Protein Chemistry. Structure, Properties, and Research Methods - Shendryk A.N. 2022

Protein Structure
Spatial Structure of Proteins
Tertiary Structure of Proteins

A peptide chain containing regions with a defined Secondary Structure typically arranges itself in space so that the elements of the secondary structure interact with one another and with disordered regions to form globules (Globular Proteins) or elongated fibers (Fibrillar Proteins). In such cases, one speaks of The formation of the Tertiary structure of the protein molecule. Every protein possesses its own unique Spatial Structure.

Fibrillar proteins. In fibrillar proteins, the peptide chains predominantly adopt a helical or pleated sheet structure. The native protein consists not of single peptide chains, but of aggregates thereof. Silk Fibroin, for example, consists of several chains with a pleated sheet structure stacked in such a way that each chain is surrounded on all four sides by chains in an antiparallel orientation. Meanwhile, proteins such as a-keratin (wool, Hair, feathers, horns, Nails) are built from large multichain structures of twisted helical chains. These chains are bound into bundles or interwound to form superstructures.

Among fibrillar proteins, Collagen is the most thoroughly studied. It is the primary component of Connective Tissue and serves as the principal structural protein of all living Cells. Approximately 30% of the body's total protein mass is accounted for by collagen. Overall, its content in the biosphere is estimated at 1 billion tons.

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Each connective tissue collagen macrofibril is an aggregate of collagen molecules. The length of a collagen molecule is about 3000Å, and its molecular mass is 300,000. The structure of the collagen molecule is a specific helix (sometimes called tropocollagen): three identical left-handed chains are intertwined to form a right-handed triple helix. Each triple chain has a significantly more elongated shape than the original monomeric a-helix.

Nearly a third of its amino acid residues are Glycine, a quarter consist of Proline and hydroxyproline, and the remainder comprises small amounts of Other Amino Acids, including hydroxylysine. The Amino Acid Sequence alternates quite regularly, with glycine occurring in almost every third position. Tripeptide fragments such as Gly-X-Pro, Gly-X-Hyp (hydroxyproline), and Gly-Pro-Hyp are very common. It is believed that the sequence:

is absolutely essential for the Formation of the tertiary structure of collagen.

The collagen triple helix is stabilized by non-covalent interactions (Hydrogen Bonds) and covalent bonds between Lysine and hydroxylysine. As a result, the tertiary structure exhibits rigidity and strength. A collagen filament 1 mm thick is capable of withstanding loads up to 100 N (about 10 kg-force).

The Biosynthesis of collagen proceeds in the following sequence. First, two different peptide chains (a₁ and a₂ chains) are formed from amino acids, including proline and lysine. Subsequently, they aggregate into a helix of the composition (a₁)₂(a₂). During the formation of the triple helix, some of the proline and lysine residues in each chain are hydroxylated. Hydroxylation is carried out by different Enzymes specific to proline and lysine. Both enzymes utilize O₂ as a source of the -OH group. There is evidence that ascorbic acid is required for maximal enzyme efficiency. It is hypothesized that hydroxyproline stabilizes the chain via hydrogen bonding. Some -OH groups are used to attach CARBOHYDRATES to collagen. Hereditary disorders of hydroxylation processes lead to severe defects, impairing the mechanical properties of Tissues (such as Skin or ligaments).

Globular proteins. In 1960, Kendrew, Perutz, and their coworkers first investigated the complete three-dimensional structure of a protein molecule using X-ray crystallography. To date, such studies have been performed on a fairly large number of proteins. As a result, it was established that, unlike fibrillar proteins, globular ones represent densely packed, folded Regions of the peptide chain. However, there is no single universal shape for all globular proteins: some are nearly regular spheres, others are elongated ellipsoids, while the majority have an intermediate and not always regular shape. Overall, these studies have led to the following generalizations.

1. The native conformation of a protein is an individual structural property of that specific protein which also determines its functional individuality; in other words, the Spatial structure of a protein is characteristic.

2. The native structure of a protein is determined by yet fully understood "instructions" embedded within its amino acid sequence, i.e., already in its Primary Structure.

3. All native protein structures share one common property: they correspond to a conformation with minimum energy, meaning they are maximally stable.

The existence of A large number of folds, turns, and bends in protein peptide chains is maintained by various stabilizing forces. The most powerful among them are covalent bonds, exemplified by disulfide bridges; however, they are absent in certain proteins. Therefore, it is generally accepted that stabilization is primarily achieved through non-covalent interactions of the following types:

> electrostatic forces of attraction between side chains with oppositely charged ionic groups (ion-ion interactions), provided the peptide chain contains amino acids with polar R-groups (lysine, Arginine, glutamic acid, and aspartic acid);

> hydrogen bonds between groups not involved in peptide bond formation, such as between Tyrosine and glutamic acid residues;

> hydrogen bonds of peptide groups formed within helical and pleated sheet structures;

> hydrophobic interactions between the nonpolar side chains of leucine, valine, isoleucine, Alanine, phenylalanine, and other nonpolar amino acids;

> interactions within the prosthetic group, for example, between a metal ion and R-groups.

Schematically, all the listed types of non-covalent intermolecular interactions stabilizing the Spatial Structure of Proteins are presented in Fig. 2.3.

It is conventionally assumed that when the distance between interacting groups is 2–3.1 Å, they participate in polar interactions, whereas at distances of 3.1–4.1 Å, they engage in nonpolar interactions. Nonpolar interactions have a rather complex mechanism and are realized primarily due to the entropic contribution of Water molecule interactions to the Free energy of the protein Structuring process.

The native conformation of a globular protein is highly sensitive to external influences and much less stable than that of a fibrillar protein.

The following rules apply to the tertiary structure of proteins.

> Peptide chains exist in their most stable state (with the lowest energy).

> All donor and acceptor groups prone to hydrogen bonding (or any other donor-acceptor complexes) are located in positions favorable for such bond formation and, as a rule, reside On the surface.

> Charged residues are typically located on the protein surface; burying charges inside the protein molecule is energetically unfavorable (increases energy). Occasionally, charges are found within the molecule, but in most cases, they belong to residues directly involved in catalytic acts or performing other specific Functions.

> Hydrophobic non-polar residues in globular proteins are generally located inside the globule;

Fig. 2.3 Schematic representation of intermolecular interactions in protein molecules that stabilize their spatial (tertiary) structure (Adapted from: Bohinsky, R. Modern Concepts in Biochemistry. 1987.-M.: Mir.- 544 p.)