Sandbox Reserved 813: Difference between revisions

There are two diffent domains in the Oct-4 sequence : the '''POU-specific domain''' (POUs) located on the N-terminal subunit and the '''POU-homeodomain''' (POUhd)located in the C-terminal subunit of the sequence.  

The first figure on the left shows an aligment between different transcription factors such as Pit-1[http://en.wikipedia.org/wiki/Pituitary-specific_positive_transcription_factor_1] , Oct-1 [http://en.wikipedia.org/wiki/Oct-1] or oct-2 [http://en.wikipedia.org/wiki/Oct-2]. We can see that there are few conserved sites between each transcription factors. We can also see the organization of the Oct-4 structure : a POUs linked to an POUh thanks to a linker which is actually an alpha helix.  

The <scene name='56/568011/Pous/1'>POU specific domain </scene> is located on the N-terminal site of the Oct-4 sequence and precisely from the 131th  amino acid to the 205th. The POU-specific domain is able to bind autonomously the DNA with the binding consensus : [gAATAT(G/T)CA]. Thanks to a helix-turn-helix[http://en.wikipedia.org/wiki/Helix-turn-helix]specific motif. As its name suggests, this pattern is composed of two α helix  [http://en.wikipedia.org/wiki/Alpha_helixlinked] by an amino acids sequence which corresponds to the turn. The second helix is the most involved in the DNA binding. Indeed, this helix is able to carry out hydrogen bonds and Van der Waals interactions with bases in the major groove of DNA. The first helix allows to stabilize the complex DNA-protein. In the Pou specific domain of the transcription factor Oct-4, there are 2 HTH motif linked by another alpha helix. The HTH motif is responsible of the DNA binding thanks to the first amino acid located in every helix in HTH. Indeed, this amino acid is a  

<scene name='56/568011/Glutamic_acide/1'>glutamic acid</scene> which is able to interact with the backbone phosphate and the adenine base in the DNA binding site. Thanks to bioinformatics tools, alignments were carried out. Very good alignment between the Oct-4 POU domain and the Lambda phage [http://en.wikipedia.org/wiki/Lambda_phage] POU domain was thus discoverded.  

The linker tethers the two POU subdomains and is hypervariable in both sequence and length. Thus the linker in Oct-4 contrarly to the linker of the other member of the POU family like Oct-1 [http://en.wikipedia.org/wiki/POU2F1], is an 17 amino acid  “alpha”-helix and is exposed to the protein surface. The Oct4 linker functions as a '''protein-protein interaction''' interface and plays a highly important role during '''reprogramming'''. This alpha 5 helix interacts with helices alpha 2 and alpha 4 of POU s mostly by Van der Waals interaction, except for the hydrogen bond between<scene name='56/568011/Liaison_25-81/1'>Tyr 25 of POUs and Gln 81</scene> of the linker. The interaction between Val 36 of POUs and the the carboxy-terminal of the helix alpha 5 of the linker plays an important role. In all known Oct-4 sequences <scene name='56/568011/Asn79_and_leu80/1'>Asn79 and Leu80 </scene> are invariant but not  conserved in other members of Oct family.  Mutation in the linker of GLn81 by an Arg leads to a complete loss-of-function phenotype. Likewise mutation of Leu80 by an Ala abolished biological activity. It is deduces that this mutation disturb an interaction surface with yet unknown additional factors. Overall mutation of the linker of the protein lead <scene name='56/568011/Asn76_asn_77_asn_79/1'>residues exposed to the surface</scene>(Asn76, Asn 77, Asn 79)  to significantly fewer function. The integrity of the linker is essential for successful reprogramming.

On the figure n°4, we can see the  surrounding of the linker. There are different hydrogen bonds to save the tridimentional structure of OCT-4: the first hydrogen bond is located between  <scene name='56/568011/Hydrogen_bond_between_33-_70/1'>the tyrosine 33 and the tryptophane 70</scene>.