Dimer crystal structure

Figure 14. Stereoviews of the defensin dimer crystal structure [coordinates courtesy of D. Eisenberg (160)7. (A) Perspective that shows the basket shape of the molecule and the van der Waals surfaces of the charged side chains. In some cases, side-chain atom positions are not defined and have been placed in a low-energy conformation. (B) Perspective that shows the beta-sheets within each dimer and the subunit interaction.

Reacting 26 with the bidentate ligands TMEDA and cod leads to the formation of the binuclear species [(if-alkyne)Ni(/i-alkyne)Ni(r/, AA -TMEDA)], 30, and the mononuclear compound [Ni(r/ -alkyne)(77 -cod)], 31, respectively (alkyne = (/i-(OH)Me2C GMe2(OH))). These compounds crystallize in a double-stranded form 30 or a polymeric chain 31. Reaction of 26 with PPhs has allowed the preparation of the mononuclear species [Ni(r7 -alkyne)(PPh3)2], 32, which forms a dimeric crystal structure, thanks to the hydrogen bonds between the OH moieties and an acetonitrile solvate. 

The folding of a monomeric version of the ROP dimer designed by Sander and co-workers was examined. The 56-nearest-lattice protein model was used to assemble the topology, followed by refinement on the 90-neighbor lattice. The predicted structures have a Ca RMSD ranging from 2.6 to 4.2 A with respect to the set of equivalent residues in the ROP dimer crystal structure. Whether this prediction is true or not awaits the experimental determination of the ROP crystal structure. 

The structure of lumazine has been studied more precisely by X-ray analysis (72AX(B)659). The crystal structure is built up of almost coplanar, hydrogen-bonded dimers of lumazine with the oxygens of the pyrimidine moiety in the keto form and the observed bond distances indicating the pyrazine ring electrons to be delocalized. 

Figure 8.4 Cro molecules from bacteriophage lambda form dimers both in solution and in the crystal structure. The main dimer interactions ate between p strands 3 from each subunit. In the diagram one subunit is green and the other is brown. Alpha helices 2 and 3, the helix-turn-helix motifs, are colored blue and red, respectively, in both subunits. (Adapted from D. Ohlendorf et al., /. Mol. Biol. 169 757-769, 1983.)...

The lac repressor monomer, a chain of 360 amino acids, associates into a functionally active homotetramer. It is the classic member of a large family of bacterial repressors with homologous amino acid sequences. PurR, which functions as the master regulator of purine biosynthesis, is another member of this family. In contrast to the lac repressor, the functional state of PurR is a dimer. The crystal structures of these two members of the Lac I family, in their complexes with DNA fragments, are known. The structure of the tetrameric lac repressor-DNA complex was determined by the group of Mitchell Lewis, University of Pennsylvania, Philadelphia, and the dimeric PurR-DNA complex by the group of Richard Brennan, Oregon Health Sciences University, Portland. 

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

Wilson, D.S., et al. Crystal structure of a paired (PAX) class cooperative homeodomain dimer on DNA. Cell 82 709-719, 1995. 

Ellenberger, T.E., et al. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted a helices crystal structure of the protein-DNA complex. Cell 71 1223-1237, 1992. 

Figure 17.12 Ribbon diagram of EMPl bound to the extracellular domain of the erythropoietin receptor (EBP). Binding of EMPl causes dimerization of erythropoietin receptor. The x-ray crystal structure of the EMPl-EBP complex shows a nearly symmetrical dimer complex in which both peptide monomers interact with both copies of EBP. Recognition between the EMPl peptides and EBP utilizes more than 60% of the EMPl surface and four of six loops in the erythropoietin-binding pocket of EBP.

In the case of phenyllithium, it has been possible to demonstrate by NMR studies that the compound is tetrameric in 1 2 ether-cyclohexane but dimeric in 1 9 TMEDA-cyclohexane. X-ray crystal structure determinations have been done on both dimeric and tetrameric structures. A dimeric structure crystallizes from hexane containing TMEDA. This structure is shown in Fig. 7.1 A. A tetrameric structure incorporating four ether molecules forms from ether-hexane solution. This structure is shown in Fig. 7.IB. There is a good correspondence between the structures that crystallize and those indicated by the NMR studies. 

Fig. 7.1. Crystal structures of phertyllithium (A) dimeric structure incorporating tetra-methylethylenediamine (B) tetrameric structure incorporating dietl l ether., (Reproduced ftom Refs. 28 and 29 with permission of Wiley-VCH and the American Chemical Society.)...

Fig. 7.3. Crystal structures of some lithium etiolates of ketones. (A) Unsolvated hexameric enolate of methyl t-butyl ketone (B) tetrahydrofuran solvate of tetramer of enolate of methyl r-butyl ketone (C) tetrahydrofuran solvate of tetramer of enolate of cyclopentanone (D) dimeric enolate of 3,3-dimethyl-4-(r-butyldimethylsiloxy)-2-pentanone. (Structural diagrams are reproduced from Refs. 66-69.) by permission of the American Chemical Society and Verlag Helvetica Chimica Acta AG.

Among the variety of nitrogen-containing fulvalenes emerging from types 7-14, X-ray structural determinations have been performed on about 20 representative examples. Tire first crystal structure determination was carried out by application of the folding-molecule method on 3,3 -diphenyl-l,l -bi-isoindolylidene 64 (R = FI) (71CB3108). Tire dimeric isoindolenine system... 

---