Textbook - BIOLOGICAL CHEMISTRY - Hubskyi Yu.I. - 2000

Chapter I. BIOMOLECULES AND CELLULAR STRUCTURES

CHAPTER 2. PROTEINS AND PEPTIDES

2.3. LEVELS OF STRUCTURAL ORGANIZATION OF PROTEIN MOLECULES

All Proteins AND Peptides possess a unique three-dimensional spatial Organization (conformation), which serves as the structural foundation for their specific biological function.

Highly Ordered Conformations of protein molecules are formed on The basis of polypeptide chains with a Covalent Structure and are stabilized through The formation of weak physicochemical bonds and interactions between amino acid residues in specific peptide regions.

Class="center">Types of bonds in protein molecules

1. Covalent bonds.

1.1. Peptide bonds — arise As a result of the interaction between the α-carboxyl and α-amino groups of the Amino Acids that form the peptide chain.

1.2. Disulfide Bonds (-S-S-) — form between Cysteine residues belonging to the same or different peptide chains.

2. Non-covalent bonds and weak interactions — physicochemical bonds involved in the interaction both between specific parts of a single peptide chain and between different, closely located chains, forming higher levels of Protein Molecule Conformation.

2.1. Hydrogen Bonds — arise between two electronegative atoms via a hydrogen atom covalently bonded to one of the electronegative atoms. They most frequently form between hydrogen belonging to =NH, -OH, or -SH groups and a neighboring oxygen atom, for example:

2.2. Ionic bonds — link ionized amine and carboxyl groups together (mainly from the side chains of diamino and dicarboxylic amino acids).

2.3. Dipole bonds — Electrostatic Interactions of permanent or induced dipoles that can form between the radicals of polar amino acids (such as Serine, Threonine, cysteine, and Tyrosine) that make up protein molecules.

2.4. Hydrophobic interactions — weak interactions that occur between the side chains of amino acids such as valine, leucine, isoleucine, and phenylalanine due to their "expulsion" from the polar (typically aqueous) phase.

Levels of Structural organization of proteins

Primary Cell/13.html">Protein Structure

The Introduction/19.html">Primary Structure of Proteins refers to the peptide (polypeptide) chain constructed from L-amino acid residues. METABOLISM/2.html">THE CONCEPT OF the primary structure of a protein or peptide includes its Qualitative and quantitative Amino Acid Composition and the sequence (order of arrangement) of individual amino acid residues.

A fragment of the primary structure of a polypeptide chain with structural parameters established on the basis of X-Ray Diffraction Analysis of peptides is presented in Fig. 2.4.

Fig. 2.4. Parameters of Structural elements of the polypeptide chain (dimensions are given in angstroms; 1Å = 0.1 nm).

In addition to peptide bonds, the primary structure of proteins is also formed by disulfide bonds that connect specific Regions of the polypeptide chain or separate peptides.

An example is the arrangement of disulfide bonds in the molecule of the protein hormone Insulin, which consists of two peptide chains (the A-chain containing 21 amino acid residues and the B-chain containing 30 residues):

The names of peptides, which determine their primary structure, are constructed as follows:

a) The amino acid residue possessing a free α-amino group (the so-called "N-terminal amino acid") is indicated first;

b) in the names of all amino acids involved in the formation of a peptide bond via their α-carboxyl group, the suffix -ine (-in) is changed to -yl;

c) the amino acid that has a free α-carboxyl group (the "C-terminal amino acid") retains its original suffix (-ine (-in)).

Example of a peptide name, alanyl-glycyl-methionyl-serine:

Using international abbreviated symbols, this tetrapeptide can be designated as follows:

Ala - Gly - Met - Ser

These abbreviated notations of peptides are of particular importance for representing proteins whose primary structure comprises many hundreds of amino acid residues.

In connection with the aforementioned ability of individual Functional groups of the peptide chain to undergo intrachain interactions, the peptide chain acquires a specific Spatial Structure (conformation). Two levels of conformation of the peptide chain (and, accordingly, of the protein molecule formed on its basis) are distinguished: secondary and tertiary structures. The secondary, tertiary, and quaternary (see below) structures are collectively referred to as the higher levels of structural organization of protein molecules.

Secondary structure of Proteins

The secondary structure of proteins is a series of conformations whose formation is driven primarily by hydrogen bonds between individual regions (predominantly peptide groups) of the peptide chain or between different peptide chains.

Two MAIN TYPES OF ordered secondary structure in protein molecules are distinguished: the α-helix and the β-structure.

