ArticleProtein science : a publication of the Protein Society2022
Spatial arrangement of proteins in planar and curved membranes by PPM 3.0.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers.
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217 citing papers in PubMed, 328 citations in OpenAlex.
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- PepMCP: a graph-based membrane contact probability predictor for membrane-lytic antimicrobial peptides.Bioinformatics (Oxford, England) · 2026Article
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157 more citing papers are in PubMed but not listed here.
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Cellular protrusions, invaginations, and many intracellular organelles have strongly curved membrane regions. Transmembrane and peripheral membrane proteins that induce, sense, or stabilize such regions cannot be properly fitted into a single flat bilayer. To treat such proteins, we developed a new method and a web tool, PPM 3.0, for positioning proteins in curved or planar, single or multiple membranes. This method determines the energetically optimal spatial position, the hydrophobic thickness, and the radius of intrinsic curvature of a membrane-deforming protein structure by arranging it in a single or several sphere-shaped or planar membrane sections. In addition, it can define the lipid-embedded regions of a protein that simultaneously spans several membranes or determine the optimal position of a peptide in a spherical micelle. The PPM 3.0 web server operates with 17 types of biological membranes and 4 types of artificial bilayers. It is publicly available at https://opm.phar.umich.edu/ppm_server3. PPM 3.0 was applied to identify and characterize arrangements in membranes of 128 proteins with a significant intrinsic curvature, such as BAR domains, annexins, Piezo, and MscS mechanosensitive channels, cation-chloride cotransporters, as well as mitochondrial ATP synthases, calcium uniporters, and TOM complexes. These proteins form large complexes that are mainly localized in mitochondria, plasma membranes, and endosomes. Structures of bacterial drug efflux pumps, AcrAB-TolC, MexAB-OrpM, and MacAB-TolC, were positioned in both membranes of the bacterial cell envelop, while structures of multimeric gap-junction channels were arranged in two opposed cellular membranes.
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