Biochemistry: The Chemical Reactions of Living Cells, Volume 1 - D. Metzler 1980

How molecules join together
Macromolecule packaging
Quasi-equivalence of subunit conformation

A quite reasonable assumption about the symmetrical packing of subunits, combined with Electron Cell/15.html">Microscopy data on their square, pentagonal, and hexagonal arrangement, led to the Conclusion that protomers tend to associate to form symmetrical structures. Let us consider The process of joining two molecules, as illustrated in Fig. 4-12. It is clear that these molecules can “dock” to form an isologous dimer only if they do not bump Nose-to-nose into each other (Fig. 4-12, A). However, despite the obvious Steric hindrances, an isologous dimer can still form in this case if one of the subunits undergoes a slight conformational change (Fig. 4-12, B). In such a Structure, the subunits are not equivalent, but rather quasi-equivalent.

Asymmetric protein dimerization appears to be a very widespread phenomenon. For example, the Enzymes malate dehydrogenase [53] and glyceraldehyde-3-phosphate dehydrogenase (Fig. 2-10) are tetramers with a Symmetry close to dihedral. When determining the crystal structures of these enzymes, it was initially assumed that all subunits were equivalent. However, it unexpectedly turned out that they are not entirely symmetric, since only one of the two polypeptide chains of malate dehydrogenase is able to bind the coenzyme NAD⁺.

The structure of the other binding site is apparently altered to such an extent that it is incapable of binding this essential coenzyme. A similar phenomenon occurs in the case of glyceraldehyde-3-phosphate dehydrogenase (Ch. 8, Sec. 3.3 and 3.5).

The hormone Insulin is a small protein consisting of two polypeptide chains (designated by the Latin letters A and B) that are linked together by disulfide bridges (Fig. 4-13, A). Fig. 4-13, B schematically depicts the structure of this protein based on X-Ray Diffraction data; only the polypeptide backbones and a few side chains are shown [54, 55]. In this figure, the B-chain is located behind the A-chain. Starting from the N-terminal phenylalanine-1, the peptide chain makes a smooth turn, then forms three α-helical turns approximately in the center of the molecule, and finally, after a sharp reversal, heads toward the upper left corner of the figure, forming an almost fully extended β-structure. The A-chain has a U-shape with two regions resembling helices. This conformation is partially achieved through The formation of a disulfide bridge between two PARTS OF THE A-chain. The A- and B-chains are connected by two disulfide bridges (one located in the upper part of the figure and the other closer to its lower part); the entire structure is stabilized by hydrophobic interactions between The amino acid side chains located in the interior of the molecule.

Class="center">

FIG. 4-12. Asymmetric binding in a dimer. A. Two molecules incapable of dimerizing. B. The problem is solved: the conformation of the polypeptide chain of molecule 1 has changed slightly, and the molecules now “dock” successfully.

FIG. 4-13. Structure of porcine insulin. A. Amino Acid Sequence of the A- and B-chains linked together by disulfide bridges. B. Spatial arrangement of the polypeptide backbones in the insulin molecule according to X-ray diffraction data. The figure also shows the arrangement of certain aromatic side groups (see also Figs. 4-14 and 4-15). C. Diagram illustrating the packing of six insulin molecules to form a hexamer stabilized by two zinc atoms.

In solution, insulin readily dimerizes, with the subunits occupying quasi-equivalent positions. Under certain conditions, three dimers form a hexamer possessing a symmetry close to dihedral (D₃); this structure is stabilized by two zinc ions. Fig. 4-13, C shows a schematic representation of the hexamer; it possesses three 2-fold (actually 3-fold) axes of symmetry and two pseudo-2-fold axes of symmetry, one of which passes between the two subunits of the dimer, and the other between neighboring dimers.

The zinc atoms are located on the 3-fold axis of symmetry and are coordinated with three imidazole rings of Histidine B-10. The Role of the zinc atoms is not entirely clear. Hexamers readily form rhombohedral crystals even inside the pancreatic Cells that synthesize insulin. The structure of insulin embodies the fundamental Features of oligomeric enzymes possessing cyclic or dihedral symmetry. As in the case of the insulin hexamer, the central parts of such molecules are often open, and the protruding amino acid side groups (imidazole groups in the case of insulin) form sort of “pockets” or “nests” that can accommodate ions or molecules regulating protein activity. However, the functional role of zinc in insulin action remains unknown for now.

Fig. 4-14 shows in greater detail how the subunits in the insulin dimer bind to each other, viewed approximately along the 2-fold axis of symmetry (marked by a cross in the center of the phenylalanine-25 ring). It can be seen that the C-termini of the B-chains are extended. Two antiparallel chains form a β-structure with two pairs of Hydrogen Bonds. If the binding were strictly isologous, these two pairs of bonds would be completely equivalent and located symmetrically relative to one another. A straight line drawn through a specific point on one chain and through the 2-fold axis of symmetry would have to pass through the corresponding point on the other chain. However, as careful analysis shows, the structure is far from symmetric.

Apparently, the most striking Asymmetry of the structure depicted in Fig. 4-14 is manifested in the center, where phenylalanine-25 of the right chain protrudes upward and to the left out of the structure. If the symmetry were ideal, the corresponding side group of the left chain would protrude upward and to the right, and these two phenylalanines would collide nose-to-nose, as schematically shown in Fig. 4-12, A. In reality, however, the side group of one of the phenylalanines in insulin is deflected, so to speak, to make room for the other.

Fig. 4-15 shows a cross-section of the insulin oligomer along a plane passing approximately through both 2-fold axes of symmetry (Fig. 4-13, C). Pay attention to the arrangement of the side groups along both axes. These groups correspond to groups c and c' in Fig. 4-9. Note that they are identical, as required for isologous binding, and are predominantly hydrophobic, aromatic, or alkyl groups (mainly leucine). The symmetry turns out to be non-ideal, and the methyl groups of the leucine residues tend to interdigitate, packing against each other more closely than would be expected under full symmetry. Thus, the results of a detailed Analysis of the dimeric and hexameric structures of insulin can, on the one hand, serve as a clear illustration of the principles of isologous protomer binding and, on the other hand, clearly demonstrate that two protomers often bind to each other in a strictly non-symmetric manner.

FIG. 4-14. Paired C-terminal Regions of the B-chains in the insulin dimer. Viewed approximately along the 2-fold axis of symmetry.

As we have already noted, the capsid subunits of icosahedral Viruses and certain Enzymes can be quasi-equivalent. This feature is responsible for the coiling of bacterial flagella, and it also underlies some interesting structural Properties of the tobacco mosaic virus. The protein subunits of the virus can be arranged either into a helix with 16.3 subunits per turn (Fig. 4-7) or into flat rings of 17 subunits each [36a]. In this case, the conformational differences are very small. The rings are capable of dimerizing, but they do not form large aggregates. Surprisingly, the dimeric rings do not possess dihedral symmetry. All subunits within them are oriented identically, but exist in two different Conformations. It has been suggested that such disks serve as an intermediate structure during viral particle assembly. According to X-ray diffraction data, the inner regions of the quasi-equivalent subunits of the disk act as a kind of trap, awaiting the moment when RNA is incorporated into the virus. After this, the disks change their conformation and form a “lock washer” or turn, initiating the growth of helical Viral Particles [36a]. These and many other interesting findings have suggested that the quasi-equivalence of protein subunits, combined with their ability to alter their conformation, underlies a wide range of biological phenomena.

FIG. 4-15. Cross-section of the insulin molecule along a plane passing through the 2-fold axes of symmetry [54].