To ameliorate this, we identified those conformational properties that produced the poorest prediction of interaction energies to reduce the parameter space for optimization. We then optimized the selected cation–peptide parameters using Boltzmann-weighted fitting and evaluated the resulting parameters in MD simulations of the N-lobe of calmodulin. We also parameterized and evaluated the CTPOL FF, which incorporates charge-transfer and polarization effects in additive FFs. This work shows how QM-driven parameter development, followed by testing in condensed-phase simulations, may yield FFs that can accurately capture the structure and dynamics of ion–protein interactions.

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Language(s): eng - English
 Dates: 2020-07-062020-09-182020-10-082020-10-14
 Publication Status: Published in print
 Pages: 15
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1063/5.0020768
 Degree: -

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Title: The Journal of Chemical Physics
  Other : J. Chem. Phys.
Source Genre: Journal
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Publ. Info: Woodbury, N.Y. : American Institute of Physics
Pages: 15 Volume / Issue: 153 (14) Sequence Number: 144102 Start / End Page: - Identifier: ISSN: 0021-9606
CoNE: https://pure.mpg.de/cone/journals/resource/954922836226