ArticleStructure (London, England : 1993)2012
Structural reorganization triggered by charging of Lys residues in the hydrophobic interior of a protein.
Article in Structure (London, England : 1993), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.Nature communications · 2025Article
- Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.Research square · 2024Article
- Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations.Journal of chemical theory and computation · 2024Article
- Protein pJournal of chemical theory and computation · 2022Article
- De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design.Biodesign research · 2022Article
- Determinants of conductance of a bacterial voltage-gated sodium channel.Biophysical journal · 2021Article
- Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework.Journal of chemical theory and computation · 2021Article
- Switching Protein Conformational Substates by Protonation and Mutation.The journal of physical chemistry. B · 2018Article
- Reservoir pH replica exchange.The Journal of chemical physics · 2018Article
- Origin of pKThe journal of physical chemistry. B · 2017Article
- Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.Biochemistry · 2017Article
- Article
- A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area.BMC bioinformatics · 2016Article
- A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.PLoS computational biology · 2015Article
- Protein stability: computation, sequence statistics, and new experimental methods.Current opinion in structural biology · 2015Review
- Buried ionizable networks are an ancient hallmark of G protein-coupled receptor activation.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Structural and thermodynamic consequences of burial of an artificial ion pair in the hydrophobic interior of a protein.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Protonation states of active-site lysines of penicillin-binding protein 6 from Escherichia coli and the mechanistic implications.Proteins · 2014Article
- Uncovering pH-dependent transient states of proteins with buried ionizable residues.Journal of the American Chemical Society · 2014Article
- Computational simulation strategies for analysis of multisubunit RNA polymerases.Chemical reviews · 2013Review
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7 authors.
Funding
Abstract
Structural consequences of ionization of residues buried in the hydrophobic interior of proteins were examined systematically in 25 proteins with internal Lys residues. Crystal structures showed that the ionizable groups are buried. NMR spectroscopy showed that in 2 of 25 cases studied, the ionization of an internal Lys unfolded the protein globally. In five cases, the internal charge triggered localized changes in structure and dynamics, and in three cases, it promoted partial or local unfolding. Remarkably, in 15 proteins, the ionization of the internal Lys had no detectable structural consequences. Highly stable proteins appear to be inherently capable of withstanding the presence of charge in their hydrophobic interior, without the need for specialized structural adaptations. The extent of structural reorganization paralleled loosely with global thermodynamic stability, suggesting that structure-based pK(a) calculations for buried residues could be improved by calculation of thermodynamic stability and by enhanced conformational sampling.
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