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AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine

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Abstract

We report a consistent set of AMBER force-field parameters for the most common phosphorylated amino acids, phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine in different protonation states. The calculation of atomic charges followed the original restrained electrostatic potential fitting procedure used to determine the charges for the parm94/99 parameter set, taking α-helical and β-strand conformations of the corresponding ACE-/NME-capped model peptide backbone into account. Missing force-field parameters were taken directly from the general AMBER force field (gaff) and the parm99 data set with minor modifications, or were newly generated based on ab initio calculations for model systems. Final parameters were validated by geometry optimizations and molecular-dynamics simulations. Template libraries for the phosphorylated amino acids in Leap format and corresponding frcmod parameter files are made available.

Schematic illustration of the systems used for parameter generation. Acid hydrogens are shown in red

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Acknowledgements

The authors wish to thank Heike Meiselbach for helpful discussions, and the Leibnitz-Rechenzentrum in Munich and the Regionales Rechenzentrum Erlangen for computational resources. This work was supported by a grant from the Deutsche Forschungsgemeinschaft (SFB473, C10) to H. Sticht. N. Homeyer acknowledges a fellowship from the BioMedTec International Graduate School of Science (BIGSS), supported by the state of Bavaria.

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Authors and Affiliations

  1. Abteilung für Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstraße 17, 91054, Erlangen, Germany

    Nadine Homeyer, Anselm H. C. Horn & Heinrich Sticht

  2. Computer-Chemie-Centrum, Nägelsbachstraße 25, 91052, Erlangen, Germany

    Harald Lanig

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  1. Nadine Homeyer
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  2. Anselm H. C. Horn
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  4. Heinrich Sticht
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Correspondence to Heinrich Sticht.

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Homeyer, N., Horn, A.H.C., Lanig, H. et al. AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J Mol Model 12, 281–289 (2006). https://doi.org/10.1007/s00894-005-0028-4

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