Architecture of Membrane Proteins

Abstract

Biological membranes are exquisite multifunctional structures that border all living cells and intracellular organelles in virtually all types of organisms from bacteria to man. In addition to the fundamental phospholipid unit, present in most bacteria and eukaryotes, and the dominant ether lipids present in many archaea, other lipids, proteins, carbohydrates and sterols contribute to the lipid bilayer. Most important, from a functional perspective, are the specialised membrane proteins of diverse functions that are embedded in or associated with membranes. Membrane architectural features and the methods used to gain relevant information are presented. Integral, peripheral and lipid‐anchored membrane proteins as well as the inhomogeneity of membranes are considered from structural, functional and evolutionary standpoints. Transport proteins that provide avenues of communication and material exchange, and toxins that target membranes and kill cells by creating transmembrane pores, are discussed in some detail, especially from mechanistic points of view.

Key Concepts:

  • Architecture of membranes and membrane proteins.

  • Functions of transmembrane proteins.

  • Membrane microcompartmentalisation.

  • Protein pore‐forming toxins.

  • Lipid rafts and caveolae.

Keywords: lipid bilayer; transporters; pore‐forming toxins; membrane lipid rafts; caveolae

Figure 1.

Model of the cellular lipid bilayer membrane, associated toxins and membrane proteins (MPs) and organisational domains. The building block of the lipid bilayer is a phospholipid, consisting of a phosphate group (P), a glycerol backbone (G) and hydrophobic saturated or unsatured fatty acid carbon chains. Some phospholipids may be glycosylated, forming glycolipids. Other types of lipids, like sphingolipids, are also part of the cell membrane. Integral MPs may be nonspanning, single‐ or multispanning and may consist of α‐helices or β‐strands. α/β‐pore‐forming toxins (PFTs) insert into the cell membrane, usually to become integral membrane channels. Without spanning the membrane, peripheral MPs interact noncovalently with the cell membrane and integral MPs, whereas lipid‐anchored MPs form covalent bonds with lipids. Finally, cell membranes consist of heterogeneous domains known as membrane lipid rafts (planar) and caveolae (invaginations), which have been shown to play important roles in multiple cellular processes.

Figure 2.

Crystal structure of XylE (PDB 4GBY; Sun et al., ), a member of the MFS (TC# 2.A.1). XylE is a 67‐kDa d‐xylose–proton symporter found in E. coli that consists of 12 transmembrane segments (TMSs). The 12 TMSs are grouped together in four 3 α‐helical bundles, consistent with other MFS TMS groupings. Both N‐ and C‐termini are located on the intracellular side, and unlike other MFS transporters, XylE contains an intracellular 4 helix domain that contains residues highly conserved in GLUT1‐4, which are sugar transporters found abundantly in humans. This domain interacts with the cytosol via extensive polar interactions. The d‐xylose ligand is found bound in the centre of the transmembrane domain, blocked from the intracellular side, yet accessible by solvents via a small, extracellular channel.

Figure 3.

Crystal structure of the A2A receptor (PDB 2YDV; Lebon et al., ), a GPCR (TC# 9.A.14). A2A is a 45‐kDa eukaryotic protein that binds adenosine or noradrenaline and is found in the basal ganglia, vasculature, T‐lymphocytes and platelets. The 7 TMS α‐helical bundle found universally across GPCRs is clearly visible, although the ligand‐binding pocket, nestled deep within the bundle, is not readily apparent. Within the binding pocket, bound adenosine and noradrenaline interact with residues in helix 7 and helix 3 via polar interactions and nonpolar interactions, respectively. Inward motion from helices 3, 5 and 7 causes contraction of the binding pocket, locking the ligand in place.

Figure 4.

Representative examples of α‐ and β‐PFTs. (a) Colicin B (PDB 1RH1; Hilsenbeck et al., ), of the channel‐forming colicin family (TC# 1.C.1) of the α‐PFT class, is a 55 kDa PFT, possessing poorly delineated N‐terminal translocation and receptor‐binding domains which are connected to a C‐terminal PF domain by a 74 Å helix. The C‐terminal PF domain consists of 10 α‐helices, of which only hydrophobic helices 8 and 9 participate in formation of a hairpin membrane‐spanning domain. Colicin B performs its cytotoxic function without multimerisation. (b) Proaerolysin (PDB 3C0N; Parker et al., ), of the Aerolysin Channel‐forming Toxin Family (TC# 1.C.4) of the β‐PFT class, is a 52 kDa protein which undergoes proteolytic activation to generate the functional 47 kDa aerolysin protein, which is yet to be crystallised. Following activation, aerolysin forms heptamers before inserting itself into the membrane and forming a large pore that destroys the permeability barrier.

Figure 5.

Detailed organisation of lipid rafts and caveolae membranes. (a) Lipid rafts: the liquid‐ordered phase is dramatically enriched in cholesterol (shown in yellow) and exoplasmic oriented sphingolipids (sphingomyelin and glycosphingolipids) (shown in orange). In contrast, the liquid‐disordered phase is composed essentially of phospholipids such as phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine (shown in green). (b) Caveolae: the liquid‐ordered and liquid‐disordered phases are illustrated as in panel (a). On integration of the caveolin‐1 protein, liquid‐ordered domains form small flask‐shaped invaginations called caveolae. Caveolin‐1 monomers assemble into discrete homooligomers (shown as dimers for simplicity) containing ∼4 to 16 individual caveolin molecules. Adjacent homooligomers are thought to be packed side by side within caveolae membranes, thereby providing the structural meshwork for caveolae invagination. Caveolin‐1 oligomers are red and the caveolin‐1 oligomerisation domain is shown in blue. Reproduced with permission from Razani et al., . © American Society for Pharmacology and Experimental Therapeutics.

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Shlykov, Maksim A, Yee, Daniel C, and Saier, Milton H(Sep 2013) Architecture of Membrane Proteins. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0004103]