ArticleProceedings of the National Academy of Sciences of the United States of America2013
Free-energy landscape of protein oligomerization from atomistic simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations.Frontiers in molecular biosciences · 2022Article
- Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: Insights from atomistic simulations.Computational and structural biotechnology journal · 2022Article
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- Thermodynamic Origin of Differential Excipient-Lysozyme Interactions.Frontiers in molecular biosciences · 2021Article
- Dynamical control by water at a molecular level in protein dimer association and dissociation.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Calculating the absolute binding free energy of the insulin dimer in an explicit solvent.RSC advances · 2020Article
- Interplay of cysteine exposure and global protein dynamics in small-molecule recognition by a regulator of G-protein signaling protein.Proteins · 2019Article
- The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results.International journal of molecular sciences · 2018Review
- Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble-based model.Protein science : a publication of the Protein Society · 2018Article
- Improving low-accuracy protein structures using enhanced sampling techniques.The Journal of chemical physics · 2018Article
- Binding Modes of Teixobactin to Lipid II: Molecular Dynamics Study.Scientific reports · 2017Article
- Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints.Journal of chemical theory and computation · 2017Article
- Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling.Nature chemistry · 2017Article
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4 authors.
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Abstract
In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage.
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