ArticleNature communications2024
Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 2026Article
- Autoinhibition of untimely DNA binding by structural disorder in the full-length peroxisome proliferator-activated receptors (PPARs).Nature communications · 2026Article
- Comparing multislice projections of MD simulations with cryo-EM exposes structural prediction errors.Biophysical journal · 2026Article
- Accurate interdomain contacts in a mixed folded protein from NMR-guided coarse-grained simulations.Physical chemistry chemical physics : PCCP · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Lipid Composition Drives Mutant Huntingtin Dimerization and Membrane Association: Insights from Computational Simulations.Molecules (Basel, Switzerland) · 2026Article
- The LOK C-terminus is an IBAR-like domain that facilitates membrane binding and ezrin colocalization.Biophysical journal · 2026Article
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- Physicochemical Principles Governing the Intrinsically Disordered Salivary Peptide Histatin 5: Ensemble Structure, Electrostatics, and Environmental Responsiveness.The journal of physical chemistry. B · 2026Review
- Integrating NMR Restraints into Coarse-Grained Simulations: Toward Accurate Conformational Ensembles of Complex Protein Systems.Journal of the American Chemical Society · 2026Article
- Concentration Effects in Peptide-Lipid Bilayer Interactions: A Coarse-Grained Molecular Dynamics Study.The journal of physical chemistry. B · 2026Article
- From Membrane Composition to Antimicrobial Strategies: Experimental and Computational Approaches to AMP Design and Selectivity.Small (Weinheim an der Bergstrasse, Germany) · 2026Review
- Comparing Multislice Projections of MD Simulations with CryoEM Exposes Structural Prediction Errors.bioRxiv : the preprint server for biology · 2026Article
- Multiscale simulations of folded and intrinsically disordered region-containing protein condensates.Biophysical journal · 2026Article
- A Coarse-Grained MARTINI Model for Mucins.Journal of chemical theory and computation · 2026Article
- Predicting Pose Distribution of Protein Domains Connected by Flexible Linkers Is an Unsolved Problem.Proteins · 2026Article
- Computational characterization of the xanthan gum glycosyltransferase GumK.PLoS computational biology · 2025Article
- Martini 3 Limitations in Phospholipid Flip-Flop.Journal of chemical theory and computation · 2025Article
- A Hybrid UA-CG Force Field for Aggregation Simulation of Amyloidogenic Peptide via Liquid-like Intermediates.Molecules (Basel, Switzerland) · 2025Article
- Microtubules in Martini: Parameterizing a heterogeneous elastic-network towards a mechanically accurate microtubule.PNAS nexus · 2025Article
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Authors and funding
6 authors.
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Abstract
Multidomain proteins with flexible linkers and disordered regions play important roles in many cellular processes, but characterizing their conformational ensembles is difficult. We have previously shown that the coarse-grained model, Martini 3, produces too compact ensembles in solution, that may in part be remedied by strengthening protein-water interactions. Here, we show that decreasing the strength of protein-protein interactions leads to improved agreement with experimental data on a wide set of systems. We show that the 'symmetry' between rescaling protein-water and protein-protein interactions breaks down when studying interactions with or within membranes; rescaling protein-protein interactions better preserves the binding specificity of proteins with lipid membranes, whereas rescaling protein-water interactions preserves oligomerization of transmembrane helices. We conclude that decreasing the strength of protein-protein interactions improves the accuracy of Martini 3 for IDPs and multidomain proteins, both in solution and in the presence of a lipid membrane.
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