The Transmembrane Domain

The transmembrane domains have different functions, according to the type of receptor. For ligand-controlled receptors, the function of the transmembrane domain is to pass the signal on to the cytosolic domain of the receptor. For ligand-controlled ion channels, the transmembrane portion forms an ion pore that allows selective and regulated passage of ions. 

The transmembrane receptors span the ca. 5 nm thick phospholipid bilayer of the cell membrane with structural portions known as transmembrane elements. The inner of a phospholipid layer is hydrophobic and, correspondingly, the surface of the structural elements that come into contact with the inner of the phospholipid double layer also has hydrophobic character. 

The transmembrane domain may be made up of one or many transmembrane elements. Generally, the transmembrane elements include 20-30 mostly hydrophobic amino acids. At the interface with aqueous medium, we often find hydrophilic amino acids in contact with the polar head groups of the phospholipids. In addition, they mediate distinct fixing of the transmembrane section in the phospholipid double layer. A sequence of 20-30 hydrophobic amino acids is seen as characteristic for membrane-spanning elements. This property is used in analysis of protein sequences, to predict possible transmembrane elements in so-called hydropathy plots . 

High-resolution structural information about the transmembrane elements of transmembrane receptors could recently be obtained on the example of rhodopsin, the light-activated G protein coupled receptor of the vision process (Fig. 5.3). These data, together with earlier data on the structures of other transmembrane proteins (e.g., bacteriorhodopsin), have confirmed that a-helices are the principal structural building blocks of the transmembrane elements of membrane receptors. The transmembrane helices are composed of 20 - 30 hydrophobic amino acids with some polar 

The transmembrane domain may consist of one or several transmembrane elements (see also Fig. 5.2). In the latter case, these are arranged in the form of bundles, as shown in Fig. 5.3 for rhodopsin. In the case of ion channels, in which several subunits are involved in the formation of the transmembrane domain, prediction of the structure of the membrane portion is very difficult. The different transmembrane elements are no longer equivalent in these cases. Part of the element is involved in formation of the inner wall of the pore other structural elements form the surface to the hydro-phobic inner of the phospholipid bilayer. It is evident that the polarity requirements for the amino acid side chains vary according to the position of the transmembrane elements (see Chapter 16). 

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FIGURE 10.32 The structures of (a) S-eudotoxiu (two views) from Bacillus thuringiensis and (b) diphtheria toxin from Cmynehacterium diphtheriae. Each of these toxins possesses a bundle of a-hehces which is presumed to form the trausmembraue channel when the toxin Is Inserted across the host membrane. In S-endotoxln, helix 5 (white) Is surrounded by 6 helices (red) In a 7-hellx bundle. In diphtheria toxin, three hydrophobic helices (white) lie at the center of the transmembrane domain (red). 

FIGURE 21.11 The structure of UQ-cyt c reductase, also known as the cytochrome hci complex. The alpha helices of cytochrome b (pale green) define the transmembrane domain of the protein. The bottom of the structure as shown extends approximately 75 A into the mitochondrial matrix, and die top of the structure as shown extends about 38 A into the intermembrane space. (Photograph kindly provided by Di Xia and Johann Deismhofer [From Xia, D., Yn, C.-A., Kim, H., Xia,J-Z., Kachnrin, A. M., Zhang, L., Yn,... 

The exchange of cations for protons occurs through the transmembrane domain, whereas regulation (fine-tuning) of the exchanger is largely exerted by the C-terminal domain. NHEs are believed to form homodimers in the membrane. 

The nAChR is cylindrical with a mean diameter of about 6.5 nm (Fig. 1). All five rod-shaped subunits span the membrane. The receptor protrades by <6 nm on the synaptic side of the membrane and by <2 nm on the cytosolic side [2]. The pore of the channel is along its symmetry axis and includes an extracellular entrance domain, a transmembrane domain and a cytosolic entrance domain. The diameter of the extracellular entrance domain is <2.5 nm and it becomes narrower at the transmembrane domain. The... 

