ArticleJournal of chemical theory and computation2013
Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- A PI(3,5)PNature communications · 2026Article
- A Coarse-Grained MARTINI Model for Mucins.Journal of chemical theory and computation · 2026Article
- Multiscale Simulation of Phosphofructokinase-1 Assemblies: Capturing the Interplay between Specific and Transient Interactions.The journal of physical chemistry. B · 2025Article
- Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- Regulation of PIEZO1 channel force sensitivity by interblade handshaking.Science advances · 2025Article
- GōMartini 3: From large conformational changes in proteins to environmental bias corrections.Nature communications · 2025Article
- Martini compatible coarse-grained model of polyethylenimine for pulmonary gene delivery.Scientific reports · 2025Article
- Refined Protein-Sugar Interactions in the Martini Force Field.Journal of chemical theory and computation · 2024Article
- Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome P450 2B4.Protein science : a publication of the Protein Society · 2024Article
- Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution.Nature communications · 2024Article
- Adsorption of monoclonal antibody fragments at the water-oil interface: A coarse-grained molecular dynamics study.APL bioengineering · 2024Article
- Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model.Journal of chemical theory and computation · 2024Article
- Thermodynamic forces from protein and water govern condensate formation of an intrinsically disordered protein domain.Nature communications · 2023Article
- Theoretical and Data-Driven Approaches for Biomolecular Condensates.Chemical reviews · 2023Review
- Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining.Journal of chemical information and modeling · 2023Article
- Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models.Journal of chemical theory and computation · 2023Article
- Structure and interaction of therapeutic proteins in solution: a combined simulation and experimental study.Molecular physics · 2023Article
- Finite-Size Effects in Simulations of Peptide/Lipid Assembly.The Journal of membrane biology · 2022Article
- Effects of cholesterol on the mechanism of fengycin, a biofungicide.Biophysical journal · 2022Article
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3 authors.
Funding
Abstract
Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.