ArticleThe journal of physical chemistry. B2021
Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids.
Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- The P134Q Sucrose Phosphorylase: Subtle Changes in the Catalytic Properties Benefit the Production of 2-O-α-Glucosyl Glycerol.Biotechnology and bioengineering · 2025Article
- Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation.The journal of physical chemistry. B · 2024Article
- Thirty years of molecular dynamics simulations on posttranslational modifications of proteins.Physical chemistry chemical physics : PCCP · 2022Review
- Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site.International journal of molecular sciences · 2022Article
- Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field.The journal of physical chemistry. A · 2022Article
- Phosphoserine inhibits neighboring arginine methylation in the RKS motif of histone H3.Archives of biochemistry and biophysics · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
Phosphorylation of select amino acid residues is one of the most common biological mechanisms for regulating protein structures and functions. While computational modeling can be used to explore the detailed structural changes associated with phosphorylation, most molecular mechanics force fields developed for the simulation of phosphoproteins have been noted to be inconsistent with experimental data. In this work, we parameterize force fields for the phosphorylated forms of the amino acids serine, threonine, and tyrosine using the ForceBalance software package with the goal of improving agreement with experiments for these residues. Our optimized force field, denoted as FB18, is parameterized using high-quality ab initio potential energy scans and is designed to be fully compatible with the AMBER-FB15 protein force field. When utilized in MD simulations together with the TIP3P-FB water model, we find that FB18 consistently enhances the prediction of experimental quantities such as
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