Dimers interfaces/surfaces

The dimer of dimers model of yCCS/ySODl interaction and copper delivery illustrated in Fig. 17 (see color insert) can be summarized as follows The positively charged (blue) yCCS dimer interface surface... 

The characteristic coiled-coil motifs found in proteins share an (abcdefg) heptad repeat of polar and nonpolar amino acid residues (Fig. 1). In this motif, positions a, d, e, and g are responsible for directing the dimer interface, whereas positions b, c, and f are exposed on the surfaces of coiled-coil assemblies. Positions a and d are usually occupied by hydrophobic residues responsible for interhelical hydrophobic interactions. Tailoring positions a, d, e, and g facilitates responsiveness to environmental conditions. Two or more a-helix peptides can self-assemble with one another and exclude hydrophobic regions from the aqueous environment [74]. Seven-helix coiled-coil geometries have also been demonstrated [75]. 

Several binding sites for Tb3+ or Cd2+ ions have been identified in the interior of the apoferritin protein shell, some of which may be iron-binding sites (Harrison et ai, 1989 Granier et ah, 1998). In HoSF and HoLF, two sites were identified on the inner surface of the B helix at the subunit dimer interface (Figure 6.15, Plate 11) which bind two Cd2+ ions. One involves Glu-57 and Glu-60 as ligands and the other Glu-61 and Glu-64 (Granier et al., 1998). In H-chain ferritins the first pair of Glu-57 and Glu-60 are both replaced by His and only a single Tb3+ is found bound to Glu-61 and Glu-64 (Lawson et al, 1991). 

The CoA binding tunnel provides access to the internal cavity. B. Molecular surface representation of the CHS-CoA complex oriented as shown in (A). In the -bottom panel, the two CHS monomers are separated and rotated slightly to highlight the flat dimerization interface along with the methionine side chain and dyad related hole in the backside of the CHS active site. 

A comparative analysis of the dimer interface between NOS isoforms is important since there are questions on significant variation in dimer stability between isoforms (84, 85). The dimer interface is extensive with approximately 2700 A of surface area buried per monomer. The interface contacts involve a mix of nonpolar and polar interactions, including hydrogen bonding. Approximately 60% of the interface in both iNOS and eNOS is hydrophobic, although the higher resolution eNOS... 

An alternative and more interesting model is the formation of rhodopsin dimers across the disk membranes, as shown in Fig. 18B. The putative tail-to-tail dimer interface is formed by side-by-side stacking of the 1 and f) 2 strands from each molecule to make a continuous antiparallel /J-sheet. The Pro-16-Pro-23 loops from each monomer interdigitate and lay over one surface of the sheet. Intermolecular salt bridges and Ca2+ binding sites formed from pairs of carboxylate residues, one from... 

Fig. 2. Structures of the extracellular domains of Ephs and ephrins. The molecular surfaces (semi-transparent) are also indicated. (A) Structure of the ligand-binding domain of EphB2. The N- and C-termini of the molecule are labeled, as are the class-specificity loop (H-I) and the ligand-binding loops that are largely disordered in the absence of bound ephrin. (B) Structure of the extracellular receptor-binding domain of ephrin-B2. Indicated is the location of the receptor-binding G-H loop. (C) Structure of the EphB2/ephrin-B2 tetramer. Eph receptors are blue and ephrins are green. The high-affinity dimerization interfaces are indicated by arrows. (See Color Insert.)...

Fig. 14. X-ray crystal structure of full-length yeast CCS [pdb code Iqup (Lamb et al., 1999)]. (a) One monomer of yCCS is in light gray and the other is in dark gray. The cysteine residues of the MXCXXC motif in domain 1 are labeled and form a disulfide bond in each subunit. Amino acid side chains that are important in the formation of the positive patch at the dimer interface (Arg-188 and Arg-217) and the solvent-exposed Trp-183 residues of loop 6 at the center of this patch are shown in ball-and-stick representation. Domain 3 is not visible in the crystal structure (see text), (b) Stereo view of the image in (a) rotated 90° in the horizontal plane of the page and then 90° counterclockwise around an axis perpendicular to the page. The side chains that form the putative ySODl interaction surface are represented as ball-and-stick. The cysteine residues of the domain 1 MXCXXC motif are also represented in ball-and-stick.

Fig. 7.1 The tetramer of eco bound to a serine protease. Visualized as a cartoon of the canonical protease and eco interaction (a), and (b), as two views of the three dimensional solution of D102N trypsin in complex with eco [3]. Each eco molecule has three protein-protein interaction surfaces. The C-terminus forms an anti-parallel p ribbon to complete the ecotin dimer interface. The 80 s and 50 s loops form the primary binding site by interacting with the protease at the active site cleft in a sub-strate-like y -sheet conformation. The 60 s and lOO s loops of eco form the secondary binding site by interacting with the C-termi-nal a-helix of the protease. Note that each eco molecule contacts both of the protease molecules. Two eco molecules (black and medium grey) form a pair of interactions each with two protease molecules (light grey). The catalytic triad residues Ser-195, Asp-102 and His-57 are in black ball and stick representation. This figure was made with Molscript [37] and Raster 3D [38].

TNF. These receptor dimers could cluster on binding TNF. The formation of receptor dimers buries large areas of the protein surface. Thus the dimerization interfaces are large. 

---