Trimer structural model

FIGURE 5-1 3 (A, B) Structure of a glutamate transporter. This bacterial glutamate transporter provides the first high-resolution model of a glutamate transporter [88]. The X-ray data indicate a trimeric structure. (A) A view of the trimer extracellularly and perpendicular to the bilayer. 

In Fig. 21, the schematic representations of the final structure model are shown according to the structure parameters determined by the Rietveld analysis. As shown in Fig. 21a, the Sc3 trimer does not reside at the center of the carbon cage but is close to the triply fused hexagonal part (not to the center of a hexagon at the other end) along the C3 axis. The nearest distance between the center of the Sc3 trimer and carbon atoms and the nearest neighbor Sc-C distance obtained from the MEM map are 3.4(1) and 2.52(2) A, respectively. Furthermore, it shows that the Sc trimer is at rest in the cage even at room temperature. 

The subject of energy transfer in phycobilisomes and their sub-structures already has a large literature (see Ref. 65 for a review), mostly beyond the scope of this chapter. However, two of these sub-structures - trimeric C-phycocyanin from the thermophilic cyanobacterium Mastigocladus laminosus and hexameric C-phycocyanin from the cyanobacterium Agmenellum quadruplicatum-have very recently become respectively the third and fourth photosynthetic pigment-protein complexes for which structural models based on single-crystal X-ray diffraction near atomic resolution are now available (Refs. 66,67 and Chapter 11). Since these are presently the only such complexes, in addition to the two already discussed (Sections 5 and 6), it seems appropriate to conclude this review of exciton effects with some brief remarks on these C-phycocyanin structures. 

Ab initio and density functional theory (DET) methods have been exploited to determine the structures and the interaction energies of 2/7-isoxazol-5-one B, and its dimer and trimer structures in the gas phase. For the cyclic trimer, the computed structural parameters resulted in excellent agreement with the X-ray determination of the supramolecular aggregate of 4-(2-methoxybenzyl)-3-phenyl-4//-isoxazol-5-one, involving very strong intermolecular H-bonds of the NH tautomeric form, interpreted in terms of the RAHB (resonance-assisted hydrogen bond) model (see Section 4.03.3.1) <2002HCA2364>. 

Nakatsubo, R, and Higuchi, T. (1980) Synthesis of trimeric lignin model compound composed of phenylcoumaran and b-O-4 structures. Mokuzai Gakkaishi 26(1), 31-36. 

Ralph, J., Rde, R. M., and Wilkins, A. L. (1986) Synthesis of trimeric lignin model compounds composed of (3-aryl ether and phenylcoumaran structures. Holzforschung 40(1), 23-30. 

Namba, H., Nakatsubo, F., and Higuchi, T. (1980) Synthesis of trimeric lignin model compound composed of b-O-4 and b-1 structures. Mokuzai Gakkaishi 26(6), 426-431. Lundquist, K., and Miksche, G. E. (1965) Nachweis eines neuen Verkniipfungsprinzips von Guajacylpropaneinheiten im Fichtenlignin. Tetrahedron Lett. (25), 2131-2136. 

A structural model of the trimeric G protein and the receptor is presented in Fig. 5.19. In this model, the known structures of the ground state of rhodopsin and the structures of the transducin Gta- GDP (fly) complex have been modeled, taking into account the location of the lipid anchors and the known interaction sites between the receptor and the G protein ( Hamm, 2001). 

A FIGURE 5-14 Structural model of one subunit of OmpX, a porin found in the E. coli outer membrane. All porins are trimeric transmembrane proteins. Each subunit Is barrel shaped, with p strands forming the wall and a transmembrane pore In the center. A band of aliphatic (noncycllc) side chains (yellow) and a border of aromatic (ring-contalning) side chains (red) position the protein In the bIlayer. [After G. E. Schulz, 2000, Curr. Opin. Struc. Biol. 10 443.]... 

Figure 2.1 The basic steps of macromolecular crystal structure solving are illustrated with respect to the enzyme, PNP MW 30000x3 D. (a) A crystal of human PNP space group R32. (b) Monochromatic oscillation diffraction photograph recorded at the Daresbury SRS resolution limit of outermost diffraction spots =3 A. (c) Electron density map, calculated at 6 A resolution, viewed down the hexagonal c axis. The diameter of the central solvent channel is =130A. Six trimers are visible. (d) A portion of the 3 A electron density map with fitted molecular model. (e) The PNP trimer molecular model, (f) The PNP trimer with bound inhibitor the protein here is represented in ribbon format for a-helix and ft sheet (see chapter 3 for details of macromolecular structure). Based on Ealick et al (1990). These figures kindly supplied by Dr S. Ealick and reproduced with permission.

Fig. 13. Segment of the LHCIIb structural model to show the close proximity between chlorophylls. Shown are regions containing Chi b2 and Chi a2, lutein (L ) and a portion of the A-helix, fortwo associated LHCIIb trimers. The distance between Chi a2 and Chi b2 is 4.06 A.

The characterization of pMMO has led to three different models of the metal center(s) discussed in Lieberman and Rosenzweig. As the crystal structure determination of pMMO from Methylococcus capsulatus (Bath) has established the nature of the metal sites details on these different models are not provided here. The pMMO structure shows that three copies each of the pmoA, pmoB, and pmoC subunits form a cylindrical trimer approximately 105 A long and approximately 90 A in diameter. A soluble region composed mainly of six /3-barrel structures, two from each protomer, extends approximately 45 A away from the membrane and is supported by 42 transmembrane (TM) helices, 14 from each protomer. A hole is formed in the center of the trimer. The trimeric structure of pMMO was not anticipated and provides the first experimental evidence for a 1 1 1 subunit ratio. 

As a structural model of the zinc(II)-OH species of carbonic anhydrase. the first mononuclear OH -bound zinc(TI) complex 6 was prepared by mixing zinc(II) ion. the ligand, and KOH. and was characterized by x-ray crystal analysis.The zinc(II)-OH complex lb is a cyclic trimer linked by three hydrogen bonds between each zinc(II)-bound hydroxide group, as shown by x-ray crystal studyP However, in aqueous solution, this trimer dissociates into monomeric zinc(II)-OH species lb. The zinc(II) complex 6 in CHCI3 reacted immediately with CO2, possibly to form a HCOa" complex 7 that ultimately and irreversibly gave a bridging carbonate complex 8. However, quantitative determination of the value for the zinc (II)-bound H2O or of the nucleophilicity of 6 was not reported. The HCOs complex 7 was characterized by IR spectroscopy [1675 and 1302 cm for zinc(n)-bound bicarbonate]. The formation of the bicarbonate com-... 

Possible trimer structure formed from cyclic poly(2-vmylpyridine) [P2VP] and model linear P2VP (L-l-L-3), from Ref. 29. 

Table 15. Structural parameters of the gold-trimer-based models (MTLTT and CHCT) of the Si(lll)- /3xV3 -Au reconstmction obtained from various surface techniques. 2/3 ML honeycomb-based models are excluded. Symbols refer to Fig. 31 [95P2]. ...

Figure 14,4 Structural models of trimeric Ana o 2. Left The sequences of Ana o 2 and its glycinin homologue are aligned with the HX-defined 2B5 and 1F5 epitopes boxed in purple and red, respectively. The denotes aa identity, the indicates aa similarity. Right The epitopes are colored similarly for the trimeric X-ray model (PDB ID 1od5). Reproduced with permission from Ref. [41]. 2011, American Chemical Society. (See insert for color representation of the figure.)...

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