ArticleBiophysical journal2008
Protein-protein interaction investigated by steered molecular dynamics: the TCR-pMHC complex.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 121 citations in OpenAlex.
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- Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules.Biophysical reviews · 2022Review
- Conformational flexibility of a free and TCR-bound pMHC-I protein investigated by long-term molecular dynamics simulations.BMC immunology · 2022Article
- Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Shock-Induced Damage Mechanism of Perineuronal Nets.Biomolecules · 2021Article
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- Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2.Scientific reports · 2021Article
- Prediction of Protein-Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets.International journal of molecular sciences · 2020Article
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- Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations.Frontiers in molecular biosciences · 2019Article
- Structural Analysis ofFrontiers in bioengineering and biotechnology · 2019Article
- Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- Phosphorylation promotes binding affinity of Rap-Raf complex by allosteric modulation of switch loop dynamics.Scientific reports · 2018Article
- Integrating Experiment and Theory to Understand TCR-pMHC Dynamics.Frontiers in immunology · 2018Review
- Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints.Journal of chemical theory and computation · 2017Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a novel steered molecular dynamics scheme to induce the dissociation of large protein-protein complexes. We apply this scheme to study the interaction of a T cell receptor (TCR) with a major histocompatibility complex (MHC) presenting a peptide (p). Two TCR-pMHC complexes are considered, which only differ by the mutation of a single amino acid on the peptide; one is a strong agonist that produces T cell activation in vivo, while the other is an antagonist. We investigate the interaction mechanism from a large number of unbinding trajectories by analyzing van der Waals and electrostatic interactions and by computing energy changes in proteins and solvent. In addition, dissociation potentials of mean force are calculated with the Jarzynski identity, using an averaging method developed for our steering scheme. We analyze the convergence of the Jarzynski exponential average, which is hampered by the large amount of dissipative work involved and the complexity of the system. The resulting dissociation free energies largely underestimate experimental values, but the simulations are able to clearly differentiate between wild-type and mutated TCR-pMHC and give insights into the dissociation mechanism.
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