ArticlePLoS computational biology2020
Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 29 citations in OpenAlex.
- Tied to Work: Topologically Knotted SPOUT Methyltransferases and UCH Deubiquitinases in Cellular Biochemistry.Journal of cellular biochemistry · 2026Review
- Novel Knotted Solenoid fold with order-shifted coil arrangement leads to nontrivial 3Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Mechanistic Insights into SAM-Dependent Methyltransferases: A Review of Computational Approaches.International journal of molecular sciences · 2025Review
- Is There a Functional Role for the Knotted Topology in Protein UCH-L1?Journal of chemical information and modeling · 2024Article
- Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model.Protein science : a publication of the Protein Society · 2024Article
- Conservation of knotted and slipknotted topology in transmembrane transporters.Biophysical journal · 2023Article
- Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study.Computational and structural biotechnology journal · 2023Article
- Are there double knots in proteins? Prediction andFrontiers in molecular biosciences · 2023Article
- Investigation of the structural dynamics of a knotted protein and its unknotted analog using molecular dynamics.Journal of molecular modeling · 2022Article
- Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.PLoS computational biology · 2021Article
- Therapeutic effect of adenosylmethionine on viral hepatitis and related factors inducing diseas.American journal of translational research · 2021Article
- MgACS catalysis · 2020Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
S-adenosylmethionine (SAM) is one of the most important enzyme substrates. It is vital for the function of various proteins, including large group of methyltransferases (MTs). Intriguingly, some bacterial and eukaryotic MTs, while catalysing the same reaction, possess significantly different topologies, with the former being a knotted one. Here, we conducted a comprehensive analysis of SAM conformational space and factors that affect its vastness. We investigated SAM in two forms: free in water (via NMR studies and explicit solvent simulations) and bound to proteins (based on all data available in the PDB and on all-atom molecular dynamics simulations in water). We identified structural descriptors-angles which show the major differences in SAM conformation between unknotted and knotted methyltransferases. Moreover, we report that this is caused mainly by a characteristic for knotted MTs compact binding site formed by the knot and the presence of adenine-binding loop. Additionally, we elucidate conformational restrictions imposed on SAM molecules by other protein groups in comparison to conformational space in water.
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