ArticleBiophysical journal2011
Direct observations of shifts in the β-sheet register of a protein-peptide complex using explicit solvent simulations.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 17 citations in OpenAlex.
- Making invisible excited-state structures of pro-interleukin-18 visible by combining NMR and machine learning.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Gating residues govern ligand unbinding kinetics from the buried cavity in HIF-2α PAS-B.Protein science : a publication of the Protein Society · 2024Article
- Volume and compressibility differences between protein conformations revealed by high-pressure NMR.Biophysical journal · 2021Article
- Fragile protein folds: Sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations.Magnetic resonance (Gottingen, Germany) · 2021Article
- Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations.Chemical science · 2019Article
- Large enhancement of response times of a protein conformational switch by computational design.Nature communications · 2018Article
- A unique binding mode of the eukaryotic translation initiation factor 4E for guiding the design of novel peptide inhibitors.Protein science : a publication of the Protein Society · 2015Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Using explicit solvent molecular dynamics simulations, we were able to obtain direct observations of shifts in the hydrogen-bonding register of an intermolecular β-sheet protein-peptide complex. The β-sheet is formed between the FHA domain of cancer marker protein Ki67 (Ki67FHA) and a peptide fragment of the hNIFK signaling protein. Potential encounter complexes of the Ki67FHA receptor and hNIFK peptide are misregistered states of the β-sheet. Rearrangements of one of these misregistered states to the native state were captured in three independent simulations. All three rearrangements occurred by a common mechanism: an aromatic residue of the peptide (F263) anchors into a transient hydrophobic pocket of the receptor to facilitate the formation of native hydrogen bonds. To our knowledge, these simulations provide the first atomically detailed visualizations of a mechanism by which nature might correct for errors in the alignment of intermolecular β-sheets.
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