From Protein Structure to Function with Bioinformatics.pdf

4 Membrane Protein Structure Prediction 93Fig. 4.1 (a) Bacteriorhodopsin from Halobacterium salinarium, a seven transmembrane helixG-protein coupled receptor (GPCR), flanked by lipid bilayer. It acts as a proton pump, usingcaptured light energy to move protons across the membrane out of the cell. PDB code 1py6. OtherGPCRs include halorhodopsin, a light-driven chloride pump, PDB code 1e12. (b) Cartoon representationof bacteriorhodopsin topologyembedded in the membrane, each of which is hydrogen-bonded to the strandsimmediately before and after it in the primary sequence, connected by extramembranousloops. The beta strands contain alternating polar and hydrophobic aminoacids so that the hydrophobic residues are orientated toward the exterior where theycontact the surrounding lipids, and hydrophilic residues are oriented toward theinterior pore. All beta-barrel transmembrane proteins have simple up-and-downtopology, which may reflect their common evolutionary origin and similar foldingmechanism. Beta-barrel TM proteins commonly form porins, 16 or 18-strandedbeta-barrels, which assemble into water-filled channels that allow the passive diffusionof nutrients and waste products across the outer membrane (Fig. 4.2). Larger,potentially toxic compounds are prevented from entering the cell by the restrictivesize of the channel. Porin-like barrel structures account for as many as 2–3% of thegenes in Gram-negative bacteria (Wimley 2003).