BIOCHEMISTRY - L. Stryer - 1984

VOLUME 1

PART I. CONFORMATION AND DYNAMICS

CHAPTER 2. INTRODUCTION TO PROTEIN STRUCTURE AND FUNCTION

2.8. Conformation of Polypeptide Chains

A striking feature of Proteins is that each possesses a precisely defined three-dimensional Structure. As shown below, when unfolded or randomly coiled, polypeptide chains are devoid of biological activity. The Functional Properties of proteins are determined by their conformation, i.e., the spatial arrangement of their atoms. The Amino Acid Sequence plays a crucial role in this process because it ultimately dictates the protein conformation.

In the late 1930s, L. Pauling and R. Corey began X-ray structural studies of Amino Acids and Peptides. They determined standard Bond Lengths and Bond Angles in order to predict protein Conformations based on these data. An important fact was discovered: the peptide unit possesses a rigid, planar structure. The hydrogen atom of the substituted amino group almost always assumes a trans configuration relative to the oxygen atom of the carbonyl group (Fig. 2.33). The bond between the carbonyl carbon atom and the nitrogen atom of the peptide unit has partial double-bond character, and consequently, rotation around this bond (Fig. 2.34) must be hindered. The bond length is 1.32 Å, which is an intermediate value between a single C—N bond (1.49 Å) and a double C=N bond (1.27 Å).

Class="center">Fig. 2.33. The peptide group has a rigid planar structure. Bond lengths are shown (in Å)

Fig. 2.34. The planarity of the peptide group is due to the nitrogen–carbon bond having partial double-bond character

Angstrom (Å) — a unit of length equal to 10^-10 m. 1 Å = 10^-10 m = 10^-8 cm = 10^-4 µm = 10^-1 nm. Named after the spectroscopist A. Ångström (1814–1874).

In contrast to the case considered above, the bond between the α-carbon atom and the carbonyl carbon atom is a true single bond. Consequently, on both sides of the rigid peptide unit, There is a high degree of rotational freedom around these bonds (Fig. 2.35). Rotations about these bonds are described by the angles and φ (Fig. 2.36).

Fig. 2.35. There is a fairly high degree of rotational freedom in the region of the bonds between the peptide groups and the α-carbon atoms

Fig. 2.36. Definition of the angles and φ: characterizes rotation about the C_α—C single bond; φ characterizes rotation about the C_α—N single bond. (Levinthal, Molecular Model Building by computer, Scientific American, Inc., 1966.)

For a complete Description of the conformation of a polypeptide backbone, it is necessary to know and φ for each amino acid residue.

2.9. Periodic Structures: Alpha Helix, Beta Pleated Sheet, Collagen Helix

Can a polypeptide chain be folded into a structure consisting of regularly repeating segments? To answer this question, Pauling and Corey compared A number of potentially possible polypeptide conformations by constructing precise molecular models. In doing so, they strictly adhered to the bond angles and interatomic distances experimentally established for amino acids and small peptides. In 1951, they proposed two periodic polypeptide structures, designated respectively as the α Helix and the β pleated sheet.

The α helix is rod-shaped. The tightly wound polypeptide backbone forms the interior of the rod, while the side chains extend outward from the backbone in a helical arrangement (Figs. 2.37 and 2.38). The α helix is stabilized by Hydrogen Bonds between the NH and CO groups of the backbone. The CO group of each amino acid is hydrogen-bonded to the NH group of The amino acid located 4 residues ahead in the linear sequence (Fig. 2.39). Thus, all backbone CO and NH groups are hydrogen-bonded to one another. Projected onto the helix axis, adjacent residues are spaced 1.5 Å apart, and the rotation angle between them is 100°, meaning there are 3.6 amino acid residues per full turn of the helix. Consequently, amino acids separated by 3 to 4 residues in the linear sequence are spatially very close to each other in the α-helical structure. Conversely, amino acids separated by two residues in the linear sequence are spatially located on opposite sides of the helix and therefore interaction between them is unlikely. The pitch of the α helix is 5.4 Å, the distance between residues along the axis is 1.5 Å, and the number of residues per turn is 3.6. The helix can be right-handed (right-handed helix) or left-handed (left-handed helix); all protein α-helices investigated so far are of the right-handed type.

