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Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models
Univ Sci & Technol Beijing, Sch Chem & Biol Engn, Dept Biol Sci & Engn, Beijing 100083, Peoples R China.
Univ Sci & Technol Beijing, Sch Chem & Biol Engn, Dept Biol Sci & Engn, Beijing 100083, Peoples R China.
Beijing Univ Chem Technol, Coll Life Sci & Technol, Beijing Key Lab Bioproc, Box 53, Beijing 100029, Peoples R China.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Uppsala University, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-7659-8526
2018 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 58, no 5, p. 1037-1052Article in journal (Refereed) Published
Abstract [en]

Thermodynamic and kinetic properties are of critical importance for the applicability of computational models to biomolecules such as proteins. Here we present an extensive evaluation of the Amber ff99SB-ILDN force field for modeling of hydration and diffusion of amino acids with three-site (SPC, SPC/E, SPC/E-b , and TIP3P), four-site (TIP4P, TIP4P-Ew, and TIP4P/2005), and five-site (TIPSP and TIP5P-Ew) water models. Hydration free energies (HFEs) of neutral amino acid side chain analogues have little dependence on the water model, with a root-mean-square error (RMSE) of similar to 1 kcal/mol from experimental observations. On the basis of the number of interacting sites in the water model, HFEs of charged side chains can be putatively classified into three groups, of which the group of three-site models lies between those of four- and five-site water models; for each group, the water model dependence is greatly eliminated when the solvent Galvani potential is considered. Some discrepancies in the location of the first hydration peak (R-RDF) in the ion-water radial distribution function between experimental and calculated observations were detected, such as a systematic underestimation of the acetate (Asp side chain) ion. The RMSE of calculated diffusion coefficients of amino acids from experiment increases linearly with the increasing diffusion coefficients of the solvent water models at infinite dilution. TIP3P has the fastest diffusivity, in line with literature findings, while the "FB" and "OPC" water model families as well as TIP4P/2005 perform well, within a relative error of 5%, and TIP4P/2005 yields the most accurate estimate for the water diffusion coefficient. All of the tested water models overestimate amino acid diffusion coefficients by approximately 40% (TIP4P/2005) to 200% (TIP3P). Scaling of protein-water interactions with TIP4P/2005 in the Amber ff99SBws and ff03ws force fields leads to more negative HFEs but has little influence on the diffusion of amino acids. The most recent FF/water combinations of ff14SB/OPC3, ffl5ipq/SPC/E-b, and fb15/TIP3P-FB do not show obvious improvements in accuracy for the tested quantities. These findings here establish a benchmark that may aid in the development and improvement of classical force fields to accurately model protein dynamics and thermodynamics.

Place, publisher, year, edition, pages
2018. Vol. 58, no 5, p. 1037-1052
National Category
Physical Chemistry
Identifiers
URN: urn:nbn:se:uu:diva-357575DOI: 10.1021/acs.jcim.8b00026ISI: 000433634900013PubMedID: 29648448OAI: oai:DiVA.org:uu-357575DiVA, id: diva2:1239695
Funder
Swedish Research Council, 2013-5947Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-08-17Bibliographically approved

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van der Spoel, David

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