ArticleScientific reports2015
Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Simulation of the trimeric globular head of C1q reveals temperature-sensitive network: implications for inflammation.Journal of molecular modeling · 2025Article
- Diffusion and Viscosity in Mixed Protein Solutions.The journal of physical chemistry. B · 2024Article
- PACSAB Server: A Web-Based Tool for the Study of Aggregation and the Conformational Ensemble of Disordered and Folded Proteins.International journal of molecular sciences · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Structure and interaction of therapeutic proteins in solution: a combined simulation and experimental study.Molecular physics · 2023Article
- Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence.Molecules (Basel, Switzerland) · 2022Article
- A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations.Frontiers in molecular biosciences · 2022Article
- Accurate Description of Protein-Protein Recognition and Protein Aggregation with the Implicit-Solvent-Based PACSAB Protein Model.Polymers · 2021Article
- Effect of the Water Model in Simulations of Protein-Protein Recognition and Association.Polymers · 2021Article
- Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization.Computational and structural biotechnology journal · 2021Article
- Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2).Communications chemistry · 2020Article
- Data-driven analysis of the number of Lennard-Jones types needed in a force field.Communications chemistry · 2020Article
- Article
- Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties.The journal of physical chemistry letters · 2019Article
- Atomic-level characterization of protein-protein association.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations.BioMed research international · 2018Article
- Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.The journal of physical chemistry. B · 2017Article
- Enhanced unbiased sampling of protein dynamics using evolutionary coupling information.Scientific reports · 2017Article
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase.Scientific reports · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.