Non-conservative residues

Fig. 6 Entrance view of the SS isomer of 3,3 -(l,2-ethanediyl)-bis[2-(3,4-dimethoxyphe-nyl)-4-thiazolidinones] into the COX-2 (a) and COX-1 (b) binding sites. In this A and B refer to thiazolidinone moieties as shown in Fig. 5. The steric effect of the non-conserved residue at position 523 (valine in a and isolucine in b) is reported to be crucial for the distinctive recognition of this compound between COX-1 and COX-2 isoenzymes. (Reprinted with permission from [85]. Copyright 2003 Elsevier Ltd.)...

Fig. 4. Folding pattern of amino acids in PS-ii D1 (A) and D2 (B) protein chains predicted by computer modeling. Non-conserved residues are represented by empty circles and conserved ones by single-letter symbols. See text for other details. Adapted from Svensson, Vass, Cedergren and Styring (1990) Structure of the donor side components in photosystem II predicted by computer modelling. The EMBO J 9 2053.

ENHANCEMENT OF THERMOSTABILITY OF LUCIOLA MINGRELICA FIREFLY LUCIFERASE BY MUTAGENESIS OF NON-CONSERVATIVE RESIDUES CYS62 AND CYS146... 

The A -16 0- and A -18 0-ACP desaturases contain nine non-conserved residues in the 30-amino acid domain described above. Using site-directed mutagenesis, these amino acids were replaced, individually or in combination, in the A -16 0-ACP desaturase with those present in the A -18 0-ACP desaturase. Several of the resulting mutants of the A -16 0-ACP desaturase displayed new activities. These included an enzyme generated by replacement of two amino acids that functioned as a A desaturase with nearly equal specificity for 16 0- and 18 0-ACP. Another mutant, which was formed by the replacement of five amino acids of the A -16 0-ACP desaturase, displayed primarily A -18 0-ACP desaturase activity. We are currently using the crystal structure of the A -18 0-ACP desaturase (4) to interpret the structural basis for the activities of these mutants. 

Fig. 11.2. Schematic representation of the primary structure of secreted AChE B of N. brasiliensis in comparison with that of Torpedo californica, for which the three-dimensional structure has been resolved. The residues in the catalytic triad (Ser-His-Glu) are depicted with an asterisk, and the position of cysteine residues and the predicted intramolecular disulphide bonding pattern common to cholinesterases is indicated. An insertion of 17 amino acids relative to the Torpedo sequence, which would predict a novel loop at the molecular surface, is marked with a black box. The 14 aromatic residues lining the active-site gorge of the Torpedo enzyme are illustrated. Identical residues in the nematode enzyme are indicated in plain text, conservative substitutions are boxed, and non-conservative substitutions are circled. The amino acid sequence of AChE C is 90% identical to AChE B, and differs only in the features illustrated in that Thr-70 is substituted by Ser.

In addition, haplotype-based methods can increase the power of association studies since the allelic architecture of the risk factor is unknown. Recent examples of association studies suggest that haplotypes can be the responsible factors [58]. The Apo E4 allele , which is associated with Alzheimer s disease, is a possible example since it results from the substitution of two of non-conservative polymorphisms encoding for residues 112 and 158 [59]. 

Figure 10. Binding site anaiysis of different species can uncover potentiai probiems with ani-mai modeis for a given target. The Cathepsin S inhibitor JNJ 10329670 (exact molecule not shown) has an activity of 34 nM in humans, but shows sub-micromolar activity in dog, monkey, and cattie, and oniy micromoiar activity in mice. These activity differences can be expiained by the fact that in the dog, monkey and bovine Cathepisin S pockets, only two of the residues are non-conserved, whiie four of the residues are non-consen/ed in mice.

The sequence and structural conservations at the P 2, Po> Pi positions define a major TRAF2 binding motif that bears the consensus sequence of px(Q/E)E, in which Pro is shown in lower case because it can be substituted for other medium sized non-charged residues. Most of the binding sequences identified so far for TRAFl, 2, 3, and 5 are consistent with the motif, thereby explaining the recognition of diverse receptor sequences by TRAF2 (Fig. 6). 

TMC-95A, a cydic peptide metabolite from Apiospra montagnei, is a potent competitive inhibitor of all active sites and forms characteristic hydrogen bonds with the protein backbone. The crystal structure of the yeast 20S proteasome in complex with TMC-95A indicates a non-covalent linkage to the active y -subunits the N-terminal threonine residues are not modified. The TMC-95A backbone adopts a -conformation and extends the -strand SI by the generation of an antiparallel P-sheet. This stmcture is similar to that seen with the aldehyde and epoxyketone inhibitors. An interactions of TMC-95A are formed with main-chain atoms and strictly conserved residues of the 20S proteasome. 

A non-conservative replacement of a Glu residue (E301) close to the exposed portion of the FAD cofactor also results in a strong inhibition of ET with Fd [63]. In this case, it was shown that the carboxyl moiety of this residue was involved in stabilizing the one-electron reduced form of the FAD (i.e. FADH"). For both this mutation and the charge-reversal mutants noted above, steady-state experiments [64] support the laser flash photolysis results. 

Two box models are used for the parameterization of water as conservative material and salts, including sulfur, as non-conservative material. For example, the first estimates were made up for the wet season. For the coastal water body budget, the following fluxes were monitored and calculated precipitation, evapotranspiration, runoff, groundwater, and residual flow. These budget estimates give the fresh water residence time as 6.2 days with residual flow equal -822.34 x 10- For Klong... 

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