Structure

Upon comparison with HSF's from several organisms including yeast, Drosophila, humans, and mice it is now clear that several domains of the HSF are evolutionarily conserved. It is likely that the common ancestor of all heat shock factor proteins contained these domains in a similar form. The major domains of conservation include:

• "Winged" Helix-Turn-Helix domain - a modified DNA binding Helix-Turn-Helix domain with a small beta sheeet and an extended appendage that protrudes out from the central core like a wing.



• Trimerization domain - an eighty residue hydrophobic pocket adjacent to the DNA binding domain which is necessary for the oligomerization of HSF monomers.



• Transactivation domain - located near the carboxy terminus, this domain is required for activation of the genes that are HSF targets.

Secondary Structure of the HSF DNA binding domain

To date only the structure of the "Winged" Helix-Turn-Helix domain of Kluyveromyces lactis HSF has been determined by x-ray crystallography. The structure reveals that this domain is formed from 3 alpha helices and 4 beta strands. I used the know structure to test how well current secondary structure prediction programs can predict stucture from sequence. Two predictions programs were used, Garnier-Robson-Osguthorpe and Rost/Sander. Neither prediction program was able to completely identify all of the correct secondary structures but the Rost/Sander program came very close.

Comparison of Secondary Structure Predictions

AA    Amino Acid (102 total)
G-R-O Garnier-Robson-Osguthorpe - Secondary Structure Prediction
R-S   Rost/Sander - Secondary Structure Prediction
PDB   Protein Database - Annonation of Secondary Structure


AA    GSRRASVGSMARPAFVNKLWSMVNDKSNEKFIHWSTSGESIVVPNRERFVQEVLPKYFKH
G-R-O CCCBTCCCCBBBAAAAAAAAAAACCCCAAAAATCCCCTTCBBBCCCTAAAAAAAATAAAC
R-S               HHHHHHHHHHHH      EEEEE    EEEE   HHHHHHHHHHH
PDB              S HHHHHHHHHHH GGGTTTSEE TTS SEEES HHHHHHHTHHHH SS

AA    SNFASFVRQLNMYGWHKVQDVKSGSMLSNNDSRWEFENERHA
G-R-O CCTCAAABTCTTTTTCBBBTTTCCCBCCCCCCCCAAAAAAAA
R-S     HHHHHHHHHH    EEEE
PDB     HHHHHHHHHHTTEEE             S  EEEEE

To better understand the details of this structure I have explored how it is classified by the program CATH. The CATH lineage for the Kluyveromyces lactis HSF is as follows:

		Mainly Alpha
		Non-Bundle
		Arc Repressor Mutant, subunit A
		TRANSCRIPTION REGULATION
		TRANSCRIPTION FACTOR
		TRANSCRIPTION FACTOR
		TRANSCRIPTION/DNA

The basis for this type of classification lineage is that although protein evolution quickly makes the sequences of two functionally similar homologs look very different, the overall fold of the proteins will be conserved. Therefore, structures are classified by there overall fold and placed into groups based on the similarity of their fold to other folds in the group. This method of classification does not take into account sequence variability allowing proteins that may be divergent at the level of amino acid sequence to be group together based on similar folds.

The DNA binding domain of the HSF from Kluyveromyces lactis consists mainly of alpha helices and is therefore grouped along with other proteins that have the same secondary structure composition in the mainly alpha class. The second classification level (Architecture) defines the orientation of secondary structural elements with relation to one another. The non-bundle designation defines domains that lack significant interaction between secondary structural elements. The Topology (overall shape and connectivity of secondary structures) of HSF is most similar to the one defined by the Arc Repressor Mutant, subunit A under which it is grouped. Moreover, HSF shares sequence homology with proteins that function as transcription factors and probably shares a common ancestor with other transcription factors (level S and H respectively). A summary image from the PDBsum website depicting the secondary structures of HSF and the connections between them is shown below.

The details of the secondary structure of HSF are further discussed in the structure-function page.