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Abstract
BackgroundPost-translational modifications (PTMs) constitute a major aspect of protein biology, particularly signaling events. Conversely, several different pathophysiological PTMs are hallmarks of oxidative imbalance or inflammatory states and are strongly associated with pathogenesis of autoimmune diseases or cancers. Accordingly, it is of interest to assess both the biological and structural effects of modification. For the latter, computer-based modeling offers an attractive option. We thus identified the need for easily applicable modeling options for PTMs.ResultsWe developed PyTMs, a plugin implemented with the commonly used visualization software PyMOL. PyTMs enables users to introduce a set of common PTMs into protein/peptide models and can be used to address research questions related to PTMs. Ten types of modification are currently supported, including acetylation, carbamylation, citrullination, cysteine oxidation, malondialdehyde adducts, methionine oxidation, methylation, nitration, proline hydroxylation and phosphorylation. Furthermore, advanced settings integrate the pre-selection of surface-exposed atoms, define stereochemical alternatives and allow for basic structure optimization of the newly modified residues.ConclusionPyTMs is a useful, user-friendly modelling plugin for PyMOL. Advantages of PyTMs include standardized generation of PTMs, rapid time-to-result and facilitated user control. Although modeling cannot substitute for conventional structure determination it constitutes a convenient tool that allows uncomplicated exploration of potential implications prior to experimental investments and basic explanation of experimental data. PyTMs is freely available as part of the PyMOL script repository project on GitHub and will further evolve.Graphical PyTMs is a useful PyMOL plugin for modeling common post-translational modifications.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0370-6) contains supplementary material, which is available to authorized users.
Highlights
Post-translational modifications (PTMs) constitute a major aspect of protein biology, signaling events
Application examples Here we provide some basic application examples of how Name of the PyMOL plugin (PyTMs) can be employed to address research questions related to PTMs, which we discuss below in the Results section: Enzyme inhibition: nitrated HPR1 The model of hydroxypyruvate reductase 1 (HPR1) from Arabidopsis thaliana was kindly provided by Dr Francisco J
In the context of altered peptide ligands (APLs) and Major Histocompatibility Complexes (MHCs), modeling can be useful to explain or predict whether an Altered Peptide Ligand (APL) can be presentable by a respective MHC allele and/or how the introduced PTM and APL may be oriented
Summary
We developed PyTMs, a plugin implemented with the commonly used visualization software PyMOL. PyTMs enables users to introduce a set of common PTMs into protein/peptide models and can be used to address research questions related to PTMs. Ten types of modification are currently supported, including acetylation, carbamylation, citrullination, cysteine oxidation, malondialdehyde adducts, methionine oxidation, methylation, nitration, proline hydroxylation and phosphorylation. Advanced settings integrate the pre-selection of surface-exposed atoms, define stereochemical alternatives and allow for basic structure optimization of the newly modified residues
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