ArticleJournal of computer-aided molecular design2015
A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation.
Article in Journal of computer-aided molecular design, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 25 citations in OpenAlex.
- Decoding the Conformational Dynamics and Hyperactivity of Histone H3K36 N-Methyltransferase in Oncogenic MutationsbioRxiv : the preprint server for biology · 2026Article
- An MD View of Ligand Binding.Molecules (Basel, Switzerland) · 2025Article
- Study of the Rv1417 and Rv2617c Membrane Proteins and Their Interactions with Nicotine Derivatives as Potential Inhibitors of Erp Virulence-Associated Factor inBiomolecules · 2023Article
- Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.Journal of molecular biology · 2022Article
- Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme.Journal of chemical information and modeling · 2022Article
- Discovery of Cofactor Competitive Inhibitors against the Human Methyltransferase Fibrillarin.Pharmaceuticals (Basel, Switzerland) · 2021Article
- Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2.Nature communications · 2021Article
- Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.PLoS computational biology · 2020Article
- Understanding the R882H mutation effects of DNA methyltransferase DNMT3A: a combination of molecular dynamics simulations and QM/MM calculations.RSC advances · 2019Article
- Parameterization of prototype organic small molecules suitable for OPVs and molecular dynamics simulations: the BTT and BPT cases.Journal of molecular modeling · 2019Article
- Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges.Journal of chemical information and modeling · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
S-Adenosylmethionine (AdoMet) is involved in many biological processes as cofactor in enzymes transferring its sulfonium methyl group to various substrates. Additionally, it is used as drug and nutritional supplement to reduce the pain in osteoarthritis and against depression. Due to the biological relevance of AdoMet it has been part of various computational simulation studies and will also be in the future. However, to our knowledge no rigorous force field parameter development for its simulation in biological systems has been reported. Here, we use electronic structure calculations combined with molecular dynamics simulations in explicit solvent to develop force field parameters compatible with the AMBER99 force field. Additionally, we propose new dynamic Hirshfeld-I atomic charges which are derived from the polarized electron density of AdoMet in aqueous solution to describe its electrostatic interactions in biological systems. The validation of the force field parameters and the atomic charges is performed against experimental interproton NOE distances of AdoMet in aqueous solution and crystal structures of AdoMet in the cavity of three representative proteins.
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