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

The Molecules We Are Made Of
Proteins
Conformations of Peptide Chains

Let us consider a chain of —СН₂ (methylene) groups — such chains form the synthetic polymer polyethylene. In a fully extended chain, the hydrogen atoms attached to carbon atoms separated by one intervening carbon actually Touch each other, meaning no larger atoms can be accommodated here.

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Even when hydrogen atoms (Structure/103.html">Van der Waals radius 0.12 nm) are replaced by fluorine atoms (radius 0.135 nm), the polymer chain cannot remain fully extended. The torsional angle, which is 180° in polyethylene, becomes 166° in polyfluoroethylene. This change is sufficient to relieve the strain in contacts between the fluorine atoms, while the fluorine atoms and adjacent carbon atoms still do not interfere with one another. The resulting helical structure resembles structural elements found in Proteins and other Biopolymers. Thus, The formation of a helical conformation is a natural consequence of the mutual steric "displacement" of certain atomic groups by others [12, 13].

The conformational properties of biopolymers are complex, yet they are significantly simplified by the rigidity of the structure in most monomeric units.

a. Peptide unit

The rigidity of Polypeptides is due to the planar nature of peptide groups, which is associated with Resonance.

The shortening of the C—N bond and the lengthening of the C = O bond expected from this resonance have been experimentally confirmed by X-Ray Structural Analysis of these structures. Each peptide unit can be depicted as a rigid flat sheet, the dimensions of which are indicated at the top of Fig. 2-3. However, the arrangement of bonds around the nitrogen atom retains a somewhat pyramidal character [14, 15] (Fig. 2-3, bottom).

FIG. 2-3. Dimensions of the peptide group. Interatomic distances are indicated, as well as the length of the Hydrogen bond formed with the adjacent peptide group. All atoms within the dashed frame lie approximately in the same plane. However, as shown at the bottom of the figure, the arrangement of bonds around the nitrogen atom partially retains a pyramidal character.

The trans-peptide bond is the most prevalent (Fig. 2-3), but cis-peptide bonds also occur (they are approximately 8 kJ∙mol^-1 less stable than the former); cis-bonds are most frequently formed at the nitrogen atom of Proline [16, 17].

A polypeptide can be viewed as a chain of interconnected flat peptide units linked end-to-end (Fig. 2-4). Each peptide unit is joined to the next through the a-carbon of an amino acid. This carbon gives rise to two single bonds in the chain around which rotation is possible (with the exception of the cyclic proline residue). The conformation of an amino acid unit in a protein chain is determined by the torsional angles about each of these single bonds. These angles are designated as φ and ψ and are taken to be 180° for a fully extended chain, as shown in Fig. 2-4 [18]. Since both φ and ψ can vary, an amino acid residue is, in principle, capable of adopting A wide variety of Conformations. Many of these, however, are immediately ruled out as sterically impossible, which is easy to verify using molecular models.

¹ Another convention is also widely used, according to which φ = ψ = 0 in a fully extended chain [13].

Nowadays, it has become common practice to computer-scan the entire range of possible values for φ and ψ. Calculations of the peptide group conformation were performed by Ramachandran.

The results of such an analysis are frequently presented as plots of φ versus ψ (Ramachandran plots, or conformational maps), in which regions of permissible combinations of the two angles are outlined. Conformational maps of Peptides (Fig. 2-5) show that the number of possible torsional angle combinations is quite large. A substantial portion of these combinations is indeed realized in proteins. At the same time, a much larger number of such angle pairs are strictly forbidden, unless one considers more flexible peptides containing Glycine (Fig. 2-5, B). Table 2-3 lists approximate torsional angle values for A number of peptides with regular structures.

FIG. 2-4. Two peptide units in a fully extended ß-conformation. Torsional angles φ_i, ψ_i, and ω_i are considered to be 0° when the backbone atoms are in the eclipsed, or cis-conformation. In a fully extended chain, all these angles are 180°.

b. ß-Structure formed by extended chain segments

As first pointed out by Linus Pauling, one of the crucial principles governing Cell/13.html">Protein Structure formation is the creation of the maximum possible number of Hydrogen Bonds between the backbone C = O and N—H groups. A simple example is a sheet of adjacent extended chains (φ=ψ=180°) interconnected by hydrogen bonds. Polyglycine adopts such a structure — which is illustrated to some extent in Fig. 2-6 (top left). Note that in this figure, neighboring chains run in opposite directions, hence the name — antiparallel ß-structure. Besides providing the most favorable conditions for interchain hydrogen bonding, the antiparallel arrangement also facilitates the chain turning around and folding back upon itself. This is a vital factor in the formation of cellular structures.

