ArticleJournal of the American Chemical Society2016
Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale.
Article in Journal of the American Chemical Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 23 citations in OpenAlex.
- Membrane Protein Folding and Biogenesis: Insights from Single-Molecule Force Spectroscopy.Chemical reviews · 2026Review
- Engineering a HyperstableJournal of the American Chemical Society · 2022Article
- Local Bilayer Hydrophobicity Modulates Membrane Protein Stability.Journal of the American Chemical Society · 2021Article
- Comparing Interfacial Trp, Interfacial His and pH Dependence for the Anchoring of Tilted Transmembrane Helical Peptides.Biomolecules · 2020Article
- GeTFEP: A general transfer free energy profile of transmembrane proteins.Protein science : a publication of the Protein Society · 2020Article
- Hydrophobic Characteristic Is Energetically Preferred for Cysteine in a Model Membrane Protein.Biophysical journal · 2019Article
- Salvaging the Thermodynamic Destabilization of Interface Histidine in Transmembrane β-Barrels.Biochemistry · 2018Article
- Comparative Analysis of TM and Cytoplasmic β-barrel Conformations Using Joint Descriptor.Scientific reports · 2018Article
- Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-Dependent Protease FtsH.Journal of the American Chemical Society · 2018Article
- Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins.Scientific reports · 2018Article
- High-resolution structure prediction ofProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Outer membrane protein folding from an energy landscape perspective.BMC biology · 2017Review
- Outer membrane protein design.Current opinion in structural biology · 2017Review
- Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein.The Journal of biological chemistry · 2017Article
- Engineering a Novel Porin OmpGF Via Strand Replacement from Computational Analysis of Sequence Motif.Biochimica et biophysica acta. Biomembranes · 2017Article
- Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins.Bioinformatics (Oxford, England) · 2017Article
- Challenges in structural approaches to cell modeling.Journal of molecular biology · 2016Review
- Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal.Journal of the American Chemical Society · 2016Article
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4 authors at 1 institution in 1 country.
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Abstract
Knowledge of the transfer free energy of amino acids from aqueous solution to a lipid bilayer is essential for understanding membrane protein folding and for predicting membrane protein structure. Here we report a computational approach that can calculate the folding free energy of the transmembrane region of outer membrane β-barrel proteins (OMPs) by combining an empirical energy function with a reduced discrete state space model. We quantitatively analyzed the transfer free energies of 20 amino acid residues at the center of the lipid bilayer of OmpLA. Our results are in excellent agreement with the experimentally derived hydrophobicity scales. We further exhaustively calculated the transfer free energies of 20 amino acids at all positions in the TM region of OmpLA. We found that the asymmetry of the Gram-negative bacterial outer membrane as well as the TM residues of an OMP determine its functional fold in vivo. Our results suggest that the folding process of an OMP is driven by the lipid-facing residues in its hydrophobic core, and its NC-IN topology is determined by the differential stabilities of OMPs in the asymmetrical outer membrane. The folding free energy is further reduced by lipid A and assisted by general depth-dependent cooperativities that exist between polar and ionizable residues. Moreover, context-dependency of transfer free energies at specific positions in OmpLA predict regions important for protein function as well as structural anomalies. Our computational approach is fast, efficient and applicable to any OMP.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.