Transmembrane helical regions

C. Potassium Channel-Binding Neurotoxins. The potassium channel plays an important role in the repolarization process in nerve transmission and is less well known than the sodium channels in the nerve. The The channel is composed of membrane protein and has six transmembrane helical regions. Both the NHz- and COOH-terminal chains are located inside the membrane. The first snake toxin found to bind is dendrotoxin. This toxin is a potent convulsant and facilitates transmitter release by inhibition of voltage-sensitive channels (Weller et al., 1985 Penner et al., 1986 Harvey and Karlsson, 1980 Black... 

Alpha helices that cross membranes are in a hydrophobic environment. Therefore, most of their side chains are hydrophobic. Long regions of hydrophobic residues in the amino acid sequence of a protein that is membrane-bound can therefore be predicted with a high degree of confidence to be transmembrane helices, as will be discussed in Chapter 12. 

Figure 12.9 Schematic diagram of the stmc-ture of a potassium channel viewed perpendicular to the plane of the membrane. The molecule is tetrameric with a hole in the middle that forms the ion pore (purple). Each subunit forms two transmembrane helices, the inner and the outer helix. The pore heJix and loop regions build up the ion pore in combination with the inner helix. (Adapted from S.A. Doyle et al., Science 280 69-77, 1998.)...

The C-terminal transmembrane helix, the inner helix, faces the central pore while the N-terminal helix, the outer helix, faces the lipid membrane. The four inner helices of the molecule are tilted and kinked so that the subunits open like petals of a flower towards the outside of the cell (Figure 12.10). The open petals house the region of the polypeptide chain between the two transmembrane helices. This segment of about 30 residues contains an additional helix, the pore helix, and loop regions which form the outer part of the ion channel. One of these loop regions with its counterparts from the three other subunits forms the narrow selectivity filter that is responsible for ion selectivity. The central and inner parts of the ion channel are lined by residues from the four inner helices. 

In contrast, the transmembrane helices observed in the reaction center are embedded in a hydrophobic surrounding and are built up from continuous regions of predominantly hydrophobic amino acids. To span the lipid bilayer, a minimum of about 20 amino acids are required. In the photosynthetic reaction center these a helices each comprise about 25 to 30 residues, some of which extend outside the hydrophobic part of the membrane. From the amino acid sequences of the polypeptide chains, the regions that comprise the transmembrane helices can be predicted with reasonable confidence. 

Figure 12.23 Hydropathy plots for the polypeptide chains L and M of the reaction center of Rhodobacter sphaeroides. A window of 19 amino acids was used with the hydrophohicity scales of Kyte and Doolittle. The hydropathy index is plotted against the tenth amino acid of the window. The positions of the transmembrane helices as found by subsequent x-ray analysis by the group of G. Feher, La Jolla, California, ate indicated by the green regions.

Like the photosynthetic reaction center and bacteriorhodopsin, the bacterial ion channel also has tilted transmembrane helices, two in each of the subunits of the homotetrameric molecule that has fourfold symmetry. These transmembrane helices line the central and inner parts of the channel but do not contribute to the remarkable 10,000-fold selectivity for K+ ions over Na+ ions. This crucial property of the channel is achieved through the narrow selectivity filter that is formed by loop regions from thefour subunits and lined by main-chain carbonyl oxygen atoms, to which dehydrated K ions bind. 

Aquaporins. Figure 1 (a) The hour-glass model. The scheme depicts the six transmembrane helices (H1-H6), the connecting loops A-E, including the helical parts of loops B ((H)B) and E (E(H)), and the conserved NPA (Asn-Pro-Ala) motif of canonical aquaporins. (b) Structure of the conserved NPA motif region, flanked by the indicated helices, (c) Crystallographic structure of AQP1 tetramer. The four water pores in atetramer are indicated [1]. 

The luminal loop (residues 79-87) between transmembrane helices Mj and M2 was proposed by MacLennan et al, [42] to serve as the low-affinity Ca " binding site. This proposal was tested by mutation of EEGEE83 into either QQGQQ or AAGAA. Neither of these mutations affected either Ca transport or Ca affinity. Therefore the Ca binding sites are not likely to involve the region of the molecule between... 

The GPCR C-terminal region, with or without a coiled-coil motif, has been implicated in the heterodimerization process of GABAb(1)-GABAb(2) (78,80), as well as in the homodimerization of 5-opioid receptor (120). However, the possibility cannot be ruled out that the indirect evidence for the involvement of the C-terminal domain results from changes produced by the deletion of the C-terminal tail, that alters the conformation of the receptors and causes decreased interactions between transmembrane helices and oligomer disruption. 

Bovine heart cytochrome bci (PDB 1BE3 and PDB IBGY) as studied by Iwata et al. exists as a dimer in the asymmetric unit cell. Each monomer consists of 11 different polypeptide subunits (SU) with a total of -2165 amino acid residues and a molecular mass of -240 kDa. The protein subunits of the complex occupy three separate regions (1) the intermembrane space (p side) occupied by cytochrome Ci (subunit 4, SU4), the iron-sulfur protein (ISP, SU5) and subunit 8 (2) the transmembrane region occupied by cytochrome b (SU3), the transmembrane helices of cytochrome Ci and the ISP, and subunits 7,10, and 11 and (3) the matrix space (n side) occupied by two large core proteins (subunits 1 and 2) as well as subunits 6 and 9. Subunit 8 is often called the hinge protein and is thought to be essential for proper complex formation between cytochrome c (the exit point for some bci complex electrons) and... 

The Na+/proline transporter of E. coli (PutP) is an integral membrane protein that is proposed to contain 13 transmembrane helices.85 Four-pulse DEER measurements found distances of 48,22, and 18 A for three doubly spin-labelled variants.The 48 A distance confirmed that those two labels were on opposite sides of the membrane. The large distance distribution widths that were observed in the pair functions reveal the substantial flexibility of the loop regions to which the spin labels were attached. 

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