ArticleBiomolecules2012
Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics.
Article in Biomolecules, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Feasibility of Combining Biomolecular Conformational Sampling Techniques for Molecular Dynamics Simulation.Journal of computational chemistry · 2025Article
- Fluorine-Thiol Displacement Stapling on the Disordered αSynlett : accounts and rapid communications in synthetic organic chemistry · 2025Article
- Some reflections on a career in science and a note of thanks to the contributors of this Special Issue.Biophysical reviews · 2022Article
- Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor.ACS omega · 2020Article
- Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism.Protein engineering, design & selection : PEDS · 2019Article
- Explicit Characterization of the Free Energy Landscape of pKID-KIX Coupled Folding and Binding.ACS central science · 2019Article
- Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review.Computational and structural biotechnology journal · 2019Review
- pKID Binds to KIX via an Unstructured Transition State with Nonnative Interactions.Biophysical journal · 2017Article
- Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling.Journal of computational chemistry · 2016Article
- Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH.Biophysical journal · 2016Article
- Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.The Biochemical journal · 2016Review
- Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.Biophysical reviews · 2016Review
- Prepaying the entropic cost for allosteric regulation in KIX.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The phosphorylated kinase-inducible activation domain (pKID) adopts a helix-loop-helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, αA and αB. We performed all-atom multicanonical molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensembles. Although the unbound pKID was disordered overall, αA and αB exhibited a nascent helix propensity; the propensity of αA was stronger than that of αB, which agrees with experimental results. In the bound state, the free-energy landscape of αB involved two low free-energy fractions: native-like and non-native fractions. This result suggests that αB folds according to the induced-fit mechanism. The αB-helix direction was well aligned as in the NMR complex structure, although the αA helix exhibited high flexibility. These results also agree quantitatively with experimental observations. We have detected that the αB helix can bind to another site of KIX, to which another protein MLL also binds with the adopting helix. Consequently, MLL can facilitate pKID binding to the pKID-binding site by blocking the MLL-binding site. This also supports experimentally obtained results.
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