Sandbox Reserved 963: Difference between revisions

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===Comparison of unliganded and liganded WO2 Fab structures===

Unliganded and liganded structures '''(Figure 4)''' superimpose very closely with an r.m.s.d. (root-mean-square deviation) of 0.3 Å on all Cα atoms (the r.m.s.d. is the measure of the average distance between the atoms of superimposed proteins[http://en.wikipedia.org/wiki/Root-mean-square_deviation]). Even the '''CDRs of liganded and unliganded states are barely distinguishable'''. Except for some small variations (<1 Å) around Ser27(E)L (L1), <scene name='60/604482/My_first_scene/11'>Lys33H</scene> ~~(H1)~~, Asp54H (H2) and Glu100(C)H (H3), there is no substantial change in the CDRs when Aβ binds with WO2.

Unliganded and liganded structures '''(Figure 4)''' superimpose very closely with an r.m.s.d. (root-mean-square deviation) of 0.3 Å on all Cα atoms (the r.m.s.d. is the measure of the average distance between the atoms of superimposed proteins[http://en.wikipedia.org/wiki/Root-mean-square_deviation]). Even the '''CDRs of liganded and unliganded states are barely distinguishable'''. Except for some small variations (<1 Å) around Ser27(E)L (L1), <scene name='60/604482/My_first_scene/11'>Lys33H (H1)</scene> , <scene name='60/604482/My_first_scene/16'>Asp54H (H2)</scene> and Glu100(C)H (H3), there is no substantial change in the CDRs when Aβ binds with WO2.

Moreover, thanks to temperature-factors analysis, it appears that CDR H1 is less flexible in the liganded structure.<ref>Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.,Miles LA, Wun KS, Crespi GA, Fodero-Tavoletti MT, Galatis D, Bagley CJ, Beyreuther K, Masters CL, Cappai R, McKinstry WJ, Barnham KJ, Parker MW J Mol Biol. 2008 Mar 14;377(1):181-92. Epub 2008 Jan 30. PMID:18237744</ref>

[[Image:Fig. 1b.png|frame|'''Figure 4 :''' Representation of Aβ (shown as ball-and-stick) in the WO2 Fab variable domain CDRs after superimposition of their Cα atoms. The unliganded Form A is in yellow and the complex with Aβ<sub>1-16</sub> is in blue<ref>Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.,Miles LA, Wun KS, Crespi GA, Fodero-Tavoletti MT, Galatis D, Bagley CJ, Beyreuther K, Masters CL, Cappai R, McKinstry WJ, Barnham KJ, Parker MW J Mol Biol. 2008 Mar 14;377(1):181-92. Epub 2008 Jan 30. PMID:18237744</ref>]]

Sandbox Reserved 963: Difference between revisions

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@@ Line 106: / Line 106: @@
 ===Comparison of unliganded and liganded WO2 Fab structures===
-Unliganded and liganded structures '''(Figure 4)''' superimpose very closely with an r.m.s.d. (root-mean-square deviation) of 0.3 Å on all Cα atoms (the r.m.s.d. is the measure of the average distance between the atoms of superimposed proteins[http://en.wikipedia.org/wiki/Root-mean-square_deviation]). Even the '''CDRs of liganded and unliganded states are barely distinguishable'''. Except for some small variations (<1 Å) around Ser27(E)L (L1), <scene name='60/604482/My_first_scene/11'>Lys33H</scene> (H1), Asp54H (H2) and Glu100(C)H (H3), there is no substantial change in the CDRs when Aβ binds with WO2.
+Unliganded and liganded structures '''(Figure 4)''' superimpose very closely with an r.m.s.d. (root-mean-square deviation) of 0.3 Å on all Cα atoms (the r.m.s.d. is the measure of the average distance between the atoms of superimposed proteins[http://en.wikipedia.org/wiki/Root-mean-square_deviation]). Even the '''CDRs of liganded and unliganded states are barely distinguishable'''. Except for some small variations (<1 Å) around Ser27(E)L (L1), <scene name='60/604482/My_first_scene/11'>Lys33H (H1)</scene> , <scene name='60/604482/My_first_scene/16'>Asp54H (H2)</scene> and Glu100(C)H (H3), there is no substantial change in the CDRs when Aβ binds with WO2.
 Moreover, thanks to temperature-factors analysis, it appears that CDR H1 is less flexible in the liganded structure.<ref>Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.,Miles LA, Wun KS, Crespi GA, Fodero-Tavoletti MT, Galatis D, Bagley CJ, Beyreuther K, Masters CL, Cappai R, McKinstry WJ, Barnham KJ, Parker MW J Mol Biol. 2008 Mar 14;377(1):181-92. Epub 2008 Jan 30. PMID:18237744</ref>
 [[Image:Fig. 1b.png|frame|'''Figure 4 :''' Representation of Aβ (shown as ball-and-stick) in the WO2 Fab variable domain CDRs after superimposition of their Cα atoms. The unliganded Form A is in yellow and the complex with Aβ<sub>1-16</sub> is in blue<ref>Amyloid-beta-anti-amyloid-beta complex structure reveals an extended conformation in the immunodominant B-cell epitope.,Miles LA, Wun KS, Crespi GA, Fodero-Tavoletti MT, Galatis D, Bagley CJ, Beyreuther K, Masters CL, Cappai R, McKinstry WJ, Barnham KJ, Parker MW J Mol Biol. 2008 Mar 14;377(1):181-92. Epub 2008 Jan 30. PMID:18237744</ref>]]