User:Fadel A. Samatey/FlhBc I: Difference between revisions

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<span style="font-size:160%"><b>Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins.</b></span><br><br>

<span style="font-size:120%">Vladimir A. Meshcheryakov, Akio Kitao, Hideyuki Matsunami and [[Fadel A. Samatey Group|Fadel A. Samatey]] ([[Fadel A. Samatey Group (Japanese)|サマテ]]). ''Acta Cryst. D69: 812-820 (2013). [http://dx.doi.org/10.1107/S0907444913002102 doi:10.1107/S0907444913002102] <span style="background-color:#ffff80;padding:3px;"><i>Open Access.</i></span></span>

<br>

Contact: [[Image:Samatey-email-address.png|160px]]

===Brief Introduction===

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==Molecular Tour: FlhBc Structures==

<!--<table cellpadding="6" style="background-color:#ffff80"><tr><td>

This page is under construction. We expect to complete additional interactive molecular scenes before May 5, 2013.

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<jmol>

<text>Do Structural Alignment</text>

</jmolButton>

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===Flexibility of N-Terminus===

Molecular dynamics simulations suggested that the mutations in 281-285 reduced flexibility of the N-terminal alpha helix, and hence that such flexibility may be important for function. Indeed, 226-267 (the N-terminal helix is 229 to about 262) is predicted to be intrinsically disordered<ref>Prediction of intrinsic disorder for ''Salmonella typhimurium'' FlhB by the FoldIndex server (image below, at right). [[Image:3b0z-FlhB-foldindex.png|frame]]</ref>. The formation of a helix seems likely to ~~be the result of~~ stabilization by crystal contacts mentioned above.

Molecular dynamics simulations suggested that the mutations in 281-285 reduced flexibility of the N-terminal alpha helix, and hence that such flexibility may be important for function. Indeed, 226-267 (the N-terminal helix is 229 to about 262) is predicted to be intrinsically disordered<ref>Prediction of intrinsic disorder for ''Salmonella typhimurium'' FlhB by the FoldIndex server (image below, at right). [[Image:3b0z-FlhB-foldindex.png|frame]]</ref>. The observed formation of a helix seems likely to depend upon stabilization by crystal contacts mentioned above.

===Evolutionary Conservation===

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There is a prominent strip of conserved residues on one side of the long N-terminal alpha helix. As mentioned above, the auto-catalytically cleaved segment, including 269 and 270, is highly conserved. In contrast (as mentioned above) the protruding loop 281-285 (which is necessary for function and suggested to be important for flexibility of the N terminus) is not conserved.

Conservation of ''A. aeolicus'' FlhBc was similar, especially in the regions mentioned above.

Conservation of ''A. aeolicus'' FlhBc (not shown) was similar, especially in the regions mentioned above.

Turning to the positive charges discussed above, <scene name='User:Fadel_A._Samatey/FlhBc_I/Conservation_st/3'>here only positively charged sidechains (Lys, Arg) are spacefilling. His is depicted in sticks.</scene> All atoms are colored by conservation.

Turning to the positive charges discussed above, <scene name='User:Fadel_A._Samatey/FlhBc_I/Conservation_st/3'>here only positively charged sidechains (Lys, Arg) are spacefilling. His is depicted in sticks.</scene> All atoms are colored by conservation. With spinning off, touch any sidechain to report its identity.

</StructureSection>

===References and Notes===

* If you have any comments, questions, or if there is any problem with this page, please contact [[Image:Samatey-email-address.png|150px]].