1. The α-Helix is a conformation formed by the spatial coiling of a polypeptide chain due to hydrogen bonds that arise between C=O and NH groups of the polypeptide chain spaced four amino acid residues apart. The hydrogen bonds in the α-helix are oriented parallel to the axis of the molecule.

The α-helix can be visualized as a line tracing the lateral surface of an imaginary cylinder. There are 3.6 amino acid residues per turn of the α-helix. The direction of coiling of the polypeptide chain in natural proteins is right-handed ("right-handed" α-helix) (Fig. 2.5).

Fig. 2.5. Model of the secondary structure of a polypeptide chain in the form of an α-helix (according to L. Pauling and R. Corey).

Geometric parameters of the α-helix: radius — 0.25 nm; pitch (identity period) — 0.54 nm; axial Translation per amino acid residue — 0.15 nm; there are 3.6 amino acid residues per turn of the α-helix.

The α-helix is a molecular structure formed under specific steric relationships between amino acid residues, and its formation depends on the amino acid COMPOSITION OF THE polypeptide chain. Certain amino acids (Pro, Gly, Glu, Asp, Arg, etc.) oppose the Formation of the α-helix or destabilize it. Consequently, Helical structures may arise that differ in their geometric parameters from the classic α-helix. An example is the helix of the Collagen protein—the major protein component of Connective Tissue, which contains 33% Glycine and 21% Proline and hydroxyproline.

Several protein molecules with helical secondary structure can interact with one another to form intermolecular complexes representing supercoiled ("super-secondary") structures.

2. The β-structure is a pleated-sheet type of structure consisting of zigzag-extended polypeptide chains arranged adjacently (two or more) — Fig. 2.6.

Fig. 2.6. β-Conformation of the polypeptide chain.

Schematic representation of three parallel chains forming a pleated-sheet structure.

β-Structures are formed through interchain hydrogen bonds linking the C=O and NH groups of adjacent Polypeptides (Fig. 2.7):

Fig. 2.7. Formation of β-structures: a - side view; b - top view.

The β-conformation is characteristic of β-Keratins, which consist of zigzag, antiparallel-oriented polypeptide chains. A typical representative of β-keratins is Fibroin, a fibrous, insoluble protein found in silk and spider webs.

In addition to ordered types (α-helices and β-structures), the secondary structure can also present an irregular, unordered (random) conformation.

In many native proteins, along a single polypeptide chain that forms the primary structure, there are both α-helical regions and zones forming a pleated sheet (β-structures) or possessing an irregular conformation. For instance, in the Chymotrypsin molecule, up to 14% of the total amino acid residues are part of α-helices, 45% belong to β-structures, and 61% form regions with an unordered structure. The polypeptide chains in Myoglobin and Tropomyosin molecules are almost entirely α-helical (80% and 100%, respectively).

Tertiary Protein Structure

The Tertiary Structure of proteins refers to the three-dimensional folding arrangement of a polypeptide chain with a specific secondary structure. Hydrogen bonds, ionic bonds, hydrophobic interactions, and other forces participate in the formation and stabilization of the tertiary structure.

Depending on their shape and the features of their three-dimensional spatial organization, proteins are classified into globular and Fibrous proteins.

Globular proteins are proteins with a rounded (spherical or ellipsoidal) shape. The ratio of the long to short axes in globular molecules ranges from 1:1 to 50:1. Examples include Blood serum albumin, Muscle myoglobin, Hemoglobin, and the majority of Enzymes.

Globular Proteins are built from one or more polypeptide chains linked by disulfide bridges and folded into compact spherical shapes. The model of the spatial structural ORGANIZATION OF THE myoglobin molecule, first proposed by J. Kendrew in 1958 based on X-ray diffraction Analysis of Protein crystals, is shown in Fig. 2.8.

Fig. 2.8. Model of the tertiary STRUCTURE OF THE myoglobin molecule. The spatial arrangement of the polypeptide chain linked to the heme group is shown.

The three-dimensional organization of globular proteins is formed through the spatial folding of the polypeptide chain, individual segments of which may contain α-helices, β-structures, and unstructured regions (see: Secondary Protein Structure).

A diagram of the spatial conformation of myoglobin, a significant portion of whose polypeptide chain is α-helical, is presented in Fig. 2.9.

Fig. 2.9. Spatial conformation of myoglobin illustrating the secondary structure Features of the polypeptide chain.

