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Document Figure 4 (Continued) Only one nitrogen atom from Arg 84 is visible, which—along with Ser 220 and His 86—interact with the acetyl group branching from the benzylic carbon. The chlorinated phenyl group is in the center of the figure, interacting with the aromatic groups in the sugar binding site. The guanine group interactions are the same as seen in Figure 4E. Figure prepared with ribbons (http://www.cmc.uab.edu/ribbons). http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_158.html (2 of 2) [4/5/2004 5:02:02 PM]
Document large solvent channels and the position of the active site. The x-ray analysis confirmed the trimeric nature of the enzyme, as the subunits are related by the crystallographic three-fold axis. Page 159 A ribbon diagram of the trimer is shown in Figure 4B. Each monomer contains an eight-stranded β sheet and a five-stranded β sheet that join to form a distorted β barrel. Seven α helices surround this β sheet structure. The active site is an irregular indentation on the surface of the enzyme, located from the position of a tightly bound sulfate ion and various substrate analogs. These investigations revealed the identity of the exact amino acids constituting the active site region; such detail was a prerequisite to drug design. Information of greater import emerged from analyses of the complexes formed when synthetic nucleosides, including previously discovered inhibitors, were diffused into the active site. B. The Active Site The structural determinations also yielded a surprise. The shape of the enzyme changes when a purine is bound. The famous lock-and-key analogy [20] has a fallacy; the shape of the lock is not static, but flexible. Awareness of these conformational changes critically aided our modeling efforts, allowing prediction of which parts of PNP could change shape to interact with a proposed inhibitor. A “swinging gate” consisting of residues 241–260 controls access to the active site (Figure 4C). These residues in the native structure had poorly defined electron density with high thermal motion. The gate opens in the native enzyme to accommodate the substrate or inhibitor. The maximum movement caused by substrate or inhibitor binding occurs at His 257, which is displaced outwards by several angstroms. After binding, the electron density becomes well defined. The gate is anchored near the central β sheet at one end and near the C-terminal helix at the other end. The gate movement is complex and appears to involve a helical transformation near residues 257–261. Consequently, initial inhibitor modeling attempts using the native PNP structure were far less successful than subsequent analyses in which coordinates for the guanine-PNP complex were used. Because of the magnitude of the changes that occur during substrate binding, it is unlikely that modeling studies based on the native structure alone would have accurately predicted the structure of PNP/inhibitor complexes. The active site is located near the subunit-subunit boundary within the trimer and involves seven polypeptide segments from one subunit and a short loop from the adjacent subunit (Figure 4D). The purine binding site employs residues Glu 201, Lys 244, and Asn 243 to form hydrogen bonds with N1, O6, and N7 of purine. The remainder of the purine binding pocket is largely http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_159.html [4/5/2004 5:02:05 PM]
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Structure-based Drug Design 14 Stru
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Page 149 and 150: Document 4 Bradykinin Receptor Anta
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Page 175 and 176: Document Figure 9 Composition of te
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Page 197 and 198: Document IV. Drug Design Progressio
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Page 205 and 206: Document References 1. Parks RE Jr.
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Page 209 and 210: Document 6 Structural Implications
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Document Page 398 with growth hormo
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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 462 strains of influe
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Document Page 488 against most of t
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Document Subsequent studies have sh
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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 Kininogen, 119 high molecu
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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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