Tag Archives: HMM

What do a TIM barrel and flavodoxin have in common?

4q37_bio_r_250Last month Birte Höcker, an experimental and theoretical protein scientist form the Max Planck Institute for Developmental Biology published an interesting article in Nature Chemical Biology.  The general challenge described is that sequences that look different on first inspection can give rise to very similar 3D structures. It also shows a nice combination of bioinformatics complemented with experimental work. Central in this case are the two folds (Figure 1, blue and green):

  • TIM barrel also known as the (βα)8-barrel  consisting of 8 β-strands in the core and 8 α-helixes around
  • Flavodoxin  which folds with 2 α-helixes on the outside sandwiching 5 βstrands in the core.

So the common theme: they both have αhelixes on the outside, sheets on the inside.

The underlaying question here is: How is one fold converted to the other?

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