Cytoplasmic loop domains

Most ZIP proteins have eight predicted transmembrane domains (Figure 7.10) and similar predicted topologies with both the N- and C-termini located on the extracytoplasmic face of the membrane with a His-rich domain frequently in the long cytoplasmic loop between transmembrane domains 3 and 4. In contrast, most CDF transporters have six predicted transmembrane domains and a His-rich domain in the loop between domains 4 and 5, but here the N- and C-termini are on the cytoplasmic side of the membrane. 

Silvanovich, A., Li, M-G., Serr, M., Mische, S., and Hays, T. S. (2003). The third P-loop domain in cytoplasmic dynein heavy chain is essential for dynein motor function and ATP-sensitive microtubule binding. Mol. Biol. Cell 14, 1355-1365. 

Fig. 1. Predicted membrane-spanning topology for mechanosensitive channels found in eukaryotes (TRPV, K2P, and DEG/ENaC channels) and bacteria (MscL and MscS). In addition to the transmembrane helices (represented as cylinders), other motifs present in these channels are designated as follows. The TRPV channels contain several cytoplasmic ankyrin domains (A) at the N terminus, and one pore-forming loop (P). K2P channels have two pore-forming loops and a self-interaction domain (SID) through which dimers are generated. DEG/ENaC sodium channels have a single pore-forming loop and three cysteine-rich domains (CRDs).

RND is a large ubiquitous superfamiiy of transporters with representations in all domains of life. Composed typicahy of about 1000 amino-acid residues, they are arranged as 12 transmembrane hehces proteins with two large hydrophilic extra-cytoplasmic loops between hehces 1 and 2 and hehces 7 and 8. It has been postulated that these proteins developed from an internal gene duplication event. The members of the RND family are also secondary active transporters that catalyze the proton-motive-force driven transport of a range of substrates, including hydrophobic drugs, bile salts, fatty acids, heavy metals, and more (22). 

The formation of a fourth cytoplasmic loop by palmitoylation of cysteine residues in the C-terminus has been shown to be crucial in G-protein coupling for some receptor subtypes. Yeagle et al constructed a polypeptide containing 43 amino acid residues of the carboxyl terminal domain of bovine rhodopsin and performed a similar study as previously described. The representative stmeture of the carboxyl terminal shows an organisation of the stmeture into three subdomains. The first subdomain, the N-terminal domain of this peptide, forms an a-helix containing 7 or 8 amino acids, which is believed to be a continuation of helix 7. The second subdomain contains the two cysteine residues, which are situated near the location of a putative lipid bilayer and therefore are accessible to palmitoylation. With the location of the cysteine residues near to the putative lipid bilayer, a loop is formed between the cysteine residues and helix 7. The third subdomain is partially composed of an antiparallel P-sheet with the two strands connected by a p-tum. This subdomain appeared to be the most exposed, which makes the phosphorylation sites readily available to rhodopsin kinase . 

Yeagle, P. L., Alderfer, J. L., Albert, A. D. Structure determination of the fourth cytoplasmic loop and carboxyl terminal domain of bovine rhodopsin. Mol. Vis., 1996,2, 12. 

Figure 1.1 Schematic model for the insertion of G-protein-coupled receptors in the plasma membrane. The seven transmembrane domains are shown as cylinders spanning the lipid bilayer. The intra- and extracellular loops are represented by black ribbons. The ligand binding site is formed by the interaction of several transmembrane domains. Coupling to transducing and desensitisation systems involves the cytoplasmic loops. Glycosylation (represented with a Y) of the N-terminus is required for proper insertion of the receptors in the membrane but not for ligand binding. Figure adapted from ref. 6.

---