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Document Figure 5 Alignment of amino acid sequences of retroviruses. See Engelman et al. [19] for details. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_91.html [4/5/2004 4:55:13 PM] Page 91
Document Page 92 The role of the N-terminus of integrase, residues 1 to 50, is still unclear. Within this region are four strictly conserved amino acids: two His and two Cys residues. In HIV-1 integrase, the spacing is His-X 3- His-X 23-Cys-X 2-Cys. This cluster of His and Cys residues is reminiscent of a zinc-binding motif, and it has been demonstrated that the full-length protein binds Zn 2+ [22,30], and that the separately expressed domain consisting only of residues 1 to 55 also binds Zn 2+ stoichiometrically [31]. However, it has not been shown that either the structural integrity or the enzymatic activities of integrase require Zn 2+. While truncation of residues from the N-terminus of HIV integrase results in loss of 3' processing and strand transfer activities [22,25], in the case of RSV integrase, the N-terminal region can be replaced <strong>by</strong> unrelated sequences, and the enzyme is still capable of all three in vitro activities [32]. B. Biophysical Properties of Full-Length Recombinant HIV-1 Integrase It has been known for some time that recombinant HIV-1 integrase is a particularly poorly behaved protein in solution. Its solubility in most usual buffers is limited to approximately 1 mg/mL, and even then only in the presence of high concentrations of NaCl. At ~1 mg/mL, HIV-1 integrase slowly precipitates out of solution, revealing one of its characteristic features, a tendency towards aggregation. These properties of the protein are not unreasonable, since in its viral environment integrase is probably never required to be a soluble protein. To maintain the integrity of preintegration complexes, it may even be advantageous for the protein to have the properties of being rather insoluble and sticking to itself, nucleic acid, and perhaps other proteins. C. Properties of Truncated Versions of HIV-1 Integrase It has been our approach to protein structure determination <strong>by</strong> x-ray crystallography that it is imperative to begin with well-characterized and well-behaved protein. In particular, it is important that the protein be reasonably soluble and monodisperse in solution. Unfortunately, as discussed above, recombinant HIV-1 integrase satisfies neither of these conditions. One approach we and others have taken to circumvent these problems has been to examine truncated versions of HIV-1 integrase to determine if removal of amino acids from either terminus or both affects solubility and aggregation properties. Although we observed that two proteins we constructed, IN 213–288 and IN 50–288, were more soluble than the full-length HIV-1 integrase, IN 1–288 [33, and unpublished observations], our first target protein for crystallization efforts was the core domain of HIV-1 integrase consisting of residues 50 to 212, IN 50–212. We reasoned that this protein domain was likely to be compact and http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_92.html [4/5/2004 4:55:15 PM]
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Structure-based Drug Design 14 Stru
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Document 2 Structural Studies of HI
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Page 67 and 68: Document Page 54 Table 2) [12,54].
Page 69 and 70: Document Page 56 It is also attract
Page 71 and 72: Document Table 3 HIV-1 RT Amino Aci
Page 73 and 74: Document ever, once an NNRTI is bou
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Page 77 and 78: Document Page 63 most of the amino
Page 79 and 80: Document Page 65 cal properties of
Page 81 and 82: Document Page 67 Biochemical data s
Page 83 and 84: Document Page 69 determining the me
Page 85 and 86: Document Chris Tantillo. The work i
Page 87 and 88: Document Page 72 16. Goldman ME, Nu
Page 89 and 90: Document 30. Coffin JM. HIV populat
Page 91 and 92: Document 45. Majumadar C, Abbotts J
Page 93 and 94: Document reverse transcriptase inhi
Page 95 and 96: Document 75. Ring CS, Sun E, McKerr
Page 97 and 98: Document 89. Hughes SH, Arnold E, H
Page 99 and 100: Document 106. Cirino NM, Cameron CE
Page 101 and 102: Document 122. Marshall WS, Beaton G
Page 103 and 104: Document dine) and didanosine (dide
Page 105 and 106: Document 149. Craig JC, Duncan IB,
Page 107 and 108: Document 163. Lacey SF, Larder BA.
Page 109 and 110: Document Figure 1 Retroviral lifecy
Page 111 and 112: Document Figure 2 In vivo reactions
Page 113 and 114: Document Page 88 transfer (Figure 3
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Page 119 and 120: Document Figure 6 Molscript stereo
Page 121 and 122: Document Page 96 region in the HIV-
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Page 127 and 128: Document Page 101 crystallized unde
Page 129 and 130: Document Figure 8 Molscript stereo
Page 131 and 132: Document proposed mechanisms. For e
Page 133 and 134: Document Page 106 on the same ring
Page 135 and 136: Document Page 108 mulate during tre
Page 137 and 138: Document when metals are bound. Fin
Page 139 and 140: Document cubation of phosphotyrosin
Page 141 and 142: Document 4. Vink C, Plasterk RHA. T
Page 143 and 144: Document Page 115 21. Kulkosky J, J
Page 145 and 146: Document 44. Cushman M, Sherman P.
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Page 149 and 150: Document 4 Bradykinin Receptor Anta
Page 151 and 152: Document Page 121 Nearly all cells
Page 153 and 154: Document Page 123 were poorly satis
Page 155 and 156: Document Page 125 binding site on t
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Page 159 and 160: Document Page 129 tolerated by the
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Document Figure 6 Rat and human B2
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Document Page 141 receptor with int
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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 IV. Drug Design Progressio
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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 6 Structural Implications
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Document IX. S2' Interactions Page
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Document 7 Structure—Function Rel
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Document Important for the validity
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Document Figure 4 Amino acids impor
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Document III. Results and Discussio
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Document Page 202 269, and valine-2
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Document Page 205 enzyme and of phe
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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 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 443 that allowed for
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Document Page 462 strains of influe
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Document B. Protein Structure Page
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Document Page 476 nM, respectively.
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Document A. The Canyon Page 491 The
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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 D ddI, 152 tumour necrosis
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Document antistasin peptides, 281 c
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Document Phosphoglycerate kinase (P
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Document [Protease targets] serinyl
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