ArticleStructure (London, England : 1993)2023
Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer.
Article in Structure (London, England : 1993), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Cholesterol-dependent dimerization and conformational dynamics of EphA2 receptors from coarse-grained and all-atom simulations.Structure (London, England : 1993) · 2025Article
- Simulation of Neurotrophin Receptor Transmembrane Helix Interactions Reveals Active States and Distinct Signaling Mechanisms.JACS Au · 2025Article
- Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A Computational Approach in the Systematic Search of the Interaction Partners of Alternatively Spliced TREM2 Isoforms.International journal of molecular sciences · 2024Article
- Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane.Journal of chemical theory and computation · 2024Article
- A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.Journal of chemical theory and computation · 2023Article
- The role of structural heterogeneity in the homodimerization of transmembrane proteins.The Journal of chemical physics · 2023Article
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Authors and funding
4 authors.
Funding
Abstract
Structures and dynamics of transmembrane (TM) receptor regions are key to understanding their signaling mechanism across membranes. Here we examine configurations of TM region dimers, assembled using the recent Martini 3 force field for coarse-grain (CG) molecular dynamics simulations. At first glance, our results show only a reasonable agreement with ab initio predictions using PREDDIMER and AlphaFold2 Multimer and with nuclear magnetic resonance (NMR)-derived structures. 5 of 11 CG TM structures are similar to the NMR structures (within <3.5 Å root-mean-square deviation [RMSD]) compared with 10 and 9 using PREDDIMER and AlphaFold2, respectively (with 8 structures of the later within 1.5 Å). Surprisingly, AlphaFold2 predictions are closer to NMR structures when the 2001 instead of 2020 database is used for training. The CG simulations reveal that alternative configurations of TM dimers readily interconvert with a predominant population. The implications for transmembrane signaling are discussed, including for the development of peptide-based pharmaceuticals.
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