Principles of Protein Structure - G. Schulz 1982

Mechanisms of polypeptide chain folding and association
Supersecondary structures
Supercoiling of α-helices

In the preceding chapters, we examined ordered segments of the main protein chain that form an energetically favorable Secondary Structure. The next, higher level of complexity involves ensembles of interacting secondary structures. The spatial architecture of such aggregates—the so-called supersecondary structure—is difficult to predict*. They can be identified only if they occur with sufficient frequency in Proteins. The very emergence of such structures indicates that they are either favored by The kinetics of the folding process or possess energetic advantages in the already folded protein.

In its most ordered form, the coiled-coil a-helix is found in Fibrous proteins. A prime example of supersecondary structure is the coiled-coil a-helix postulated by Crick [210]. In this structure, two a-helices are twisted around each other to form a left-handed superhelix with an identity period of approximately 140 Å (Fig. 5.11, a). Coiled-coil a-helices have been detected in the fibrous proteins a-keratin [211, 212], Tropomyosin [213], paramyosin [214], and the light meromyosin chain [215]. Short stretches of this supersecondary structure have been observed in Globular proteins containing a-helices packed approximately parallel or antiparallel to one another. The most well-known Examples of nearly linear helix packing include hemerythrin [216, 217], tobacco mosaic virus coat protein [180, 218], Bacteriorhodopsin [219], bacteriophage fd coat [220], and tyrosyl-tRNA synthetase [221].

* In a broader sense, the definition of supersecondary structure should also encompass ß-sheets, which represent ensembles of regular strands. However, supersecondary structure is typically understood to refer only to systems of regularly arranged peptide chains within ß-sheets.

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Fig. 5.11. Twisted two-stranded a-helix. a — general view of a left-handed two-stranded superhelix with an identity period of 140 Å. The dimensions of the individual a-helices are shown. Both helices are parallel; b — superposition of cylindrical projections of two parallel a-helices. The dashed line indicates the central axis of the superhelix. Ca atoms are indicated by bold dots. At a 10° tilt, all aa', dd', etc. contacts lie along the superhelix axis. Side chains - d', etc. (indicated by short ticks pointing in directions opposite to the C_a - C_β bond orientations) are located between the a, e, d side chains and the side chain of the next turn. Thus, all side chains in the contact regions between a, d, etc., and a', d' form a tight knob-into-hole packing. c — cross-section of a parallel two-stranded a-helix. The positions of C_a atoms are denoted in alphabetical order along The polypeptide chains; positions a and a' are at the same height.

Tight packing of side chains without significant distortion of the a-helices is possible within the superhelix. The structure of the superhelix can be visualized by overlaying the cylindrical nets of two neighboring a-helices. This can be done in such a way (Fig. 5.11, b) that a contact line is formed along which the side-chain interactions of alternating residues of both helices take place. Such interaction can proceed unhindered if both helices form a left-handed superhelix with a contact line in the form of a straight axis. The pitch of the superhelix can be determined using the contact line on one of the cylindrical nets—specifically, by the segment of the net cut off by the double intersection of the contact line with it. At an interhelical angle of about 10° (Fig. 5.11, b), the pitch is approximately 140 Å. The torsion angle values (∅, ψ) deviate slightly from those characteristic of an ideal single a-helix. The repeating structural unit in each chain is a heptapeptide (Fig. 5.11, c), with the seventh residue occupying an equivalent position relative to the superhelix axis (Fig. 5.11, b). This 7.0-residue repeat is slightly smaller than twice the pitch height of a single a-helix (2∙3.6 = 7.2 residues per turn). If the Amino Acid Sequence of the chain is represented by the formula (abcdefg)_m, then all residues a (or, correspondingly, b, c, d, e, f, g) will occupy structurally equivalent positions (Fig. 5.11, c).

Supercoiling of the a-helix is energetically favorable because side-chain packing promotes The formation of additional advantageous Van der Waals contacts between the a-helices. If the interacting side chains are hydrophobic, the decrease in the Free energy of such a structure is particularly pronounced, since the side chains are thereby shielded from contact with solvent molecules as they run along the superhelix axis. Indeed, in tropomyosin [222] and a-keratin [212], whose Amino acid sequences are known, positions a and d within the superhelix are occupied by hydrophobic residues (Fig. 5.11, c). Polar residues are typically located on the outer surface, at positions b, c, and f. In tropomyosin, positions e and g are frequently occupied by charged residues that form salt bridges with the oppositely located residues g' and e', respectively.

The superhelix model is applicable to both parallel and antiparallel a-helices. All the considerations presented above apply to both parallel and antiparallel a-helices. However, only the parallel arrangement satisfies the packing mode shown in Fig. 5.11, b; since the C_a—C_β bond of an a-helical residue is not perpendicular to the a-helix axis, but is oriented at an angle of about 45° in the direction opposite to the helix sense, the side chains share this same orientation. They pack together effectively only in the case of parallel helices (Fig. 5.11, c). For antiparallel helices, the fitting scheme differs somewhat from that shown in Fig. 5.11, b. To eliminate steric clashes between side chains, a relative shift of the helices along the contact line by approximately 1 Å is required. If, for example, the helix shown in Fig. 5.11, c with abcdе residues is inverted, steric repulsion between the side chains of residues a and d' is eliminated by shifting the helix 1 Å downward. The resulting closer approach of the side chains of residues a' and d will not lead to steric hindrance, as these chains point in opposite directions. Thus, neither helix orientation appears to be inherently preferred.

Chemical data, alongside results from X-Ray Diffraction Analysis and Electron Cell/15.html">Microscopy, have demonstrated that the a-helices are parallel in tropomyosin [213, 223, 224] and light meromyosin [215]. This presumably also holds true for a-keratin, given that the long a-keratin chain can be fully synthesized and stabilized before a superhelix can form from antiparallel a-helices. In contrast, the helix packing is antiparallel in the globular proteins hemerythrin [216, 217] and tobacco mosaic virus coat [180, 218].

Three other preferred relative orientations involving different contacts between two a-helices have been proposed [225]. These were derived from an analysis of cylindrical nets and likewise correspond to favorable side-chain packing. However, they are not yet strongly supported by experimental data.