Complexes between

Fig. 7.15 The variation in torsion angles can be effectively represented as a series of dials, where the time corresponds to the distance from the centre of the dial. Data from a molecular dynamics simulation of an intermolecular complex between the enzyme dihydrofolate reductase and a triazine inhibitor [Leach and Klein 1995].

Linear molecules belong to the axial rotation group. Their symmetry is intermediate in complexity between nonlinear molecules and atoms. 

To determine the formula for the complex between Fe + and o-phenanthroline, a series of solutions was prepared in which the total concentration of metal and ligand was held constant at 3.15 X 10 M. The absorbance of each solution was measured at a wavelength of 510 nm. Using the following data, determine the formula for the complex. 

Hemin is the complex between protoporphyrin and iron in the +3 oxidation state. Iron is in the +2 state in the heme of hemoglobin. The molecule has the following structure ... 

Most chiral chromatographic separations are accompHshed using chromatographic stationary phases that incorporate a chiral selector. The chiral separation mechanisms are generally thought to involve the formation of transient diastereomeric complexes between the enantiomers and the stationary phase chiral ligand. Differences in the stabiHties of these complexes account for the differences in the retention observed for the two enantiomers. Often, the use of a... 

Fig. 8. A hydrophobic inclusion complex between a chiral analyte and a cyclodextrin.

The chiral recognition mechanism for these types of phases was attributed primarily to hydrogen bonding and dipole—dipole interactions between the analyte and the chiral selector in the stationary phase. It was postulated that chiral recognition involved the formation of transient five- and seven-membered association complexes between the analyte and the chiral selector (117). 

MX Separation Process. The Mitsubishi Gas—Chemical Company (MGCC) has commercialized a process for separating and producing high purity MX (104—113). In addition to producing MX, this process gready simplifies the separation of the remaining Cg aromatic isomers. This process is based on the formation of a complex between MX and HF—BF. MX is the most basic xylene and its complex with HF—BF is the most stable. The relative basicities of MX, OX, PX, and EB are 100, 2, 1, and 0.14, respectively. 

Mercurous fluoride [13967-25 ] Hg2p2, is less effective than Hgp2. The addition of chlorine or iodine to the reagent increases its reactivity owing to the formation of a complex between Hgp2 and HgX2 (4,12). 

The principle of this method depends on the formation of a reversible diastereomeric complex between amino acid enantiomers and chiral addends, by coordination to metal, hydrogen bonding, or ion—ion mutual action, in the presence of metal ion if necessary. L-Proline (60), T.-phenylalanine (61),... 

Iodine Complexes. The small molecule/PVP complex between iodine and PVP is probably the best-known example (95) and can be represented as follows ... 

Many examples are known of complexes between metal cations and both neutral azoles and azole anions. Overlap between the cf-orbltals of the metal atom and the azole rr-orbitals is believed to increase the stability of many of these complexes. 

A simple spectrophotometric procedure for the determination of hydroxyurea (HU) has been developed. This procedure is based on the complex formation between HU and FeCl. The violet colored complex between HU and FeCl 560 nm) was not sufficiently stable to allow... 

Figure 10 Models of complexes between BLBP and two different fatty acids. The fatty acid ligand IS shown in the CPK representation. The small spheres in the ligand-bmdmg cavity are water molecules, (a) Model of the BLBP-oleic acid complex, in which the cavity is not filled, (b) Model of the BLBP-docosahexaenoic acid complex, m which the cavity is filled. The figure was prepared using the program MOLSCRIPT [236].

The protein-DNA interactions have been analyzed in detail at high resolution in the complex between the 434 repressor fragment and the ORl containing 20mer DNA. A pseudo-twofold symmetry axis relates the halves of this complex. The symmetry is not exact since the nucleotide sequence of the DNA is slightly different in each half (see Table 8.2). However, the interactions between one protein subunit and one half of the DNA are very similar to those between the second subunit and the other half of the DNA since most of the bases that interact with the protein are identical in both halves. Details of the interaction are very similar to those in the complex with the palindromic synthetic 14mer of DNA shown in Figures 8.14 and 8.15. The base pairs at one end of the DNA, 1-14, 2-13, etc. are called base pairs 1, 2, etc. 

Figure 8.14 Overall view of the complex between 434 repressor fragment and a palindromic synthetic 14mer of DNA (see Table 8.2). The two binding sites of the repressor dimer to the DNA are identical.

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

Figure 9.S Schematic diagram illustrating the structure of the complex between TBP and a DNA fragment containing the TATA box. Both the stirmps and the underside of the saddle are in contact with the DNA. (Adapted from V. Kim et al., Nature 365 514-520, 1993.)...

Figure 9.10 Schematic diagrams illustrating the complex between DNA (orange) and one monomer of the homeodomain. The recognition helix (red) binds in the major groove of DNA and provides the sequence-specific interactions with bases in the DNA. The N-terminus (green) binds in the minor groove on the opposite side of the DNA molecule and arginine side chains make nonspecific interactions with the phosphate groups of the DNA. (Adapted from C.R. Kissinger et al Cell 63 579-590, 1990.)...

Figure 13.17 Schematic diagram of the structure of a complex between phosducin and the transducin Gpy dimer. The p subunit of transducin is light red and the seven WD repeats are represented as seven orange blades of a propeller. The y subunit is yellow and the phosducin molecule is blue. The helical domain of phosducin interacts with Gp in the same region that Gq binds, thereby blocking the formation of a trimeric Gapy complex.

The complex between GH and GHR contains one molecule of the hormone and two molecules of the receptor, even though the hormone does not have a pseudosymmetric structure with two similar binding sites. Instead, there are two completely different binding sites on the hormone, each of which binds to similar sites on the receptor molecules. These interactions are so far unique. 

Figure 13.20 Ribbon diagram of the structure of a 1 2 complex between the human growth hormone and the extracellular domains of two receptor molecules. The two receptor molecules (blue) bind the hormone (red) with essentially the same loop regions (yellow).

---