ArticleBiophysical journal2013
Molecular simulations of a dynamic protein complex: role of salt-bridges and polar interactions in configurational transitions.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Targeted protein degradation: advances in drug discovery and clinical practice.Signal transduction and targeted therapy · 2024Review
- Revolutionizing Drug Targeting Strategies: Integrating Artificial Intelligence and Structure-Based Methods in PROTAC Development.Pharmaceuticals (Basel, Switzerland) · 2023Review
- Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers.Scientific reports · 2022Article
- Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations.Polymers · 2021Article
- Factors underlying asymmetric pore dynamics of disaggregase and microtubule-severing AAA+ machines.Biophysical journal · 2021Article
- U-shaped caveolin-1 conformations are tightly regulated by hydrogen bonds with lipids.Journal of computational chemistry · 2019Article
- The Sam-Sam interaction between Ship2 and the EphA2 receptor: design and analysis of peptide inhibitors.Scientific reports · 2017Article
- A role of the SAM domain in EphA2 receptor activation.Scientific reports · 2017Article
- Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIα.Biochemistry · 2017Article
- Molecular Dynamics Simulations Reveal Isoform Specific Contact Dynamics between the Plexin Rho GTPase Binding Domain (RBD) and Small Rho GTPases Rac1 and Rnd1.The journal of physical chemistry. B · 2017Article
- Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.Biophysical journal · 2016Article
- Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.Nucleic acids research · 2016Article
- Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB.Proteins · 2015Article
- Binding and function of phosphotyrosines of the Ephrin A2 (EphA2) receptor using synthetic sterile α motif (SAM) domains.The Journal of biological chemistry · 2014Article
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Authors and funding
2 authors.
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Abstract
Ion charge pairs and hydrogen bonds have been extensively studied for their roles in stabilizing protein complexes and in steering the process of protein association. Recently, it has become clear that some protein complexes are dynamic in that they interconvert between several alternate configurations. We have previously characterized one such system: the EphA2:SHIP2 SAM-SAM heterodimer by solution NMR. Here we carried out extensive all-atom molecular-dynamics simulations on a microsecond time-scale starting with different NMR-derived structures for the complex. Transitions are observed between several discernible configurations at average time intervals of 50-100 ns. The domains reorient relative to one another by substantial rotation and a slight shifting of the interfaces. Bifurcated and intermediary salt-bridge and hydrogen-bond interactions play a role in the transitions in a process that can be described as moving along a "monkey-bar". We notice an increased density of salt bridges near protein interaction surfaces that appear to enable these transitions, also suggesting why the trajectories can become kinetically hindered in regions where fewer of such interactions are possible. In this context, even microsecond molecular-dynamics simulations are not sufficient to sample the energy landscape unless the structures remain close to their experimentally derived low-energy configurations.
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