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Document Figure 2 A number of ALR2 inhibitors that have entered clinical trails. structures show the protein to fold into a (β/α) 8 barrel (Figure 3). This fold has emerged as the most common enzyme motif [19] although most of the proteins adopting this structure share no sequence homology. The ALR2 enzyme is, however, the first NAD(P)H binding protein to adopt this fold. It contains an extra β hairpin preceding the first β strand, which caps the N-terminal end of the barrel. It also has two helices that are not part of the regular barrel. One precedes α7 and the other follows α8. A. Cofactor Binding The NADPH cofactor is bound in an extended conformation across the C-terminal end of the β barrel. The catalytically active nicotinamide moiety is located http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_232.html (1 of 2) [4/5/2004 5:08:09 PM] Page 232
Document Figure 3 C α trace of the ALR2 holoenzyme looking down the (β/α) 8 barrel. The NADPH cofactor is seen bound across the carboxy-terminal end of the β-barrel with the active nicotinamide moiety in the center. Figure produced using the MOLSCRIPT program [48]. Page 233 at the center of the barrel while the adenosine extends away to bind between α7 and α8. A belt composed of residues 213 to 227 folds over the pyrophosphate of the NADPH to sequester a large part of the cofactor from the solvent. It is fastened to the other side of the NADPH binding site via Asp216 on the loop that forms bifurcated salt links with Lys21 and Lys262. The dominant interactions holding the coenzyme in place are directional hydrogen bonds and salt links from positively charged side chains to the phosphates. The interaction between the 2' phosphate on the NADPH and the side chains from Lys262 and Arg268 account for the enzyme's preference for NADPH over NADH. Earlier biochemical studies had shown that it is the 4-pro-R hydride that is transferred from the nicotinamide to the substrate [20]. This is ensured <strong>by</strong> a hydrogen-bonding network using side chains from Ser159 and Asn160 and the main chain of Gln183 to orient the amide. It is also determined <strong>by</strong> the stacking interactions with Tyr209, which is adjacent to the 4-pro-S side of the nicotinamide. B. Mechanism The catalytic site was unambiguously identified using the location of the nicotinamide moiety of the NADPH cofactor in the holoenzyme structure. The region surrounding the catalytic site is a 12-Å deep groove that measures http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_233.html (1 of 2) [4/5/2004 5:08:15 PM]
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Structure-based Drug Design 14 Stru
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Document dine (3TC), and 2',3'-dide
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Document Analysis of various HIV-1
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Document Page 54 Table 2) [12,54].
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Document Table 3 HIV-1 RT Amino Aci
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Document ever, once an NNRTI is bou
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Document Chris Tantillo. The work i
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Document Page 72 16. Goldman ME, Nu
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Document reverse transcriptase inhi
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Document 106. Cirino NM, Cameron CE
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Document 122. Marshall WS, Beaton G
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Document dine) and didanosine (dide
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Document 149. Craig JC, Duncan IB,
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Document 163. Lacey SF, Larder BA.
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Document Page 106 on the same ring
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Document Page 108 mulate during tre
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Document when metals are bound. Fin
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Document cubation of phosphotyrosin
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Document 4 Bradykinin Receptor Anta
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Document Page 121 Nearly all cells
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Document Page 125 binding site on t
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Document receptor, it has not yet b
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Document Figure 6 Rat and human B2
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Document Figure 9 Composition of te
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Document B. Pharmacology Figure 1 T
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Document We determined the structur
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Document Figure 3 Previously known
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Document Table 1 Inhibition Data fo
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Document Page 166 As predicated, th
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Document References 1. Parks RE Jr.
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Document 17. Ealick SE, Rule SA, Ca
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Document 6 Structural Implications
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Page 257 and 258: Document 29. Baker ME. Genealogy of
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Document 12 Polypeptide Modulators
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Document 16 Progress in the Design
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Document Table 1 Known Three-Dimens
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Document Page 398 with growth hormo
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Document All effects of the IL-1 fa
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Document Figure 13 The identified p
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Document Page 425 Antinflammatory D
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Document 5. Dinarello CA. On the Bi
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Document 39. Saurat JH, Schfferli J
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Document 17 Structure and Functiona
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Document Table 1 Approval Indicatio
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Document Page 438 proteins. One pot
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Document II. Type IFNs A great deal
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Document Page 441 sequence of the m
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Document Page 443 that allowed for
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Document Figure 4 Stereo view of IF
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Document Figure 5 Velcro-key model
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Document Figure 6 Proposed receptor
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Document Page 451 with the cytoplas
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Document for directed subcellular t
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Document Page 462 strains of influe
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Document B. Protein Structure Page
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Document Figure 5 (a) Stereo image
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Document Page 471 molecules in the
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Document hydroxy, and 6 Neu5Ac2en -
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Document Figure 8 Stereo image of t
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Document Page 476 nM, respectively.
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Document VI. Conclusion Page 480 It
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Document 21. Both GW, Sleigh MJ, Co
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Document 64. Ward CW, Elleman TC, A
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Document Page 488 against most of t
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Document A. The Canyon Page 491 The
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Document Subsequent studies have sh
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Document Page 495 of the RNA and pr
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Document Figure 4 A ribbon diagram
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Document Figure 5 Some compounds wh
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Document Figure 7 HRV14 VP1 hydroph
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Document C. Structure-Activity Rela
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Document Page 545 protein binding s
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Document Figure 32 PTP and PTB 3D s
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Document Acknowledgments Page 620 I
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Document 18. Sawyer TK. In: Peptide
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Document Med Biol 1991; 306:9-21; (
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Document site, 52, 55, 61 triad, 24
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Document factors, 247 Combination t
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Document Cyclotheonamide A (CtA), 2
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Document D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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Document fragment-based programs, 5
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Document [Human immunodeficiency vi
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Document overview, 103-104, 108-109
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Document antagonistic activity, 416
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Document Kininogen, 119 high molecu
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Document Matrix-metalloproteinase (
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Document RT inhibitor, 41, 56 Nonpe
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Document Phosphoglycerate kinase (P
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Document [Protease targets] serinyl
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