Alpha helices have been mentioned in green colour and beta sheets are blue in colour.
Alignment of NcGRA9 and TgGRA9 protein sequences resulted in a high sequence identity of 60%, and TgGRA9 also exhibited similar hydrophilicity, hydrophobic domains, and
alpha helices. Other T.
So, most of the studied proteins contain both alpha helices and beta strands.
For this in silico experiment, we used alpha helices, beta strands, four types of coil regions (BCH: coil between beta strand and alpha helix; HCB: coil between alpha helix and beta strand; BCB: coil between two beta strands; and HCH: coil between two alpha helices), and four types of supersecondary structural motifs (B-BCH-H: beta strand and alpha helix separated by a region of coil; HHCB-B: alpha helix and beta strand separated by the region of coil; B-BCB-B: two beta strands and coil between them; H-HCH-H: two alpha helices and coil between them).
Even though the most commonly distributed kind of secondary structural motif (beta strand-major binder-random coil) is characteristic for Glu residues binding [Mn.sup.2+], in proteins encoded by GC-rich genes glutamic acid residues from alpha helices became able to bind that ion too.
According to the results of several studies [7, 8], the number of amino acid residues in 3/10 helices is about 10 times lower than the number of residues in alpha helices. However, that ratio between the number of residues in 3/10 helices and the number of residues in alpha helices cannot be considered as an argument towards justifying the extreme rarity of 3/10 helices.
Yet another popular theory states that 3/10 helices are usually situated before or after alpha helices [1, 4, 9].
Towards this goal, Compugen developed a sequence-based computational method for the prediction of intra-molecular interacting
alpha helices. We hypothesized that adding peptides corresponding to one of the interacting helices would interfere with the formation of the helix-helix interaction, thereby capturing the target protein in its 'open' conformation.
The researchers found that the chains folded into spiral structures resembling
alpha helices in proteins, suggesting that hydrogen bonds are not central to the folding of
alpha helices.
Previous work had shown that combinations of just three amino acids are sufficient to form bundles of spiral-shaped structures called
alpha helices. The bundles are rather formless, however.
Alpha helices were found to be easiest to predict, with various researchers correctly predicting the location of seven, eight or nine of the molecule's 10 helices.
Photo: Part of the tertiary structure of the enzyme lactate dehydrogenase, showing the spatial arrangement of its alpha helices and beta-pleated sheets.