ArticleNature communications2018
Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Computational insights into the aggregation mechanism and amyloidogenic core of aortic amyloid medin polypeptide.Colloids and surfaces. B, Biointerfaces · 2024Article
- DNA controls the dimerization of the human FoxP1 forkhead domain.Cell reports. Physical science · 2024Article
- The molecular basis for cellular function of intrinsically disordered protein regions.Nature reviews. Molecular cell biology · 2024Review
- A complex network of interdomain interactions underlies the conformational ensemble of monomeric TDP-43 and modulates its phase behavior.Protein science : a publication of the Protein Society · 2024Article
- Endothelial leakiness elicited by amyloid protein aggregation.Nature communications · 2024Article
- Deciphering the influence of Y12L and N17H substitutions on the conformation and oligomerization of human calcitonin.Soft matter · 2024Article
- Co-aggregation of α-synuclein with amyloid-β stabilizes β-sheet-rich oligomers and enhances the formation of β-barrels.Physical chemistry chemical physics : PCCP · 2023Article
- Unveiling Medin Folding and Dimerization Dynamics and Conformations via Atomistic Discrete Molecular Dynamics Simulations.Journal of chemical information and modeling · 2023Article
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- DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility.iScience · 2023Article
- Dissecting the Self-assembly Dynamics of Imperfect Repeats in α-Synuclein.Journal of chemical information and modeling · 2023Article
- Domain tethering impacts dimerization and DNA-mediated allostery in the human transcription factor FoxP1.The Journal of chemical physics · 2023Article
- Coevolution and smFRET Enhances Conformation Sampling and FRET Experimental Design in Tandem PDZ1-2 Proteins.The journal of physical chemistry. B · 2023Article
- Structural Perturbation of Monomers Determines the Amyloid Aggregation Propensity of Calcitonin Variants.Journal of chemical information and modeling · 2023Article
- Different Forms of Disorder in NMDA-Sensitive Glutamate Receptor Cytoplasmic Domains Are Associated with Differences in Condensate Formation.Biomolecules · 2022Article
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Authors and funding
11 authors.
Funding
Abstract
Previous studies of the N-terminal PDZ tandem from PSD-95 produced divergent models and failed to identify interdomain contacts stabilizing the structure. We used ensemble and single-molecule FRET along with replica-exchange molecular dynamics to fully characterize the energy landscape. Simulations and experiments identified two conformations: an open-like conformation with a small contact interface stabilized by salt bridges, and a closed-like conformation with a larger contact interface stabilized by surface-exposed hydrophobic residues. Both interfaces were confirmed experimentally. Proximity of interdomain contacts to the binding pockets may explain the observed coupling between conformation and binding. The low-energy barrier between conformations allows submillisecond dynamics, which were time-averaged in previous NMR and FRET studies. Moreover, the small contact interfaces were likely overridden by lattice contacts as crystal structures were rarely sampled in simulations. Our hybrid approach can identify transient interdomain interactions, which are abundant in multidomain proteins yet often obscured by dynamic averaging.
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