Polypeptide alternate helical

Alternate Helical Structures. Since Pauling and Corey s description of the a helix [76], many other helical structures for polypeptides have been proposed and described. However, most of them are rare or found only in homopolymeric systems. These include the helix, the it helix, and the an helix. 

Figure 2 Composite structure of hair at various length-scales (a) filament protein with alternating helical/linker sections (helical section is shown atttie bottom) (b) coiled coil of filament proteins (in a polar environment two polypeptide chains naturally coil around each other in parallel, as this leaves the hydrophobic groups shielded in the centre) (c) intermediate filament with 16 coils (d) filament embedded in matrix (e) macrofibril (f) cortical call enclosed by cell-membrane complex.

The secondary structure of a protein is the shape adopted by the polypeptide chain—in particular, how it coils or forms sheets. The order of the amino acids in the chain controls the secondary structure, because their intermolecular forces hold the chains together. The most common secondary structure in animal proteins is the a helix, a helical conformation of a polypeptide chain held in place by hydrogen bonds between residues (Fig. 19.19). One alternative secondary structure is the P sheet, which is characteristic of the protein that we know as silk. In silk, protein... 

FIGURE 19.20 One of the four polypeptide chains that make up the human hemoglobin molecule. The chains consist of alternating regions of a helix and p sheet. The a-helix regions are represented by red helices. The oxygen molecules that we inhale attach to the iron atom (blue sphere) and are curried through the bloodstream. 

Figure 5-6. Examples of tertiary structure of proteins. Top The enzyme triose phosphate isomerase. Note the elegant and symmetrical arrangement of alternating p sheets and a helices. (Courtesy of J Richardson.) Bottom Two-domain structure of the subunit of a homodimeric enzyme, a bacterial class II HMG-CoA reductase. As indicated by the numbered residues, the single polypeptide begins in the large domain, enters the small domain, and ends in the large domain. (Courtesy ofC Lawrence, V Rod well, and C Stauffacher, Purdue University.)...

All the above-mentioned proteins have single-stranded folds based on solenoidal windings of one polypeptide chain. Recently, however, several triple-stranded /1-helices (alternatively, triple-stranded /l-solenoids ) have been described in bacteriophage tail proteins (Kanamaru et al., 2002 Smith et al., 2005 Stummeyer et al., 2005 van Raaij et al, 2001). In these structures, three identical chains wind around a common axis and their coils have an axial rise of 14.5 A, that is, 3 x 4.83 A (for details see Sections IV and V.D). In this chapter, triple-stranded /l-solenoids will be abbreviated as TS /l-solenoids, while the term /1-solenoid, if not otherwise qualified, will apply to the predominant group of single-stranded /l-solenoids. 

Current investigations on dilute polymer solutions are still largely limited to the class of macromolecular solutes that assume randomly coiled conformation. It is therefore natural that there should be a growing interest in expanding the scope of polymer solution study to macromolecular solutes whose conformations cannot be described by the conventional random-coil model. The present paper aims at describing one of the recent studies made under such impetus. It deals with a nonrandom-coil conformation usually referred to as interrupted helix or partial helix. This conformation is a hybrid of random-coil and helix precisely, a linear alternation of randomly coiled and helical sequences of repeat units. It has become available for experimental studies through the discovery of helix-coil transition phenomena in synthetic polypeptides. 

Inasmuch as this form of rotatory dispersion is in principle characteristic of the interaction of like chromophores, one would wish to employ it in the investigation of ordered polypeptide structures. But, as will become evident in the experimental use to which Eq. (18) has been put, it possesses in addition the distinct practical advantage that Xo of helices is close to Xc for disordered pol3q)eptide chains, that is, about 220 m/j, so that one equation can characterize mixtures of disordered chains and helices and at the same time yield a parameter, 6o, uniquely related to helical content. This feature is highlighted by a lack of similar adaptability displayed by alternative empirical equations proposed to describe helical dispersion. Yang and Doty (1957) have fitted data for helical poly-y-benzyl-L-gluta-mate to an abbreviated two-term Drude equation. 

These polypeptides nonetheless present a problem for characterizing the dispersion of the helix itself. If X for these disordered chains does not equal Xo, with the consequence that bo does not vanish when the helical form is destroyed, should not the foregoing derivation, based on the equality of Xc and Xo, be rejected It will be retained for reasons that are discussed below, but let us first consider an alternative device for assimilating simple dispersion to the Moffitt form, one which circumvents this assumption. What can be adequately represented with two constants, Xc and a°, can equally well be described with three, Xo, a , and bo. Consequently, the reduced mean residue rotation for the disordered form may be written... 

Note Added in Proof. Alternative explanations have recently been put forward to account for the height and shape of the transition in certain synthetic polypeptide monolayers (38). These do no however account for many of the results here presented or for the general pattern of behavior observed in monolayers when the a-helical conformation is present (5). 

P barrel The folding of a polypeptide chain to form a barrel-shaped structure with eight p strands as the lining. Eight a helices lie outside this p sheet. Both the a helices and the P strands follow a right-handed spiral around the axis of the barrel. The amino acid sequence in such a protein is such that p sheet and a helix alternate to give Pa)s- This motif was first seen in triose phosphate isomerase, and has since been observed in many other protein structures. 

---