Positioning of proteins in membranes: a computational approach.

摘要: A new computational approach has been developed to determine the spatial arrangement of proteins in membranes by minimizing their transfer energies from water lipid bilayer. The membrane hydrocarbon core was approximated as a planar slab adjustable thickness with decadiene-like interior and interfacial polarity profiles derived published EPR studies. Applicability accuracy method verified for set 24 transmembrane whose orientations have studied spin-labeling, chemical modification, fluorescence, ATR FTIR, NMR, cryo-microscopy, neutron diffraction. Subsequently, optimal rotational translational positions were calculated 109 transmembrane, five integral monotopic 27 peripheral protein complexes known 3D structures. This can reliably distinguish water-soluble based on penetration depths. accuracies hydrophobic thicknesses tilt angles ∼1 2°, respectively, judging deviations different crystal forms same proteins. ranged 21.1 43.8 depending type biological membrane, while respect bilayer normal varied zero symmetric 26° asymmetric Calculated boundaries are located ∼5 lower than phosphates correspond depth parameter spin-labeled residues. Coordinates all be found Orientations Proteins Membranes (OPM) database:http://opm.phar.umich.edu/.