A comprehensive comparison of transmembrane domains reveals organelle-specific properties.
Bottom Line: The various membranes of eukaryotic cells differ in composition, but it is at present unclear if this results in differences in physical properties.In addition, TMDs from post-ER organelles show striking asymmetries in amino acid compositions across the bilayer that is linked to residue size and varies between organelles.The pervasive presence of organelle-specific features among the TMDs of a particular organelle has implications for TMD prediction, regulation of protein activity by location, and sorting of proteins and lipids in the secretory pathway.
Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.Show MeSH
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Mentions: To quantify trends in hydropathy, the mean hydrophobicity over all the sequences in each dataset was plotted relative to residue position. As noted above, the hydropathy plots for the fungal proteins from the early Golgi and late Golgi were found to be very similar, and so the datasets were combined to form a “Golgi” set (Figure S1 available online). For both fungi and vertebrates, the plasma membrane TMDs were on average hydrophobic for a greater length than those of the ER and Golgi (Figures 3A and 3B). For fungi the hydrophobicity values of the Golgi and plasma membrane TMDs were highly significantly different between positions 16 and 24 (p < 1 × 10−10 from two-sample independent t test, Figure S2A). For vertebrates, the difference between Golgi and plasma membrane TMDs was highly significant for positions 17 to 23 (Figure S2A).
Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.