Architecture of Membrane Proteins

Maksim A Shlykov, University of California at San Diego, San Diego, California, USA
Daniel C Yee, University of California at San Diego, San Diego, California, USA
Milton H Saier, University of California at San Diego, San Diego, California, USA

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.

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.

Slatin SL, Nardi A, Jakes KS, Baty D and Duche D (2002) Translocation of a functional protein by a voltage‐dependent ion channel. Proceedings of the National Academy of Sciences of the USA 99: 1286–1291.