Protein Chemistry - Part 1 - General Protein Chemistry - Ashmarin I. P. 1968

Spatial Organization of the Protein Molecule
Secondary Structure of Polypeptides

One of the distinctive features of synthetic polypeptide molecules is the presence of a strict spatial configuration, in the establishment and maintenance of which Hydrogen Bonds play the primary role.

It is precisely due to The formation of A large number of hydrogen bonds that the potential energy of the macromolecule decreases while its stability increases. Therefore, the search for the true Structure of Polypeptides focused on finding a configuration with minimal potential energy—that is, a model that would ensure the maximum possible formation of hydrogen bonds with minimal distortion of valence angles and bonds.

The a-Helix. Out of numerous hypotheses regarding The structure of polypeptide chains, only a few hold more than historical interest. Among the latter, Pauling and Corey's theory of the a-helix has gained universal recognition, supported by direct experimental evidence. The authors developed this structure based on general stereochemical principles and X-Ray Diffraction data concerning covalent and Hydrogen bond lengths as well as valence angle values. These data have been presented previously and are summarized here more concisely. Thus, a model of the spatial configuration of a polypeptide chain must satisfy the following fundamental principles.

1. The entire quartet of atoms of the amide group lies in a single plane (is coplanar). This is a consequence of the partially double-bond character of the peptide bond. Any significant deviations from coplanarity are energetically unfavorable.

2. Each amino acid residue is situated relative to its neighbors and to the helix as a whole in an absolutely identical manner to all the others (THE PRINCIPLE OF equivalence of all amino acid residues).

3. The maximum possible number of hydrogen bonds is formed between peptide groups (two per group) while maintaining the greatest possible compactness of the helix. The length of the hydrogen bond (the distance between the N and O atoms) is 2.8 Å, the C = O and N—H groups are collinear, and the allowable deviation from collinearity does not exceed 20°.

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Fig. 18. Scheme and model of the polypeptide a-helix (after Pauling, 1955).

Only a single structure satisfies these requirements—the a-helix (Fig. 18). All other models fail to allow for the maximum formation of H-bonds or do not comply with the principle of equivalence of all amino acid residues. Upon examining Fig. 18, one can readily observe several Characteristic Features of the a-helix. For instance, the first feature, representing The most significant deviation from known helical systems, is its non-integral nature. There are 3.6 amino acid residues per turn of the helix; thus, the identity period along the axis of the a-helix spans 5 turns, or 18 residues. Consequently, another designation for it is the 3.6-residue helix. With a pitch of 5.4 Å per turn, the Translation—that is, the displacement along the axis per amino acid residue—is 1.5 Å. Furthermore, while shifting along the axis by 1.5 Å, each residue rotates around it by 100°. The inner diameter of the helix, which is the diameter of the cylinder On the surface of which all a-carbon atoms are located, equals 10.1 Å.

The second feature of the a-helix is related to the Formation of the maximum possible number of hydrogen bonds—two for each peptide group. The Hydrogen bonds are approximately parallel to the axis of the helix, with each peptide nitrogen being hydrogen-bonded to the carbonyl oxygen of the third nearest residue. Consequently, each hydrogen bond spans three amino acid residues and holds them in an ordered configuration independently of the other two H-bonds. For a disruption of the rigid a-helix structure to occur in a localized region, at least three consecutive hydrogen bonds must be broken. This circumstance is crucial in imparting high stability to the a-helix, as well as sharpness to the helix-to-coil transition.

Finally, the third feature of this conformation is that The amino acid side chains point outward. Without taking direct part in forming the carbon backbone of the a-helix, these side chains can induce strains incompatible with the helical configuration and cause the rupture of hydrogen bonds, thereby leading to the formation of amorphous regions. Thus, the a-helix structure allows for maximum Variability in protein architecture and, consequently, ensures an exceptional diversity in the chemical Specificity of Proteins. The arrangement of the amino acid side chains is also highly significant from another perspective. If we consider an a-helix constructed from natural L-Amino Acids (Fig. 19), with a left-to-right direction of rotation (right-handed helix), all side chains will be oriented along the axis from the C-terminus to the N-terminus—that is, in the direction opposite to that of the polypeptide chain. Conversely, if the helix is left-handed, the side radicals will be directed along the axis in the direction of the polypeptide chain. Since there are 3.6 such radicals per turn of the helix, their packing and interaction will be entirely different for each type of helix. It must be emphasized that this specific interaction determines the choice of the direction of helical rotation. Unfortunately, the Pauling-Crick theory cannot predict what this direction should be, as it is completely immaterial for the construction of the model. For the majority of investigated polypeptides, it has been found that Natural Amino Acids form right-handed helices; these have also been discovered in A number of proteins.

