Posted: Jul 22, 2010 12:32 pm
One thing I don't want to do is get into a Monty Python type argument about IC and things seem to be heading that way. That is why I would prefer to get into more detail and I'm concentrating on the flagellar hook because I see this as possibly the strongest position to argue for the IC of the flagellum. So if anyone can convince me that this is easily explained by unguided natural means, I'm ready to listen.
There is a problem with just saying it has homologs and that's it. Here is a link and an excerpts so that you can see some of the difficulties. It explains one domain of a single hook protein:
http://structbio.vanderbilt.edu/chazin/classnotes/Hybrid-methods-paper1.pdf
There is a problem with just saying it has homologs and that's it. Here is a link and an excerpts so that you can see some of the difficulties. It explains one domain of a single hook protein:
http://structbio.vanderbilt.edu/chazin/classnotes/Hybrid-methods-paper1.pdf
Domain
D1 has a rather complex, unusual fold composed of many different folding motifs: a stack of four horizontal b-hairpins one above another, alternating their orientations with crossing angles of about 1208 (Asn 79–Leu 115 and Gly 324–Gln 337, on the left side in Fig. 1); a triangular loop (Thr 116–Pro 135, on the right side in front); a four-stranded (Leu 288–Ile 314 and Asn 357–Ser 363) and a two-stranded (Val 315–Asn 321 and Ser 339–Thr 346) b-sheet (in the upper and lower half, respectively, both on the back side); two consecutive b-turns (Thr 346–Phe 352, behind the triangular loop); and a vertically extended chain (Pro 135–Ala 144, in the centre front of the upper half). This extended chain seems to be a backbone around which the other motifs assemble. A three-dimensional structural similarity search using software DALI25 resulted in no match for domain D1, confirming its unique fold. The longest dimensions of domain D1 and D2 are about 50 and 45A ° , respectively, and these two domains are connected along their long axes with an angle of about 708.
As predicted from amino acid sequences and expected from farultraviolet circular dichroic spectra, the structure of FlgE31 is very different from that of the F41 fragment of flagellin21,26, which consists of three domains with domain D1, which consists of three a-helices and a b-hairpin, domain D2, which is formed from many b-hairpins, and domain D3, which is made of a tight b-barrel. It is curious that these two molecules with completely different structures both form the tubular structures with basically the same architecture and helical symmetry.