ArticleStructure (London, England : 1993)2012
Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions.
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 46 papers.
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Who cites it
46 citing papers in PubMed.
- Membrane Protein Folding and Biogenesis: Insights from Single-Molecule Force Spectroscopy.Chemical reviews · 2026Review
- Conformational Flexibility of Transmembrane Helices: How it Works and Where it Matters.Chemical reviews · 2026Review
- Capturing Unanticipated Drug Toxicities Using an Ensemble Machine Learning Approach.Research square · 2025Article
- Sequence-dependent scale for translocon-mediated insertion of interfacial helices in membranes.Science advances · 2025Article
- Implicit model to capture electrostatic features of membrane environment.PLoS computational biology · 2024Article
- SARS-CoV-2 Omicron Subvariants Balance Host Cell Membrane, Receptor, and Antibody Docking via an Overlapping Target Site.Viruses · 2023Article
- Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes.Membranes · 2022Review
- Article
- How physical forces drive the process of helical membrane protein folding.EMBO reports · 2022Review
- Spatial arrangement of proteins in planar and curved membranes by PPM 3.0.Protein science : a publication of the Protein Society · 2022Article
- Multifaceted membrane binding head of the SARS-CoV-2 spike protein.Current research in structural biology · 2022Article
- Spiers Memorial Lecture: Analysis andFaraday discussions · 2021Article
- BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins.Frontiers in bioinformatics · 2021Article
- How bilayer properties influence membrane protein folding.Protein science : a publication of the Protein Society · 2020Review
- Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding.ACS chemical biology · 2020Article
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- A paradigm of thermal adaptation in penguins and elephants by tuning cold activation in TRPM8.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Review
- A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.Biophysical journal · 2018Article
- Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins.Scientific reports · 2018Article
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Authors and funding
7 authors.
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Abstract
The complex hydrophobic and hydrophilic milieus of membrane-associated proteins pose experimental and theoretical challenges to their understanding. Here, we produce a nonredundant database to compute knowledge-based asymmetric cross-membrane potentials from the per-residue distributions of C(β), C(γ) and functional group atoms. We predict transmembrane and peripherally associated regions from genomic sequence and position peptides and protein structures relative to the bilayer (available at http://www.degradolab.org/ez). The pseudo-energy topological landscapes underscore positional stability and functional mechanisms demonstrated here for antimicrobial peptides, transmembrane proteins, and viral fusion proteins. Moreover, experimental effects of point mutations on the relative ratio changes of dual-topology proteins are quantitatively reproduced. The functional group potential and the membrane-exposed residues display the largest energetic changes enabling to detect native-like structures from decoys. Hence, focusing on the uniqueness of membrane-associated proteins and peptides, we quantitatively parameterize their cross-membrane propensity, thus facilitating structural refinement, characterization, prediction, and design.
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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.