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@@ Line 4: / Line 4: @@
 <span style="font-size:160%"><b>Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins.</b></span><br><br>
 <span style="font-size:120%">Vladimir A. Meshcheryakov, Akio Kitao, Hideyuki Matsunami and [[Fadel A. Samatey Group|Fadel A. Samatey]] ([[Fadel A. Samatey Group (Japanese)|サマテ]]). ''Acta Cryst. D69: 812-820 (2013). [http://dx.doi.org/10.1107/S0907444913002102 doi:10.1107/S0907444913002102] <span style="background-color:#ffff80;padding:3px;"><i>Open Access.</i></span></span>
+<br>
+Contact: [[Image:Samatey-email-address.png|160px]]
 ===Brief Introduction===
@@ Line 11: / Line 13: @@
 ==Molecular Tour: FlhBc Structures==
-<StructureSection size='450' frame='true' align='right' caption='Cytoplasmic domain of FlhB' scene='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st/6' >
+<!--<StructureSection size='400' frame='true' align='right' caption='Cytoplasmic domain of FlhB' scene='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st/6' >-->
+<StructureSection load='' size='400' side='right' caption='Cytoplasmic domain of FlhB' scene='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st/6'>
 <!--<table cellpadding="6" style="background-color:#ffff80"><tr><td>
 This page is under construction. We expect to complete additional interactive molecular scenes before May 5, 2013.
@@ Line 34: / Line 37: @@
 <jmol>
 <jmolButton>
-<script>if ({1.2}.count > 0); compare {1.1} {1.2} SUBSET {*.ca} {246-269:A} {240-263:C} {272-280:B} {266-274:D} {285-351:B} {279-345:D} ATOMS rotate translate; zoomto *1.5;spin y; else; set echo bottom left; color echo white; font echo 20 sansserif;echo "Please display both structures first!"; delay 4; set echo off; endif;</script>
+<script>if ({1.2}.count > 0); compare {1.1} {1.2} SUBSET {*.ca} {246-269:A} {240-263:C} {272-280:B} {266-274:D} {285-351:B} {279-345:D} ATOMS rotate translate 3; zoomto *1.5;spin y; else; set echo bottom left; color echo white; font echo 20 sansserif;echo "Please display both structures first!"; delay 4; set echo off; endif;</script>
 <text>Do Structural Alignment</text>
 </jmolButton>
@@ Line 49: / Line 52: @@
 ===Flexibility of N-Terminus===
-Molecular dynamics simulations suggested that the mutations in 281-285 reduced flexibility of the N-terminal alpha helix, and hence that such flexibility may be important for function. Indeed, 226-267 (the N-terminal helix is 229 to about 262) is predicted to be intrinsically disordered<ref>Prediction of intrinsic disorder for ''Salmonella typhimurium'' FlhB by the FoldIndex server (image below, at right). [[Image:3b0z-FlhB-foldindex.png|frame]]</ref>. The formation of a helix seems likely to be the result of stabilization by crystal contacts mentioned above.
+Molecular dynamics simulations suggested that the mutations in 281-285 reduced flexibility of the N-terminal alpha helix, and hence that such flexibility may be important for function. Indeed, 226-267 (the N-terminal helix is 229 to about 262) is predicted to be intrinsically disordered<ref>Prediction of intrinsic disorder for ''Salmonella typhimurium'' FlhB by the FoldIndex server (image below, at right). [[Image:3b0z-FlhB-foldindex.png|frame]]</ref>. The observed formation of a helix seems likely to depend upon stabilization by crystal contacts mentioned above.
 ===Evolutionary Conservation===
@@ Line 56: / Line 59: @@
 There is a prominent strip of conserved residues on one side of the long N-terminal alpha helix. As mentioned above, the auto-catalytically cleaved segment, including 269 and 270, is highly conserved. In contrast (as mentioned above) the protruding loop 281-285 (which is necessary for function and suggested to be important for flexibility of the N terminus) is not conserved.
-Conservation of ''A. aeolicus'' FlhBc was similar, especially in the regions mentioned above.
+Conservation of ''A. aeolicus'' FlhBc (not shown) was similar, especially in the regions mentioned above.
-Turning to the positive charges discussed above, <scene name='User:Fadel_A._Samatey/FlhBc_I/Conservation_st/3'>here only positively charged sidechains (Lys, Arg) are spacefilling. His is depicted in sticks.</scene> All atoms are colored by conservation.
+Turning to the positive charges discussed above, <scene name='User:Fadel_A._Samatey/FlhBc_I/Conservation_st/3'>here only positively charged sidechains (Lys, Arg) are spacefilling. His is depicted in sticks.</scene> All atoms are colored by conservation. With spinning off, touch any sidechain to report its identity.
 </StructureSection>
 ===References and Notes===
+* If you have any comments, questions, or if there is any problem with this page, please contact [[Image:Samatey-email-address.png|150px]].
 <references />
 <!--