The unhindered formation of a ß-structure from fully extended chains is possible only for polyglycine; the presence of side (R) chains in Other Amino Acids inevitably causes structural distortion. For example, Silk Fibroin is characterized by a repeat distance of 0.70 nm, whereas a fully extended chain has a repeat distance of 0.72 nm (Fig. 2-4). As Pauling and Corey showed, this chain shortening can result from a ~40° change in the φ angle (to —140°) and a ~55° change in the ψ angle in the opposite direction (to +135°), producing a "pleated" multi-chain structure known as a pleated sheet (Fig. 2-6). Parallel ß-structures are also frequently found in proteins.

FIG. 2-5. A. Ramachandran-calculated diagram (conformational map) of allowed values for the angles φ and ψ. For the two regions on the left enclosed by solid outlines, there are no steric restrictions. Note that the pleated ß-sheet, Collagen structure, and a-helix fall within these regions. Regions marked with dots feature small steric barriers, yet the corresponding conformations can still occur. B. Ramachandran plot for Insulin B-chains (Chap. 4, Sec. D.7); φ and ψ angle values were obtained by constructing molecular models based on X-Ray Diffraction data at 0.19 nm resolution. The majority of conformations correspond to a distorted a-helix or are close to a ß-structure. 8, 20, and 23 are glycine residues. (Blundell T., Dodson G., Hodgkin D., Mercola D., Adv. Protein Chem., 26, 279—402, 1972.)

Table 2-3 Approximate torsional angle values for some regular peptide structures^a

^а Based on data from the IUPAC-IUB Commission on Biochemical Nomenclature, Biochemistry, 9, 3471—3479, 1970.

^б The torsion angles for a fully extended chain can equivalently be designated as +180° or —180°, as these are completely interchangeable. For easier comparison with other structures, it is convention here to set φ = —180° and ψ = +180°.

^в The set of three angles corresponds to the three residues forming the repeating sequence (Pro-Gly-Pro)_n, which predominates in collagen (Yonath A., Traub W., JMB, 43, 461—477, 1969.)

FIG. 2-6. STRUCTURE OF THE pleated ß-sheet formed by extended chains. The left panel shows the antiparallel structure found in silk fibroin. The axial repeat of 0.70 nm is slightly shorter than that of a fully extended chain. The amino acid side chains (R) project alternately above and below the folds shown in the diagram (which resemble accordion bellows). Pairs of interchain hydrogen bonds impart high stability to the structure. The chain can reverse its direction (via a ß-turn or ß-bend) and double back on itself. At the midpoint of the ß-turn, the peptide group is oriented almost perpendicular to the plane of the pleated sheet. A similar structure is formed by parallel chains (right panel), although the hydrogen-bonding geometry is slightly less favorable in this case. The bottom portion shows a stereoscopic view of the peptide backbone of the enzyme Carboxypeptidase A [26]. Although Hydrogen bonds are omitted from this drawing and only the positions of the a-carbon atoms are displayed, eight distinct chain segments running from the upper left to the lower right of the molecule can be discerned. These chains (comprising both parallel and antiparallel arrangements) are linked by an extensive network of hydrogen bonds. The illustration can be viewed using stereoscopic glasses, but with a little practice, the 3D effect can also be perceived unaided—a very useful skill to acquire, as many molecular structures are now published in journals as stereograms. Place the well-lit drawing at a distance of 20—30 cm from your eyes. Relax your focus as if gazing into infinity. Out of the four resulting images, fuse the two central ones into a single image, which yields the stereoscopic effect. A rather clear diagram of the chain backbone in the ß-structure region can be found in Dickerson and Geis (p. 89) [13].

b. Polyglycine II and collagen

Another form of polyglycine is known in which each amino acid residue is rotated by 120° relative to the preceding one around a 3rd-order screw axis (an end-on view is shown in Fig. 2-7, A). The ψ angle for each residue is approximately 150°, and φ is roughly —80°. The axial Translation per residue is 0.31 nm, with a repeat distance of 0.93 nm. These molecules can form either right-handed or left-handed helices. In this structure, the N—H and C = O groups project perpendicularly to the helix axis. Consequently, much like in the ß-structure, hydrogen bonds are formed between adjacent chains.

