Biological Chemistry - Berezov T. T., Korovkin B. F. 1998

Chemistry of Proteins
Structural Organization of Proteins
Secondary Protein Structure

X-ray structural crystallography solves two major problems in Protein Chemistry: the regular patterns in The sequence of amino acid residues within a polypeptide chain and the conformational geometry of the protein molecule.

The first protein X-Ray Diffraction patterns, obtained back in the 1930s by W. Astbury, and later by L. Pauling and R. Corey, revealed that Proteins contain linear polypeptide chains alongside segments folded in a specific manner.

Protein Secondary Structure refers to the configuration of the polypeptide chain—that is, the way the chain is folded, coiled, or packed into a helical or other conformation. This process does not occur randomly, but strictly According to the program encoded in the Primary Structure. Two primary configurations of polypeptide chains that satisfy both structural requirements and experimental data have been studied in detail: the a-helix and the ß-Structure.

Thanks to the research of L. Pauling*, the a-helix is considered the most probable structural motif for Globular proteins (Fig. 1.17). The coiling of the polypeptide chain proceeds in a clockwise direction (right-handed helix), which is determined by the L-Amino Acid Composition of natural proteins. The driving force behind The formation of a-helices (as well as ß-structures) is the ability of Amino Acids to form Hydrogen Bonds. Several regular patterns have been discovered in The structure of a-helices. Each turn (pitch) of the helix contains 3.6 amino acid residues. The pitch of the helix (the distance along its axis) is 0.54 nm per turn, with 0.15 nm allotted to each amino acid residue. The helix rise angle is 26°, and after 5 turns (18 amino acid residues), the structural configuration of the polypeptide chain repeats. This means that the repeat (or identity) period of the a-helical structure is 2.7 nm.

Each protein is characterized by a specific degree of helicity in its polypeptide chain. The degree of helicity is determined by measuring the optical rotation of polarized light. Changes in optical rotation are directly proportional to the degree of coiling of the protein molecule. Not all globular proteins are helical throughout their entire polypeptide chain. In a protein molecule, a-helical regions alternate with linear segments. Specifically, while the a- and ß-chains of Hemoglobin are about 75% helical, Lysozyme is 42% helical, and Pepsin is only 30% helical.

* L. Pauling was awarded the Nobel Prize in Chemistry (1954) for his Discovery of the Fine Structure of proteins using X-ray Diffraction Analysis of native proteins and synthetic Polypeptides.

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Fig. 1.17. Structure and parameters of the a-helix.

Thus, the Stability of the secondary structure is maintained primarily by hydrogen bonds (with primary valence bonds, such as peptide and Disulfide Bonds, also making a certain contribution).

A Hydrogen bond is a weak electrostatic attraction (interaction, bond) between an electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently bonded to a second electronegative atom. The types of Hydrogen bonds are discussed below.

According to modern concepts, a hydrogen bond involves not only electrostatic forces of attraction between polar groups (the interaction of hydrogen atoms with electronegative elements like oxygen, nitrogen, and chlorine), but also electronic linkages similar to those found in certain coordination compounds. Being non-covalent, hydrogen bonds are characterized by low bond energy. For instance, while breaking covalent interatomic bonds requires from 84 to 8400 kJ, breaking a single hydrogen bond requires a mere 6.3 kJ per mole. Because the number of hydrogen bonds in a protein molecule is exceptionally large (all peptide groups are involved in hydrogen bonding), their cumulative effect drives the coiling of the polypeptide chain into a helical structure, imparting both compactness and stability.

The Mechanism of hydrogen bond formation can be illustrated in its elementary form using the interaction of two Water molecules (dipoles). As is well known, in a water dipole, an excess of positive charge resides on the hydrogen atoms, while an excess of negative charge resides on the oxygen atom.

Due to the structural Properties of the hydrogen atom, when two water molecules approach each other closely enough, an electrostatic interaction arises between the oxygen atom of one molecule and the hydrogen atom of the second water molecule. This results in a weakening of the bond between the hydrogen and oxygen atoms within each individual water molecule and, consequently, the formation of a new, relatively weak bond (indicated by a dashed line) between the hydrogen atom of the first molecule and the oxygen atom of the second water molecule. This fragile bond is designated as a hydrogen bond.

In a protein molecule, the most important hydrogen bonds are formed between a covalently bound hydrogen atom carrying a partial positive charge and a negatively charged, covalently bound oxygen atom. Examples of hydrogen bonds in a protein molecule are shown below: a) between peptide chains; b) between two hydroxyl groups; c) between an ionized COOH group and a Tyrosine OH group; d) between a Serine OH group and a peptide bond.

Depending on the Chemical Nature of the acceptor atom, hydrogen bonds vary in strength. The number of hydrogen bonds in a protein molecule is estimated using isotopic Methods, specifically by measuring the exchange rate of hydrogen atoms involved in hydrogen bonding with deuterium (upon treating the protein with heavy water D₂O, which contains the heavy hydrogen isotope deuterium instead of standard hydrogen).

Another type of polypeptide chain conformation, found in Hair, silk, Muscle, and other Fibrous proteins, is known as the ß-structure. In this case, two or more linear polypeptide chains, running parallel or, more frequently, antiparallel, are strongly linked by interchain hydrogen bonds between the NH and CO groups of adjacent chains, forming a pleated-sheet structure (Fig. 1.18).

Fig. 1.18. ß-Structure of polypeptide chains.

However, there are proteins in nature whose structures correspond to neither the ß- nor the a-structure. A classic example of such a protein is Collagen—a fibrous protein that constitutes the primary mass of Connective Tissue in Human and Animal organisms (see Chapter 21).

X-ray diffraction analysis has recently proven the existence of two additional Levels of Protein structural Organization that serve as intermediates between the secondary and tertiary structures. These are the so-called Supersecondary structures and Structural domains.

Supersecondary structures are aggregates of polypeptide chains possessing their own secondary structure, which form in certain proteins As a result of thermodynamic or kinetic stability. For instance, globular proteins have been found to contain aß-motifs (consisting of two parallel ß-strands connected by an x-segment), ßaßaß-motifs (consisting of two a-helical segments inserted between three parallel ß-strands), and others. Large globular proteins sometimes contain distinct structural domains that perform different Functions, much like homologous domains within a single monomeric protein, which likely arise either from Gene effects in the first case or Gene Duplication In the second. Domains are formed by the combination and alternation of a-helices and ß-sheets, interspersed with more loosely packed structural regions (Fig. 1.19).

A domain is a compact globular structural unit within a polypeptide chain. Domains can perform distinct functions and fold into independent, compact globular structural units connected by flexible regions within the protein molecule. Numerous proteins (such as IMMUNOGLOBULINS) have been discovered that consist of structurally and functionally diverse domains encoded by different genes.