ArticlePLoS computational biology2013
A systematic framework for molecular dynamics simulations of protein post-translational modifications.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
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- Structural Study of a Peptide Epitope Bearing Multiple Post-Translational Modifications in Rheumatoid Arthritis.International journal of molecular sciences · 2025Article
- Molecular Dynamics Simulations of Plasma-Antifolate Drug Synergy in Cancer Therapy.Biomolecules · 2025Article
- Protein editing using a coordinated transposition reaction.Science (New York, N.Y.) · 2025Article
- Identification and inhibition of PIN1-NRF2 protein-protein interactions through computational and biophysical approaches.Scientific reports · 2025Article
- Deacetylation of HSC70 by SIRT2 promotes chaperone mediated autophagy.Autophagy reports · 2025Article
- Targeting serotonin receptors with phytochemicals - an in-silico study.Scientific reports · 2024Article
- Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution.Journal of chemical information and modeling · 2024Article
- Effect of plasma-induced oxidation on NK cell immune checkpoint ligands: A computational-experimental approach.Redox biology · 2024Article
- Protein Oxidative Modifications in Neurodegenerative Diseases: From Advances in Detection and Modelling to Their Use as Disease Biomarkers.Antioxidants (Basel, Switzerland) · 2024Review
- An Integrated Analytical Approach for Screening Functional Post-Translational Modification Sites in Metabolic Enzymes.ACS omega · 2024Article
- Article
- Top-Down Machine Learning of Coarse-Grained Protein Force Fields.Journal of chemical theory and computation · 2023Article
- TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins.Cell death & disease · 2023Article
- Review
- Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site.International journal of molecular sciences · 2022Article
- Engineering of enzymes using non-natural amino acids.Bioscience reports · 2022Review
- O-GlcNAc modification of leucyl-tRNA synthetase 1 integrates leucine and glucose availability to regulate mTORC1 and the metabolic fate of leucine.Nature communications · 2022Article
- Molecular Dynamics Study of Citrullinated Proteins Associated with the Development of Rheumatoid Arthritis.Proteomes · 2022Article
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Authors and funding
5 authors.
Funding
Abstract
By directly affecting structure, dynamics and interaction networks of their targets, post-translational modifications (PTMs) of proteins play a key role in different cellular processes ranging from enzymatic activation to regulation of signal transduction to cell-cycle control. Despite the great importance of understanding how PTMs affect proteins at the atomistic level, a systematic framework for treating post-translationally modified amino acids by molecular dynamics (MD) simulations, a premier high-resolution computational biology tool, has never been developed. Here, we report and validate force field parameters (GROMOS 45a3 and 54a7) required to run and analyze MD simulations of more than 250 different types of enzymatic and non-enzymatic PTMs. The newly developed GROMOS 54a7 parameters in particular exhibit near chemical accuracy in matching experimentally measured hydration free energies (RMSE=4.2 kJ/mol over the validation set). Using this tool, we quantitatively show that the majority of PTMs greatly alter the hydrophobicity and other physico-chemical properties of target amino acids, with the extent of change in many cases being comparable to the complete range spanned by native amino acids.
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