Conserved binding site

An alternative mechanism for loss of membrane integrity is via the solubilization of phospholipids by thionins." This revised version of the carpet model is based on the observation of a conserved binding site for phospholipids head groups in thionins, their tendency to form oligomers," " and small-angle X-ray scattering... 

The two iron-binding sites in most transferrins are similar to each other, with each consisting of two tyrosines, one aspartic acid and one histidine. In some transferrins, however, conservation of the binding site residues is reduced for example, cockroach transferrin lacks the histidine in the N-lobe binding site, while several other invertebrate transferrins lack conserved binding site residues in the C-lobe. This may contribute to a lack of binding in the C-lobe of invertebrate transferrins. ... 

Baker HM, Basu I, Chung MC et al. Crystal structures of the staphylococcal toxin SSL5 in complex with sialyl Lewis X reveal a conserved binding site that shares common features with viral and bacterial sialic acid binding proteins. J Mol Biol 2007 374 1298-1308. 

If tliere are n independent binding sites per receptor, conservation of mass dictates tliat s = nb - c, where /jq is tire... 

In the middle of the accuracy spectrum are the models based on approximately 35% sequence identity, corresponding to 85% of the Ca atoms modeled within 3.5 A of their correct positions. Eortunately, the active and binding sites are frequently more conserved... 

The central 10 base pairs of the palindromic DNA molecule have a regular B-DNA structure. Between base pairs 5 and 6 in each half of the fragment (base pairs are counted from the center) there is a 40° kink which causes these base pairs to be unstacked (Figure 8.24a). After this localized kink the two end regions have an essentially B-DNA structure. The kink occurs at a TG step in the sequence GTG. These TG steps at positions 5 and 6 are highly conserved in both halves of different CAP-binding sites, presumably in part because they facilitate kinking. 

Five of the six loop regions (G1-G5 in Figure 13.4) that are present at the carboxy end of the p sheet in the Ras structure participate in the GTP binding site. Three of these loops, G1 (residues 10-17), G3 (57-60), and G4 (116-119), contain regions of amino acid sequence conserved among small GTP-binding proteins and the Ga subunits of trimerlc G proteins. 

The peptide-binding site is a hydrophobic groove flanked by the RT loop between pi and p2 and the n-Src loop between p3 and P4 (see Figure 13.28a). The latter is so named because neuronal Src has an insertion of six residues in this loop. The groove is lined with conserved aromatic residues. 

FIGURE 15.9 Monod-Wyman-Changeux (MWC) model for allosteric transitions. Consider a dimeric protein that can exist in either of two conformational states, R or T. Each subunit in the dimer has a binding site for substrate S and an allosteric effector site, F. The promoters are symmetrically related to one another in the protein, and symmetry is conserved regardless of the conformational state of the protein. The different states of the protein, with or without bound ligand, are linked to one another through the various equilibria. Thus, the relative population of protein molecules in the R or T state is a function of these equilibria and the concentration of the various ligands, substrate (S), and effectors (which bind at f- or Fj ). As [S] is increased, the T/R equilibrium shifts in favor of an increased proportion of R-conformers in the total population (that is, more protein molecules in the R conformational state). 

Approximately 500 of the 820 amino acid residues of the myosin head are highly conserved between various species. One conserved region, located approximately at residues 170 to 214, constitutes part of the ATP-binding site. Whereas many ATP-binding proteins and enzymes employ a /3-sheet-a-helix-/3-sheet motif, this region of myosin forms a related a-f3-a structure, beginning with an Arg at (approximately) residue 192. The /3-sheet in this region of all myosins includes the amino acid sequence... 

C2 domains (phosphokinase C conserved 2 domains) mediate membrane targeting of diverse peripheral proteins. A C2 domain consists of approximately 130 residues and was first discovered as the Ca2+-binding site in conventional phosphokinase Cs. 

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