Evidence for the existence of the a-helix was obtained by Bamford et al. through The Study of X-ray diffraction patterns from synthetic polypeptide films and certain proteins. These diffraction patterns exhibited reflections corresponding to periods of 1.5, 5.1, and 9.8 Å, which represent the axial distance between successive residues, the pitch, and the diameter of the helix, respectively.

The β-Structure. The a-helix with intramolecular hydrogen bonds is the most stable configuration of the polypeptide chain, as represented in the majority of investigated proteins. However, it is not their only possible configuration.

Fig. 19. Arrangement of side groups in left- and right-handed helices (Steiner, 1965).

Another variant of Secondary structure that satisfies all the aforementioned principles is the structure featuring intermolecular hydrogen bonds connecting adjacent polypeptide chains (the β-structure). The polypeptide chains in this structure must be extended, and their peptide groups must lie approximately in a single plane (Fig. 20). The carboxyl (amino) groups of every second residue point in the same direction, while the transition to the neighboring residue is accomplished by a translation of 3.6 Å along the chain axis and a 180° rotation around it. The ordinary extended form of polyglycine has approximately this configuration. The identity period of the chain is 7.2 Å; the chains are arranged parallel to one another and exhibit a zigzag conformation. The side radicals of adjacent amino acid residues project from the polypeptide backbone in opposite directions and lie perpendicular to the plane of the drawing.

The most interesting feature of this configuration is the orientation of the C = O and N—H groups, which lie within a single plane and are oriented in such a way that they can form hydrogen bonds with the corresponding groups of neighboring chains. In this arrangement, the alternating amino and carboxyl groups of a given chain are hydrogen-bonded on both sides to the carboxyl and amino groups of two other chains located on either side of it. Such chains are termed antiparallel, and the structures formed by them are referred to as pleated-sheet structures.

Fig. 20. Scheme and model of the polypeptide ß-Structure:

1 — model of the chain (viewed along the direction of the hydrogen bonds; carboxyl and Amino groups are oriented perpendicular to the plane of the drawing), 2 — model of the pleated-sheet structure (ß-carbon radicals are positioned perpendicular to the plane of the drawing).

The pleated-sheet structure with antiparallel chains is characteristic of Fibrous proteins such as Silk Fibroin. The X-ray diffraction patterns of this protein clearly reveal reflections corresponding to periods of 6.97 and 9.4 Å, which match the identity period along the polypeptide chain and the distance between alternating equivalent chains (9.5 Å, According to the molecular model).

A distinctive hallmark of the ß-structure is the arrangement of adjacent ß-carbon atoms on opposite sides of the sheet, perpendicular to its plane (alternating above and below the sheet). Since all ß-carbon atoms on each side of the sheet are in "phase" with one another—that is, at equivalent points relative to the fiber axis—large troughs are formed between adjacent rows of ß-carbon atoms. This enables the tight packing of neighboring sheets, wherein the ß-carbon atoms (side radicals) of one sheet fit into the gaps between the ß-carbon atoms of the other. Admittedly, these side radicals cannot be excessively large (in fibroin, these are the CH₃ radical of Alanine and the CH₂OH radical of Serine), as otherwise the order of the simplified model would be disrupted.

In Conclusion, it should be noted that the configuration of synthetic polypeptides is largely determined by The Nature of the solvent from which the polypeptide film is cast. If the solvent is formic or dichloroacetic acid, a ß-structure with intermolecular hydrogen bonds is obtained; if cresol or dimethylformamide is used, a structure with intramolecular bonds—namely, the a-helix—is formed. From certain Solvents, polypeptide films with a random amorphous configuration can be obtained.