Sandbox Reserved 829: Difference between revisions

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Moreover, the two conformations of the Pdx1/DNA complex contained invariant contacts found in both conformations A and B, and variant contacts specific to each conformation.  
Moreover, the two conformations of the Pdx1/DNA complex contained invariant contacts found in both conformations A and B, and variant contacts specific to each conformation.  
[[Image:Final.jpg|right|1000px|thumb|'''Differences between conformation A and B'''  <ref name= "binding" />]]   
[[Image:Final.jpg|right|1000px|thumb|'''Differences between conformation A and B'''  <ref name= "binding" />]]   




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''* The N-terminal arm ''




The N-terminal arm  (residues 1 to 9) of PDX-1 homeodomain, first contacts the core TAAT bases of the DNA through the minor groove and contributes to the binding specificity. In PDX-1, the N-terminal sequence contains three basic residues :  Lys 2, Arg 3 and Arg 5.
In both PDX-1 conformations, Arg 5 forms hydrogen bonds with the bases of Thy 1 and Gua -1* through the minor groove, and van der Waals contact with Ade 2.


In conformation B, the N-terminal arm is more ordered with Lys 2 hydrogen bonded with the bases Ade 3 and Thy 2* in the minor groove, whereas in the conformation A, the N-terminal arm is mostly disordered. Scientists attributed the different contacts between the two conformations, to differences in DNA bending.


Arg 3 and Arg 43  help the stabilization of the N-terminal arm. In fact, the contact by Arg 3 and Arg 43 from the major groove with the phosphate backbone correlates with stabilizing the N-terminal arm. Moreover, these residues are more mobile in conformation A than in conformation B.


So, the most stable  configuration for the N-terminal arm of Pdx1 consists of Lys 2 inserted in the minor groove and Arg 3 outside of the minor grove contacting the phosphate backbone and Arg 43.






''* The N-terminal arm ''




The N-terminal arm  (residues 1 to 9) of PDX-1 homeodomain, first contacts the core TAAT bases of the DNA through the minor groove and contributes to the binding specificity. In PDX-1, the N-terminal sequence contains three basic residues :  Lys 2, Arg 3 and Arg 5.
In both PDX-1 conformations, Arg 5 forms hydrogen bonds with the bases of Thy 1 and Gua -1* through the minor groove, and van der Waals contact with Ade 2.
In conformation B, the N-terminal arm is more ordered with Lys 2 hydrogen bonded with the bases Ade 3 and Thy 2* in the minor groove, whereas in the conformation A, the N-terminal arm is mostly disordered. Scientists attributed the different contacts between the two conformations, to differences in DNA bending.


Arg 3 and Arg 43  help the stabilization of the N-terminal arm. In fact, the contact by Arg 3 and Arg 43 from the major groove with the phosphate backbone correlates with stabilizing the N-terminal arm. Moreover, these residues are more mobile in conformation A than in conformation B.


So, the most stable  configuration for the N-terminal arm of Pdx1 consists of Lys 2 inserted in the minor groove and Arg 3 outside of the minor grove contacting the phosphate backbone and Arg 43.




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Furthermore, the DNA curvature in conformation A or B differs from each other. The curvature of the DNA in conformation B is around 34° while the conformation A enable a curvature around 16°.  
Furthermore, the DNA curvature in conformation A or B differs from each other. The curvature of the DNA in conformation B is around 34° while the conformation A enable a curvature around 16°.  




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