Fig. 2.37. Model of a right-handed α helix. A. Only the α-carbon atoms are shown on the helix. B. Only the nitrogen (N) atoms forming the molecular backbone, the α-carbon (C_α) atoms, and the carbonyl carbon (C) atoms are shown. C. Full representation of the helix. Hydrogen bonds (indicated by red dots in Fig. C) between the NH and CO groups stabilize the helix

Fig. 2.38. Cytology/practical/72.html">Cross section of the α helix. Note that the side chains (shown in green) are on the outside of the helix. The Van der Waals radii of the atoms are actually larger than depicted in the figure, consequently leaving almost no free space inside the helix

Fig. 2.39. In the α-helix, the NH group of the n-th residue is hydrogen-bonded to the CO group of the (n-4) residue

The content of α-helices in proteins studied to date is extremely variable. In some proteins, such as Myoglobin and Hemoglobin, the α-helix forms The basis of their structure. Other proteins, such as the digestive enzyme Chymotrypsin, are virtually devoid of α-helical structure. The single α-helix discussed above is generally quite short, usually less than 40 Å in length. Variants of α-helices are utilized to form long strands reaching 1000 Å and more in length. Two or more α-helices can twist around one another like the strands of a rope. Such a structure—a coiled-coil α-helix—is found in many proteins: in Hair keratin, Muscle Myosin and Tropomyosin, Skin epidermis, and Blood fibrin clot. The coiled "ropes" of these Proteins perform a mechanical role by forming dense bundles of fibers.

"If we accept that the fibrillary Proteins of the epidermis, proteins of keratinized Tissues, the major muscle protein myosin, and now also blood fibrinogen all share the same underlying molecular architecture and therefore likely represent adaptive variants of a single foundational principle, then we are evidently encountering one of the great Milestones in the evolution of biological molecules."

K. Bailey, W.T. Astbury, K. M. Rudall, Nature, 1943

The structure of the α-helix was predicted by Pauling and Corey 6 years before it was experimentally elucidated using X-Ray Diffraction Analysis of myoglobin. The Discovery of the α-helix structure represents a major milestone in The Development of molecular biology, as it proved that the conformation of a polypeptide chain can be predicted if The properties of its component parts are known with precision.

That same year, Pauling and Corey discovered another variant of periodic structure, which they named the β-pleated sheet (designated as β because it was the second structure they discovered after the α-helix). The β-pleated sheet differs significantly from the α-helix in that it has a flat rather than rod-like shape. The polypeptide chains in β-pleated sheets are almost fully extended (Fig. 2.40) rather than tightly coiled as in the α-helix. The axial distance between two adjacent amino acids is 3.5 Å rather than 1.5 Å as in the α-helix. Another feature of the β-pleated structure is that it is stabilized by hydrogen bonds between the NH and CO groups of different polypeptide strands, whereas in the α-helix, Hydrogen bonds are formed between these groups within the same polypeptide chain. Adjacent strands in a pleated β-sheet can run in the same direction (parallel β-sheet) or in opposite directions (antiparallel β-sheet). For example, Silk Fibroin consists almost entirely of "stacks" of antiparallel β-pleated sheets (Fig. 2.41). Similar regions of β-pleated sheets are found in many other proteins. Structural units consisting of 2 to 5 parallel or antiparallel β-sheets are particularly widespread.

Fig. 2.40. Conformation of a dipeptide unit in a pleated β-sheet. The polypeptide chain is shown in an almost fully extended state

Fig. 2.41. Antiparallel β-pleated sheet. Adjacent polypeptide strands run in opposite directions. The structure is stabilized by hydrogen bonds between the NH and CO groups of adjacent strands. Side chains (shown in green) lie above and below the plane of the sheet

The third type of periodic structure—the Collagen helix—will be discussed in detail in Chapter 9. This specialized structure provides high tensile strength and elasticity to collagen, the primary component of skin, bones, and tendons.