Homodimerization

As Eq. (29) shows, corresponds to the arithmetic mean and to the geometric mean of the homodimeric parameters AA and BB. 

Firefly. Firefly luciferase (EC 1.13.12.7) is a homodimeric enzyme (62 kDa subunit) that has binding sites for firefly luciferin and Mg ATP . Amino acid sequence analysis has iadicated that beetle luciferases evolved from coen2yme A synthetase (206). Firefly bioluminescence is the most efficient bioluminescent reaction known, with Qc reported to be 88% (5), and at 562 nm (56). At low pH and ia the presence of certain metal ions (eg, Pb ", ... 

AH three nitrogenases comprise two separately puriftable component proteins. Each has a specific homodimeric Fe protein. The Fe... 

It is not clear why some organisms have two 14-3-3 isoforms while others have up to 12. Binding 14-3-3 inhibits the plant enzyme nitrate reductase and there appears to be no selectivity between plant 14-3-3 isoforms in fact yeast and human isoforms appear to work equally as well in vitro. The best example where selectivity has been demonstrated is human 14-3-3o. 14-3-3o Preferential homodimerizes with itself and crystallization revealed a structural basis for this isoform s dimerization properties as well as for its specific selectivity for target binding proteins. Here partner specificity is the result of amino acid differences outside of the phosphopeptide-binding cleft. 

Like VEGF165, native VEGF is a heparin-binding homodimeric glycoprotein of 45 kDa. In contrast, VEGFi2i lacks heparin-binding properties. VEGF i89... 

Scheme 94 Total synthesis of the natural compound dehydrohomoancepsenolide (473) through sequential application of chemoselective ruthenium-catalyzed RCM and tungsten-catalyzed alkyne homodimerization [191]...

When a mixture of compounds is treated, cross-dimerization and homodimerization take place statistically, for example ... 

The HIV-1 protease, like other retroviral proteases, is a homodimeric aspartyl protease (see Fig. 1). The active site is formed at the dimer interface, with the two aspartic acids located at the base of the active site. The enzymatic mechanism is thought to be a classic acid-base catalysis involving a water molecule and what is called a push-pull mechanism. The water molecule is thought to transfer a proton to the dyad of the carboxyl groups of the aspartic acids, and then a proton from the dyad is transferred to the peptide bond that is being cleaved. In this mechanism, a tetrahedral intermediate transiently exists, which is nonconvalent and which is mimicked in most of the currently used FDA approved inhibitors. 

Cluster Fx was also identified via its EPR spectral features in the RCI photosystem from green sulfur bacteria 31, 32) and the cluster binding motif was subsequently found in the gene sequence 34 ) of the (single) subunit of the homodimeric reaction center core (for a review, see 54, 55)). Whereas the same sequence motif is present in the RCI from heliobacteria (50), no EPR evidence for the presence of an iron-sulfur cluster related to Fx has been obtained. There are, however, indications from time-resolved optical spectroscopy for the involvement of an Fx-type center in electron transfer through the heliobacterial RC 56). 

Finally, also isolated from D. vulgaris was another homodimeric protein (subunit molecular mass of 27 kDa) named nigerythrin (43). Spectroscopic characterization revealed that this protein is similar to Rr. The function of nigerythrin is also unknown. It should be noted that genes coding for two similar Rr proteins were also found in Arch-aeoglobus fulgidus. 

Figure 5-6. Examples of tertiary structure of proteins. Top The enzyme triose phosphate isomerase. Note the elegant and symmetrical arrangement of alternating p sheets and a helices. (Courtesy of J Richardson.) Bottom Two-domain structure of the subunit of a homodimeric enzyme, a bacterial class II HMG-CoA reductase. As indicated by the numbered residues, the single polypeptide begins in the large domain, enters the small domain, and ends in the large domain. (Courtesy ofC Lawrence, V Rod well, and C Stauffacher, Purdue University.)...

TKase is a homodimeric protein with a subunit of about 70kDa. The X-ray structures of TKase of E. colif S. cerevisiaeX Leishmania mexicana and mize have been solved. In addition, the crystal structures of a number of site-directed mutants have been determined. Schneider and co-workers have reported a series of studies in which they have mutated important residues of active site of TKase to elucidate the reaction mechanism and explain the origin of the stereospecificity of the C—C bond-forming process (Table The conserved... 

For CBCA synthase hardly any information has been pubhshed. The enzyme was characterized after it was purified from C. sativa extracts and until this moment no sequence has been deposited. After purification of the protein it was found to be a homodimeric enzyme, meaning that enzyme is formed by two identical domains. This was observed after the purification, when the enzyme had a molecular weight of 136 kDa, and after denatured electrophoresis, when it had a molecular weight of 71 kDa. Furthermore, the CBCA synthase has shown to bear higher affinity for CBGA (1717 M S ) than THCA synthase and CBDA synthase (respectively 1382M s and 1492 M s ), which is probably due to its homodimeric nature [40]. 

Another reagent that has found use in pinacolic coupling is prepared from VC13 and zinc dust.264 This reagent is selective for aldehydes that can form chelated intermediates, such as (3-formylamides, a-amidoaldehydes, a-phosphinoylaldehydes,265 and 8-ketoaldehydes.266 The vanadium reagent can be used for both homodimerization and heterodimerization. In the latter case, the reactive aldehyde is added to an excess of the second aldehyde. Under these conditions, the ketyl intermediate formed from the chelated aldehyde reacts with the second aldehyde. 

Figure 5.10. Protein complementation assay using murine DHFR. The F[l,2] and F[3] fragments are each fused to the homodimerizing GCN4 leucine zipper protein. A. Transformation of both Z-F[l,2] and Z-F[3] constructs results in reconstituted DHFR and growth of E. coh on agar plates containing trimethoprim. B. Transformation of Z-F[l,2] or Z-F[3] alone does not result in trimethoprim resistant E. coli cells. Figure adapted from Pelletier et al. (1998).

The use of pairs of matched spectral variants of GFP, like cyan and yellow or GFP and mRed, to differentially tag proteins and look for interactions, is now in routine use. The approach can be readily applied to homodimerization of molecules that differ only by their living color or epitope tag. For example, homomultimer-ization of a viral coat protein can be observed by imaging a mixture of cyan and yellow tagged homomeric molecules [46], whereas oc-synuclein stacking can be detected by utilizing a-synuclein transcripts that encoded different epitope tags for detection by immunostaining [47],... 

Apparently, the dimerization of 4 is considerably more facile than that of MCP or BCP, resembling those of (dichloromethylene)cyclopropane (455) and radicophilic olefins with a capto-dative substitution pattern [125], some of which are known to cyclodimerize even at room temperature. Indeed, the capto-datively substituted methylenecyclopropane 85 undergoes the homodimerization at 60 °C (Scheme 65) [126]. 

Konakahara and co-workers reported the first direct synthesis of a quinoline skeleton 99 via homodimerization of ethynylanilines 98 in the presence of InBr3 in refluxing methanol <06JOC3653>. 

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