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Document Table 2 HIV-1 RT Amino Acid Residues Composing the Putative dNTP-Binding Sites and the Locations of NRTI- Resistance Mutations (see also [12]) dNTP-Binding Site Nucleoside <strong>Drug</strong>-Resistance Mutation Site Residue Location Mutation Location Possible Effects References Asp110 β6 Met41Leu αA template binding 55 Asp113 β6-αC loop Ile50Thr β2 unclear 154 Try115 αC Lys65Arg β3–β4 template binding 154 Phe116 αC Asp67Asn β3–β4 template binding 155 Gln151 β8-αE Thr69Asp β3–β4 template binding 156 Phe160 αE Lys70Arg β3–β4 template binding 155 Asp185 β9–β10 Leu74Val β4 template binding 8 Asp186 β9–β10 Val75Thr β4 template binding 163 Lys219 β11 Glu89Gly β5 dsDNA binding 157 Tyr115Phe αC dNTP binding 170 Ile135Thr β7–β8 unclear 158,159 Gln151Met β8-αE dNTP binding Met184Val, Ile β9–β10 dNTP-binding/fidelity 154,160,161 Thr215Tyr, Phe, Cys β11 indirect effect/dNTP binding 155,162 Lys219Gln β11 dNTP binding 155 Page 52 site can accommodate both the normal dNTP substrates and dideoxynucleoside analogs. The majority of mutations that confer resistance to NRTIs are not located at the dNTP-binding site; however, they appear to influence the geometry of the dNTP-binding site indirectly in a way that permits RT to discriminate between a normal dNTP and a modified nucleoside triphosphate (see discussion in the next section). http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_52.html (1 of 2) [4/5/2004 4:49:26 PM]
Document Analysis of various HIV-1 RT structures has revealed an unusual β-turn geometry for the YMDD motif at the polymerase catalytic site of p66 [33,34,41–43]. The energetically unfavorable main chain conformation of Met184 (torsion angles φ~60° and ϕ~-120°) is stabilized <strong>by</strong> a hydrogen bond of its carbonyl oxygen to the side chain of either Gln182 [33,41,43] or Gln161 [42]. It has been suggested that this novel β-turn geometry might be required to position the aspartic acids in precisely the correct way for catalysis [41]. IV. Mechanism of NRTI-Resistance Mutations Development of resistance to NRTIs has been a major problem with clinical use of these drugs. Careful analysis of mutations that confer resistance to different http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_52.html (2 of 2) [4/5/2004 4:49:26 PM]
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Structure-based Drug Design 14 Stru
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Document D ddI, 152 tumour necrosis
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