Sandbox Reserved 973

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PAS-A domains don't have the same conformation in the two subunits. In BMAL1, we can observe 3 loops involving about 60 residues whereas in CLOCK there are only 25 residues in a single loop. Nevertheless, this two PAS-A domains adopt a typical PAS fold. The core of these domains contains a five-stranded antiparallel β sheet (AβBβGβHβIβ) as well as numerous α helices (Cα, DαEαFα). They also contain an N-terminal A'α helix that does not belong to the canonical PAS fold. Those helices pack in between the β-sheet faces and are involved in the dimerization interactions.
PAS-A domains don't have the same conformation in the two subunits. In BMAL1, we can observe 3 loops involving about 60 residues whereas in CLOCK there are only 25 residues in a single loop. Nevertheless, this two PAS-A domains adopt a typical PAS fold. The core of these domains contains a five-stranded antiparallel β sheet (AβBβGβHβIβ) as well as numerous α helices (Cα, DαEαFα). They also contain an N-terminal A'α helix that does not belong to the canonical PAS fold. Those helices pack in between the β-sheet faces and are involved in the dimerization interactions.
The two PAS-A domains are mostly linked thanks to hydrophobic bonds. Indeed, Phe104, Leu105, and Leu113 on the A′α helix of CLOCK are interacting with the
The two PAS-A domains are mostly linked thanks to hydrophobic bonds. Indeed, Phe104, Leu105, and Leu113 on the A′α helix of CLOCK are interacting with the
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residues Leu159 on strand Aβ, Thr285 and Tyr287 on Hβ, Val315 and Ile317 on strand Iβ, of the BMAL1 subunit. The same kind of bonds are occuring between the A'α helix of BMAL1 and the β-sheet of CLOCK.
+
residues Leu159 on strand Aβ, Thr285 and Tyr287 on Hβ, Val315 and Ile317 on strand Iβ, of the BMAL1 subunit. The same kind of bonds are occuring between the A'α helix of BMAL1 and the β-sheet of CLOCK. Thus the 2 PAS-A domains form a

Revision as of 21:29, 6 January 2015

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This Sandbox is Reserved from 15/11/2014, through 15/05/2015 for use in the course "Biomolecule" taught by Bruno Kieffer at the Strasbourg University. This reservation includes Sandbox Reserved 951 through Sandbox Reserved 975.
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Contents

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This is a default text for your page '. Click above on edit this page' to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.

Function and overall structure

The heterodimeric complex CLOCK:BMAL1 is a transcriptionnal factor responseable for the activation of 2 genes; Period(Per1,Per2) and Cryptochrome(Cry1,Cry2), by interacting with the E-box DNA. This is a central mechanism in the circadian cycle regulation as the downstream products PER and CRY can accumulate dimerize too, so they can rpress transcription of Bmal1 and Clock at night, creating an autregulatory feedback loop. The two peptides involved in the dimere have very similar sequences. Chez mus musculusBMAL1 is 387 residues long when CLOCK is 361. Both of these subunits are basic helix-loop-helix-PAS proteins (bHLH-PAS) which contains the same 3 domains: a bHLH domain, a PAS-A domain and a PAS-B domain. They are involved in DNA binding and dimerization abilities. Mutations that affects the heterodimer interfaces can then disturb the activity of the complex and therefore the persistence and periodicity of the circadian cycle.


Domains

PAS-A domains don't have the same conformation in the two subunits. In BMAL1, we can observe 3 loops involving about 60 residues whereas in CLOCK there are only 25 residues in a single loop. Nevertheless, this two PAS-A domains adopt a typical PAS fold. The core of these domains contains a five-stranded antiparallel β sheet (AβBβGβHβIβ) as well as numerous α helices (Cα, DαEαFα). They also contain an N-terminal A'α helix that does not belong to the canonical PAS fold. Those helices pack in between the β-sheet faces and are involved in the dimerization interactions. The two PAS-A domains are mostly linked thanks to hydrophobic bonds. Indeed, Phe104, Leu105, and Leu113 on the A′α helix of CLOCK are interacting with the residues Leu159 on strand Aβ, Thr285 and Tyr287 on Hβ, Val315 and Ile317 on strand Iβ, of the BMAL1 subunit. The same kind of bonds are occuring between the A'α helix of BMAL1 and the β-sheet of CLOCK. Thus the 2 PAS-A domains form a


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Structural highlights

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</StructureSection>

References

  1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
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