Domain III

Gether U, Lin S, Ghanouni P, Ballesteros JA, Weinstein H, Kobilka BK. Agonists induce conformational changes in transmembrane domains III and VI of the beta2 adrenoceptor. EMBO J 1997 16(22) 6737-6747. 

Figure 5.11 Individual transferrin receptor domains. Ribbon diagrams for domain I, the protease-like domain (a) domain II, the apical domain (b) and domain III, the helical domain (c). Secondary structure elements are labelled and are referred to in the text first with respect to the domain number, then with respect to the linear order of the elements within the domain. For example aI-3 refers to the third helix in the first domain. In (a), the two grey spheres indicate the positions that would be occupied by Zn2+ in an authentic protease. Reprinted with permission from Lawrence et ah, 1999. Copyright (1999) American Association for the Advancement of Science.

Holst, B., Elling, C. E., and Schwartz, T. W. (2000) Partial agonism through a zinc-ion switch constructed between transmembrane domains III and VII in the tachykinin NK(1) receptor. Mol. Pharmacol. 58, 263-270. 

Ponce, J., Biton, B Benavides, J., Avenet, P, and Aragon, C. (2000) Transmembrane domain III plays an important role in ion binding and permeation in the glycine transporter GLYT2. J. Biol. Chem. 275, 13856-13862. 

Several block copolymer systems have shown only domains I and III upon self-nucleation. This behavior is observed in confined crystallizable blocks as PEO in purified E24EP57EO1969 [29]. Crystallization takes place for the PEO block at - 27 °C after some weak nucleating effect of the interphase. Domain II is absent and self-nucleation clearly starts at Ts = 56 °C when annealed crystals are already present, i.e., in domain III (Fig. 17b). The absence of domain II is a direct consequence of the extremely high... 

In those cases where the injection of self-nuclei in every MD is most difficult in view of the very large number of MDs, domain III is split into two domains. Evaluation of the self-nucleation of the PE block within S35E15C50219 shows that not only domain II is absent, but upon decreasing Ts, the PE block is annealed before any detectable self-nucleation occurs (Fig. 17c). Therefore two subdomains were defined [98] domain IIIa, where annealing without previous self-nucleation occurs and domain IIIsa> where self-nucleation and annealing are simultaneously observed for Ts < 88 °C. Domain IIIsa would be the exact equivalent to the standard domain III established by Fillon et al. [75]. 

The way in which calcium binding changes the tyrosine fluorescence of calmodulin was initially a controversial issue. In 1980, Seamon(n5) examined the binding of Ca2+ and Mg2+ by NMR and concluded that both Tyr-99 and Tyr-138 were perturbed by the first two calcium ions. Although Tyr-138 was also perturbed by the binding of the fourth calcium, both residues appeared to be associated with high-affinity domains (III and IV). 

The fluorescence of the two tyrosine residues in bovine testes calmodulin was investigated by Pundak and Roche.(123) Upon excitation at 278 nm, a second emission, in addition to tyrosine fluorescence, was observed at 330-355 nm, which they characterized as being due to tyrosinate fluorescence. The tyrosinate fluorescence appeared to be from Tyr-99, which has an anomalously low pKa of about 7 for the phenol side chain. Pundak and Roche(123) reasoned that since tyrosinate emission is apparently not being seen in other species of calmodulin, it is possible that the bovine protein contains a carboxylate side chain in domain III which is amidated in other species. They further argued that the tyrosinate emission from bovine testes calmodulin arises from direct excitation of an ionized tyrosine residue. This tyrosinate fluorescence is discussed in more detail in Section 1.5.2. 

FlC. 8. Interdomain influence on the rate of refolding of Domain III of albumin (residues 377-381), later time points. All conditions were the same as for Fig. 7. 

This protein is fixed in the cell membrane, and is sensitive to voltage. When the cell is sufficiently depo adzed, a conformational change occurs in the protein, allowing flow of Na+ across the membrane. After several milliseconds, an inactivation gate closes, ceasing the flux of Na+. The inactivation gate is likely located on an intracellular loop between domains III and IV. 

Fig. 16.8. Model of inactivation of voltage-gated Na and K channels, a) Inactivation of the Na channel. On inactivation of the Na channel, the loop, which binds domain III and domain IV of the a-subunit, positions itself in the cytoplasmic entrance of the pore and closes it. The indicated hydrophobic amino acids of the connecting loop are involved in the inactivation, b) Inactivation of the K channel. The model assumes that a compact structural part of the C terminus of the P subunit is aligned in the pore and transiently closes it. The inactivating structural part is linked to the pore via a flexible structural element and contains a functionally important leucine residue and a lot of positive charges. According to CatteraU, (1995).

Domain III shares no sequence homology with other known proteins, its structure resembling the C2 domains found in phospholipase C, protein kinase C and synap-totagmin (Rizo and Sudhof, 1998). In addition to linking the Ca2+-binding domain of the molecule to the catalytic domain (domain II), domain III appears to be involved in phospholipids and Ca2+ binding (Tompa et al., 2001). 

Fig. 5. Ribbon diagram of TnC (from Herzberg and James, 1985). The structural C-terminal lobe (consisting of alpha helices E, F, G, and H in domains III and IV) has higher affinity for Ca2+ ions than does the regulatory N-terminal lobe (consisting of alpha helices A, B, C, and D in domains I and II). The D/E linker between the two lobes is often flexible, but when ordered it adopts an a-helical conformation with three turns fully exposed to solvent (see text).

A cancer research group with Abbott Laboratories and Idun Pharmaceuticals studied compounds that bind and inhibit the activity of Bcl-XL, a protein associated with B-cell lymphoma. The team developed compound 7.6 as a moderately active inhibitor of Bcl-XL (Figure 7.9). Compound 7.6, however, lost almost all its inhibitory activity when screened in the presence of human serum. The group determined that 7.6 binds domain III of human serum albumin (HS A-III) with a KD of 0.1 /U.M through two key interactions. The 4-fluorophenyl... 

Balian, R. and Bloch, C. (1972). Distribution of eigenfrequencies for the wave equation in a finite domain III. Eigenfrequency density oscillations, Annals of Physics 69, 76-160. 

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