Poly(L-proline) adopts a helical structure remarkably similar to that of polyglycine II. Due to the presence of bulky side chains, the left-handed helix is energetically favored. It should be noted that for a polypeptide chain composed of L-amino acids, any given helical folding mode will result in different stabilities for the right- and left-handed helices.

Collagen is present in very large quantities in animal organisms, serving as the principal protein component of Connective Tissue, basement membranes, and other structures. The structural unit of collagen is tropocollagen, which is believed to be a triple-helical segment measuring 1.5 × 280 nm. It resembles polyglycine II (Fig. 2-7, A) but consists of only three chains. Furthermore, the individual left-handed helical chains are additionally coiled into a right-handed superhelix.

The predominance of a single amino acid in proteins is a relatively rare occurrence. However, collagen contains 33% glycine, 21% proline plus hydroxyproline, and 11% alanine. This composition is necessitated by the fact that bulky side chains cannot be accommodated within the interior of the triple helix. The same principle applies to silk fibroin, which consists primarily of the repeating sequence

(—Glу—Ser—Glу—Аlа—Glу—Аlа—)_n.

In this arrangement, when the pleated sheet forms, all the Serine and alanine side chains project to one side of the sheet, while only the hydrogen atoms of glycine face the opposite side. As a result, the sheets pack together much more closely—the alanine and serine side chains of one layer nestle into the gaps between the side chains of the adjacent layer [19].

c. The a-helix

A particularly interesting set of conformations is realized when both torsion angles, φ and ψ, are close to —60°. This angular region corresponds to Helical structures stabilized by intrachain hydrogen bonds. Of primary interest is the a-helix (Fig. 2-8), where the right-handed helix of L-amino acids is significantly more stable than the left-handed one. To date, only right-handed a-helices have been found in nature. Note that in the a-helix, all C = O and N—H groups involved in peptide bonds are approximately parallel to the helix axis; each carbonyl group forms a hydrogen bond with the fourth N—H group further along the chain. The number of amino acid residues per turn of the helix is 3.61. The pitch of the helix (which can be determined experimentally using X-ray crystallography) is 0.541 nm.

FIG. 2-7A. Structure of polyglycine II and collagen. A. View of the polyglycine II structure looking down the helical axis. Note the presence of the 3rd-order screw axis. Polyproline forms a similar structure, whereas collagen appears to be a triple "rope" composed of three peptide chains whose structures are also close to the one depicted here, though featuring right-handed supercoiling. B. Electron micrograph of a basement membrane (between arrows) and underlying collagen fibrils in an amphibian Skin section. The 1.5-nm filaments within the basement membrane region (indicated by arrows) presumably represent individual tropocollagen molecules arranged in parallel with a "quarter-stagger," which gives rise to the 64-nm axial periodicity. Some fibrils are visible in cross-section (marked with a cross). (Kindly provided by Elizabeth D. Hay.)

The stratum corneum of the skin, Hair, Nails, and porcupine quills are all structures constructed from a family of proteins known collectively as Keratins. One of the principal components of keratin¹, the so-called "low-sulfur protein," is composed of a-helices with a pitch of 0.51 nm rather than the standard 0.54 nm. This reduction in pitch is explained by the coiling of two or three right-handed a-helices around one another to form a left-handed superhelix, which further assembles into microfibrils approximately 2.0 nm in diameter [19—21]. A structurally analogous arrangement is believed to form The basis of the Muscle Proteins Myosin [22] and Tropomyosin [23] (Chap. 4, Sec. E.1). Both of these proteins are typically depicted as two-stranded "ropes" in which the hydrophobic side chains of one chain fit into grooves On the surface of the neighboring chain².

Other helical structures also exist, possessing diameters either larger or smaller than that of the a-helix, and they similarly play a role in protein architecture [13]. The 3₁₀-helix contains exactly three residues per turn; each carbonyl group is hydrogen-bonded to the third N—H group along the chain. Consequently, this helix is more tightly wound than the a-helix. The п-helix contains 4.4 residues per turn and has a larger diameter than the a-helix. Although 3₁₀- and п-helixes are not major Structural elements of proteins, they do occur, most frequently as single-turn terminations at the ends of regular helices.

¹ It is generally accepted that the other proteins comprising keratin form an amorphous "matrix" penetrated by microfibrils. One such matrix component is the "high-sulfur protein," which is rich in Cysteine and features a high degree of cross-linking. Human hair has a particularly high cysteine content.

² The tendency to intertwine and form rope-like structures arises because the stabilizing, periodically repeating interchain bonds can only form if the chains wind around one another [23а].