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Document Figure 5 Exploitable structural differences between T.brucei(full) and human (dashed) TIM. The inhibitor 2-phosphoglycolate as observed in the structure of the human enzyme indicates the location of the active site. Drug design targets are the T.brucei Ala100-Tyr101, which are considerably different from their human counterpart His-Val. (From Ref.25. Copyright 1994 by Cambridge University Press.) http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_373.html (2 of 2) [4/5/2004 5:36:17 PM]
Document Figure 6 Stereoview of NAD binding by trypanosomal GAPDH (full black). For clarity only 2 of the 4 subunits are shown. A substantial deviation of the protein backbone occurs in human GAPDH (open gray, only one subunit shown) near the adenosine part of the cofactor. The nearby cleft (marked by an asterisk) is important for introducing selectivity in inhibitor binding and has therefore been termed “selectivity cleft.” Page 374 glycosomal GAPDH has been overexpressed in E. coli [59] while human erythrocyte GAPDH is available from commercial suppliers. The sequences of the two enzymes are only 55% identical [60]. The crystal structure of the parasite enzyme was solved from Laue data at 3.2 Å resolution in our group (Figure 6) and in a second crystal form at 2.8 Å [26]. The structure of the human muscle enzyme was solved at 3.5 Å resolution in the group of the late Herman Watson [28]. Its resolution was improved to 2.3 Å in our group [26,29]. Both structures were of the holo-enzyme, i.e., the enzyme in presence of the cofactor. The active site and the nicotinamide-binding site of the two enzymes are very well conserved. This is reflected in similar K m (glyceraldehyde-3-phos-phate) values of 0.15 and 0.17 mM for the trypanosomal and human enzyme, respectively [61]. Surprisingly, the K m (NAD +) values differ by a factor ten: 0.45 mM for T. brucei and 0.04 mM for human GAPDH [61]. In view of the conservation of the nicotinamide and pyrophosphate binding sites, the substantial difference in K m (NAD +) has to be ascribed to the adenosine binding environment. Indeed, some of the residues embracing the adenine ring of the cofactor are not identical. In the trypanosomal enzyme the adenine is sandwiched in between a Thr in the back and a Met in the front. This Met is replaced by Pro and Phe in the human enzyme (Figure 7). A second difference involves the residue flanking the C2 atom of the purine ring. It is a Val in the trypanosomal enzyme, and Asn in the human enzyme. These differences apparently account for a ten-fold lower affinity for the cofactor. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_374.html (1 of 2) [4/5/2004 5:38:25 PM]
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Structure-based Drug Design 14 Stru
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