![]() In this mode, a side-chain ridge lies in a groove formed by other regions of the protein (example in Fig. and residues in helices are listed in the legend of Fig. As a result, the final pool contained 12 proteins for a total of 13 helices (Protein Data Bank accession nos. These reports only name a small fraction of the structures included in their studies. In an effort to verify this idea, we performed a visual inspection of long 3 10 helices containing at least two turns (seven or more residues) in protein structures listed in three different papers ( Peters et al., 1996 Pal and Basu, 1999 Enkhbayar et al., 2006). Intuitively, this disposition imposes specific structural requirements for the packing of long 3 10 helices with other protein regions. In contrast, as a result of the ∼3.2 residues per helical turn in 3 10 helices, side chains are disposed in a more restrictive fashion they form ridges along the helix ( Fig. This arrangement therefore imposes few structural restrictions on the interacting partners and increases the probability of the stabilization of long α helices in a protein. In an α helix, the 3.6 residues per turn positions side chains every 100° around the helical axis, staggering the side chains and offering an extensive set of modes of interaction ( Fig. For α helix packing in proteins, it has been shown that there is a maximization of the interaction surface between helices ( Bowie, 1997). Interestingly, the authors concluded that 3 10 helices are para-helices, helices where long-range order is not maintained.Ĭlearly, the stability of a helix in a protein structure is very dependent on the packing interactions established with other protein regions. ![]() This study also classified individual 3 10 helices as regular or irregular, according to the level of variation of stereochemical parameters along the helix, and found that the percentage of irregular helices increased rapidly with length. As expected, the large majority was composed of helices with fewer than two helical turns, but a significant number spanned more than seven residues: 53 helices were 8 residues long, 13 helices were 9 residues long, 4 helices spanned 10 residues, and 1 helix was 11 residues long. More recently, a structural analysis of 689 protein chains with low sequence identity (≤20%) and solved at better than 1.6-Å resolution found 1,774 3 10 helices spanning five residues or more ( Enkhbayar et al., 2006). A 1999 survey found 132 cases of 3 10 helices with six amino acids or more ( Pal and Basu, 1999). The very large number of protein structures currently available has revealed that long 3 10 helices are present in proteins. The authors also concluded that 3 10 helices in proteins differed from the canonical conformation by having an average of 3.2 residues per turn instead of three residues, and noticed that 3 10 helices are in general irregular, presenting a wide variability in their main-chain torsion angle distribution. ![]() In contrast, they found that the 3 10 conformation was present in only 3.4% of the total number of residues 3 10 helices had a mean length of 3.3 residues, with just one helix spanning six residues. Later, in a comparative study of protein structures, Barlow and Thornton (1988) analyzed 57 protein structures and showed that 32% of the total number of residues were involved in the formation of α helices α helices presented a mean length of 10 residues, with the longest extending over 27 residues. When Pauling, Corey, and Branson proposed the α-helical and the 3 10-helical conformations as protein structural motifs, they concluded that the 3 10 helix had a distorted hydrogen bond network and was most likely unstable ( Pauling et al., 1951). This idea has its origins in the classical studies of the helical conformation of polypeptides. There is a generalized belief among structural biologists that 3 10 helices are inherently unstable and are, therefore, relatively rare and short, not spanning more than three to four residues. Because of their potential functional impact, it is worthwhile focusing our attention on two characteristics of 3 10 helices, stability and dynamics. ![]()
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