Sandbox Reserved 712: Difference between revisions
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=== X-ray structure analysis of 3ggu === | === X-ray structure analysis of 3ggu === | ||
[[Image:Positions_of_the_mutations_in_PR_variants_used_for_structural_studies.jpg|left|320px|thumb| Fig. | [[Image:Positions_of_the_mutations_in_PR_variants_used_for_structural_studies.jpg|left|320px|thumb| Fig.1 Positions of the mutations in PR variants used for structural studies. <ref name="Molecular" />]] | ||
[[Image: Structural_changes_in_PRdrv5_mutant.jpg|right|200px|thumb| Fig. | [[Image: Structural_changes_in_PRdrv5_mutant.jpg|right|200px|thumb| Fig.2 Structural changes in PR<sub>DRV5</sub> mutant relative to wild-type PR. <ref name="Molecular" />]] | ||
[[Image: Detailed_view_of_darunavir-enzyme_interactions.jpg|right|200px|thumb| Fig. | [[Image: Detailed_view_of_darunavir-enzyme_interactions.jpg|right|200px|thumb| Fig.3 Detailed view of the darunavir-enzyme interactions. <ref name="Molecular" />]] | ||
The crystal structure was determined in complex with [[darunavir]] with 1.8-Å resolutions. The crystal is formed out of one PR dimer in the asymmetric unit with two inhibitor molecules bound in alternative orientations. | The crystal structure was determined in complex with [[darunavir]] with 1.8-Å resolutions. The crystal is formed out of one PR dimer in the asymmetric unit with two inhibitor molecules bound in alternative orientations. | ||
Surface residues <scene name='Sandbox_Reserved_712/R45/1'>R45</scene> and <scene name='Sandbox_Reserved_712/R55/1'>R55</scene> have disordered side chains, but the other amino acid residue changes could be modeled into well-defined electron density maps. | Surface residues <scene name='Sandbox_Reserved_712/R45/1'>R45</scene> and <scene name='Sandbox_Reserved_712/R55/1'>R55</scene> have disordered side chains, but the other amino acid residue changes could be modeled into well-defined electron density maps. | ||
PR<sub>DRV5</sub> contains darunavir mutations <scene name='Sandbox_Reserved_712/V82t/1'>V82T</scene> and | PR<sub>DRV5</sub> contains darunavir mutations <scene name='Sandbox_Reserved_712/V82t/1'>V82T</scene> and | ||
<scene name='Sandbox_Reserved_712/I84v/2'>I84V</scene> (see Fig. | <scene name='Sandbox_Reserved_712/I84v/2'>I84V</scene> (see Fig.1, Part B, indicated in bold print) that are directly involved in substrate-darunavir-interactions (change of S2/S2' subsites). | ||
The other 18 mutations are outside the binding cleft, but some are still in direct contact with the binding residues (e.g. <scene name='Sandbox_Reserved_712/L10i/1'>L10I</scene>, K20M, <scene name='Sandbox_Reserved_712/L33f/1'>L33F</scene>, <scene name='Sandbox_Reserved_712/I54v/1'>I54L/V</scene> and <scene name='Sandbox_Reserved_712/L90m/1'>L90M</scene>). | The other 18 mutations are outside the binding cleft, but some are still in direct contact with the binding residues (e.g. <scene name='Sandbox_Reserved_712/L10i/1'>L10I</scene>, K20M, <scene name='Sandbox_Reserved_712/L33f/1'>L33F</scene>, <scene name='Sandbox_Reserved_712/I54v/1'>I54L/V</scene> and <scene name='Sandbox_Reserved_712/L90m/1'>L90M</scene>). | ||
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<scene name='Sandbox_Reserved_712/Mutations_flap/1'>Mutations</scene> <scene name='Sandbox_Reserved_712/L33f/1'>L33F</scene>, <scene name='Sandbox_Reserved_712/M36l/1'>M36L</scene>, <scene name='Sandbox_Reserved_712/N37t/1'>N37T</scene>, | <scene name='Sandbox_Reserved_712/Mutations_flap/1'>Mutations</scene> <scene name='Sandbox_Reserved_712/L33f/1'>L33F</scene>, <scene name='Sandbox_Reserved_712/M36l/1'>M36L</scene>, <scene name='Sandbox_Reserved_712/N37t/1'>N37T</scene>, | ||
<scene name='Sandbox_Reserved_712/P39s/1'>P39S</scene>, <scene name='Sandbox_Reserved_712/K45r/1'>K45R</scene>, M46I, <scene name='Sandbox_Reserved_712/I54v/1'>I54V</scene> and <scene name='Sandbox_Reserved_712/K55r/1'>K55R</scene> cause structural changes in the flap region and the flap hinge. | <scene name='Sandbox_Reserved_712/P39s/1'>P39S</scene>, <scene name='Sandbox_Reserved_712/K45r/1'>K45R</scene>, M46I, <scene name='Sandbox_Reserved_712/I54v/1'>I54V</scene> and <scene name='Sandbox_Reserved_712/K55r/1'>K55R</scene> cause structural changes in the flap region and the flap hinge. | ||
The pictures on the right (Fig. | The pictures on the right (Fig.2 and Fig.3) show the regions (indicated in blue) that undergo structural changes caused by the mutations. | ||
To see the full images, with changes in PR<sub>DRV1</sub> and comparative structure of wild-type, PR<sub>DRV1</sub> and PR<sub>DRV5</sub> follow the links: | To see the full images, with changes in PR<sub>DRV1</sub> and comparative structure of wild-type, PR<sub>DRV1</sub> and PR<sub>DRV5</sub> follow the links: | ||
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2738195/figure/f4/ Structural changes in PR<sub>DRV</sub> mutants relative to wild-type PR] and | [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2738195/figure/f4/ Structural changes in PR<sub>DRV</sub> mutants relative to wild-type PR] and | ||
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It was discovered that the inhibitor substituents can adjust their positions depending on changes of the substrate binding pockets. Among them the P2' aminophenyl moiety undergoes the biggest changes. <ref name="Molecular" /> | It was discovered that the inhibitor substituents can adjust their positions depending on changes of the substrate binding pockets. Among them the P2' aminophenyl moiety undergoes the biggest changes. <ref name="Molecular" /> | ||
== '''Phenotypic susceptibility and enzymatic analysis''' == | == '''Phenotypic susceptibility and enzymatic analysis''' == | ||