ArticleJournal of computational chemistry2016
Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling.
Article in Journal of computational chemistry, 2016. 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.
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- Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday.Biophysical reviews · 2022Article
- Conformational Changes of Glutamine 5'-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations.Frontiers in chemistry · 2021Article
- Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties.Informatics in medicine unlocked · 2021Article
- Pyrazinamide resistance of novel mutations inRSC advances · 2020Article
- myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling.Biophysics and physicobiology · 2020Article
- Mechanistic Insights into the Effect of Ligands on Structural Stability and Selectivity of Sulfotransferase 2A1 (SULT2A1).ACS omega · 2019Article
- Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance.Scientific reports · 2019Article
- Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review.Computational and structural biotechnology journal · 2019Review
- Insight into novel clinical mutants of RpsA-S324F, E325K, and G341R ofComputational and structural biotechnology journal · 2018Article
- Adaptive Steered Molecular Dynamics Combined With Protein Structure Networks Revealing the Mechanism of Y68I/G109P Mutations That Enhance the Catalytic Activity of D-psicose 3-Epimerase FromFrontiers in chemistry · 2018Article
- Understanding the differences of the ligand binding/unbinding pathways between phosphorylated and non-phosphorylated ARH1 using molecular dynamics simulations.Scientific reports · 2017Article
- Variation of free-energy landscape of the p53 C-terminal domain induced by acetylation: Enhanced conformational sampling.Journal of computational chemistry · 2016Article
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9 authors.
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Abstract
The C-terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non-neutralized. Because of the flexibility of the unbound CTD, a free-energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized. The fragments were expressed by an all-atom model and were immersed in an explicit solvent. The acetylation and charge-neutralization varied FEL greatly, which might be convenient to exert a hub property. The acetylation slightly enhanced alpha-helix structures that are more compact than sheet/loop conformations. The charge-neutralization produced hairpins. Additionally, circular dichroism experiments confirmed the computational results. We propose possible binding mechanisms of CTD to partners by investigating FEL. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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