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Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications

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    Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications
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    Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States
    *E-mail: [email protected]. Phone: 609-258-4595. Fax: 609-258-0211.
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    Journal of Chemical Theory and Computation

    Cite this: J. Chem. Theory Comput. 2013, 9, 12, 5653–5674
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    https://doi.org/10.1021/ct400556v
    Published November 22, 2013
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    Abstract

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    In this work, we introduce Forcefield_PTM, a set of AMBER forcefield parameters consistent with ff03 for 32 common post-translational modifications. Partial charges were calculated through ab initio calculations and a two-stage RESP-fitting procedure in an ether-like implicit solvent environment. The charges were found to be generally consistent with others previously reported for phosphorylated amino acids, and trimethyllysine, using different parametrization methods. Pairs of modified structures and their corresponding unmodified structures were curated from the PDB for both single and multiple modifications. Background structural similarity was assessed in the context of secondary and tertiary structures from the global data set. Next, the charges derived for Forcefield_PTM were tested on a macroscopic scale using unrestrained all-atom Langevin molecular dynamics simulations in AMBER for 34 (17 pairs of modified/unmodified) systems in implicit solvent. Assessment was performed in the context of secondary structure preservation, stability in energies, and correlations between the modified and unmodified structure trajectories on the aggregate. As an illustration of their utility, the parameters were used to compare the structural stability of the phosphorylated and dephosphorylated forms of OdhI. Microscopic comparisons between quantum and AMBER single point energies along key χ torsions on several PTMs were performed, and corrections to improve their agreement in terms of mean-squared errors and squared correlation coefficients were parametrized. This forcefield for post-translational modifications in condensed-phase simulations can be applied to a number of biologically relevant and timely applications including protein structure prediction, protein and peptide design, and docking and to study the effect of PTMs on folding and dynamics. We make the derived parameters and an associated interactive webtool capable of performing post-translational modifications on proteins using Forcefield_PTM available at http://selene.princeton.edu/FFPTM.

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    Supporting Information

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    Instructions for importing new parameters into AMBER, forcefield parameters for each PTM grouped by scaffold residue, images of each parametrized PTM grouped by scaffold residue, an explanation of the methodology used to curate the pairs of modified and unmodified protein structures contained in the PDB, the identities of post-translationally modified proteins in the PDB as a function of the number of modifications, an explanation of how the background secondary and tertiary structure dissimilarity was assessed to establish background control levels, the methodology for filling in missing residues and homology modeling of the pairs of modified/unmodified proteins curated, a derivation of the restrained electrostatic potential (106) (for completion), energetic and structural statistics collected over the course of 5 ns all-atom MD simulations for 17 pairs of modified/unmodified structures, supplementary discussion on 2L5J/2L5I deviation in simulation, plots of energetics, secondary structure, and tertiary structure space sampled for pairs of modified/unmodified proteins, images of the torsion angles assessed using ab initio rotational profiles, and a forcefield file capable of being directly imported into AMBER. This material is available free of charge via the Internet at http://pubs.acs.org.

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    Cite this: J. Chem. Theory Comput. 2013, 9, 12, 5653–5674
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    Published November 22, 2013
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