Figure 3.4 Transmembrane topology of a 7-TM domain G-protein receptor such as the P-adrenoceptor. Agonist binding is predicted to be within the transmembrane domains. The extracellular structure is stabilised by the disulphide bond joining the first and second extracellular loop. The third intracellular loop is the main site of G-protein interaction while the third intracellular loop and carboxy tail are targets for phosphorylation by kinases responsible for initiating receptor desensitisation...

Ligand binding outside the transmembrane domains on cell surface... 

While the agonist binding domain is thought to be within the transmembrane domains for the monoamine and nucleotide receptors, neuropeptides are thought to bind close to the membrane surface on the extracellular domains of the receptor. It is still not clear whether non-peptide antagonists bind at the same or a different site on the receptor. 

These receptors are unlike the well-characterised rhodopsin-like family in that they have a large extracellular N-terminus and hormone binding seems to be dominated by this domain rather than the transmembrane domains. Receptors in this class include... 

In the Ca-ATPase from sarcoplasmic reticulum, oligonucleotide-directed, site-specific mutagenesis has been applied to identify amino acids involved in Ca binding. Mutation of 30 glutamate and aspartate residues, singly or in groups, in a stalk sector near the transmembrane domain has little effect on Ca " -transport. In contrast mutations to Glu ° , Glu, Asn , Thr , Asp ° or Glu ° resulted in loss... 

Combining structural and biochemical information, MacLennan and his colleagues [8,11,42,45,48,87] constructed a hypothetical model of the tertiary structure of Ca " -ATPase that has interesting mechanistic implications (Fig. 2). The structure was divided into three major parts, designated as the cytoplasmic headpiece, the stalk domain and the transmembrane domain each was assigned distinct functional... 

Fig. 1. Diagrammatic representation of CCR7 showing the arrangement of the transmembrane domains, the intra- and extracellular loops, and the amino-terminus and carboxy-terminus.

Compared to US and its subsequent variants, the ABF method obviates the a priori knowledge of the free energy surface. As a result, exploration of is only driven by the self-diffusion properties of the system. It should be clearly understood, however, that while the ABF helps progression along the order parameter, the method s efficiency depends on the (possibly slow) relaxation of the collective degrees of freedom orthogonal to . This explains the considerable simulation time required to model the dimerization of the transmembrane domain of glycophorin A in a simplified membrane [54],... 

Fig. 20.13. Potential H-bonding energy, released upon interaction with the transmembrane domains of P-gp (in arbitrary energy units, EU) for progesterone (1), propranolol (2), amitriptyline (3), diltiazem (4), amiodarone (5), colchicine (7), gramicidin S (8), daunorubicin (9), vinblastine (10), cyclosporin A, in comparison with verapamil...

The transmembrane domain in the RPTK is a hydrophobic segment of 22-26 amino acids inserted in the cell membrane. It is flanked by a proline-rich region in the N-terminus and a cluster of basic amino acids in the C-ter-minus. This combination of structures secures the transmembrane domain within the lipid bilayer. There is a low degree of homology in the transmembrane domain, even between two closely related RPTKs, suggesting that the primary sequence contains little information for signal transduction. 

Slow-channel syndrome. Abnormally long-lived openings of mutant AChR channels result in prolonged endplate currents and potentials, which in turn elicit one or more repetitive muscle action potentials of lower amplitude that decrement. The morphologic consequences stem from prolonged activation of the AChR channel that causes cationic overload of the postsynaptic region - the endplate myopathy - with Ca2+ accumulation, destruction of the junctional folds, nuclear apoptosis, and vacuolar degeneration of the terminal. Some slow-channel mutations in the transmembrane domain of the AChR render the channel leaky by stabilization of the open state, which is populated even in the absence of ACh. Curiously, some slow-channel mutants can be opened by choline even at the concentrations that are normally present in serum. Quinidine, an open-channel blocker of the AchR, is used for therapy. 

Monnot, C., Bihoreau, C., Conchon, S., Cumow, K. M., Corvol, P., and Clauser, E. (1996) Polar residues in the transmembrane domains of the type 1 angiotensin II receptor are required for binding and coupling. Reconstitution of the binding site by co-expression of two deficient mutants. J. Biol. Chem. 271,1507-1513. 

Repacking of the transmembrane domains of P-glycoprotein during the transport ATPase cycle. EMBO Journal, 20, 5615-5625. 

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