The tertiary structure of the globular enzyme hexokinase, whose polypeptide chain forms both α-helices and pleated sheets, is depicted in Fig. 2.10.

Fig. 2.10. Three-dimensional organization of the hexokinase enzyme. In this figure and in Fig. 2.13, α-helices are conventionally represented as cylinders, and β-structures as arrows (after A.Ya. Nikolayev, 1989).

The stabilization of the compact globule is achieved through Hydrogen bonds and other weak interactions between the side chains of amino acid residues, which fix specific segments of the polypeptide chain (or chains linked by S-S bonds) relative to one another.

A distinctive feature of the tertiary Structure of Globular proteins, which determines their crucial physicochemical and biological properties, is the specific arrangement of polar and nonpolar amino acid residues. In most globular proteins, polar (hydrophilic) residues are located On the surface of the globule, where they interact with the aqueous phase, whereas nonpolar radicals are buried within the internal Hydrophobic core of the molecule. These Structural Features of protein globules determine their degree of solubility and The Nature of their interactions with other proteins and ligands of various chemical properties.

Fibrous proteins are proteins whose structural hallmark is an elongated molecular shape. They tend to form multimolecular thread-like complexes called fibrils, which consist of several parallel polypeptide chains.

Fibrous proteins serve as Structural components of connective tissue and other supportive Tissues in the Organism. Examples of structural fibrous proteins include collagen, the most abundant protein in The Human Body, accounting for up to 30% of total tissue proteins; Elastin in connective tissue; and α-keratin in supportive tissues, the epidermis of the Skin, and Hair.

The formation of many biologically important fibrous proteins occurs through The Development of supersecondary (supercoiled) structures, specifically:

1. Tropocollagen molecules are the structural units of collagen fibrils in connective tissue. Tropocollagen molecules consist of three polypeptide chains (collagen helices) wound around each other like a tight rope. The stabilization of tropocollagen is achieved via hydrogen bonds between the C=O and NH groups of adjacent polypeptide chains.

2. α-Keratin proteins are the primary type of fibrous proteins that make up the outer protective coverings of vertebrate animals (human skin epidermis, hair, and Nails; animal wool, feathers, and horny structures). α-Keratins are microfibrils approximately 2 nm in diameter, composed of three α-helical polypeptide chains assembled into a coiled-coil superhelix. Individual microfibrils, linked together by interchain disulfide bonds, form multi-stranded cable-like structures that provide mechanical strength to hair and other tissues rich in α-keratins.

The Mechanism of fibrous protein formation via supercoiling of individual polypeptide chains adopting an α-helical conformation is illustrated in Fig. 2.11.

Fig. 2.11. Model of fibrous protein formation from individual α-helical polypeptides: a — a polypeptide chain representing a "major" helix formed on the basis of a "minor" α-helix; in the depicted model, the pitch of the "minor" helix (1) is 12.5 times smaller than the pitch of the "major" helix (2); b — a multi-stranded cable-type superhelix composed of seven α-helical polypeptides.

Quaternary Protein Structure

Quaternary protein structure arises from the association (aggregation) of multiple polypeptide chains or protomers, each possessing its own characteristic ordered conformation.

Individual protomers (subunits) in proteins with quaternary structure are held together by non-covalent interactions, making them relatively easy to dissociate upon Changes in the PHYSICOCHEMICAL PROPERTIES OF the environment. At the same time, such dissociation leads to the loss of the protein-specific biological activity, which is characteristic only of the intact oligomeric assembly.

Examples of proteins with quaternary structure include Oligomeric Proteins with a molecular weight above 50 kD, as listed in Table 2.1.

Of significant physiological and clinical interest is the erythrocyte protein hemoglobin (Hb), which serves as the oxygen carrier in humans and higher vertebrates. It is a classic representative of proteins with quaternary structure. The Molecular Weight of hemoglobin is 68 kD; its molecule is built from four pairwise identical subunits — two α- and two β-polypeptide chains, each associated with a non-protein heme group, a porphyrin derivative that binds the oxygen molecule (Fig. 2.12):

Fig. 2.12. Quaternary Structure of the hemoglobin molecule.

Proteins with quaternary structure may comprise either identical protomers (as in the case of hemoglobin) or different ones. Many enzyme proteins contain diverse protomers that perform distinct biochemical Functions (specifically, catalytic and regulatory).

Domain Proteins

Domains are structural regions of protein molecules that form globular units within proteins exhibiting tertiary structure. A globular domain has an average diameter of 2.5 nm and typically consists of 100–150 amino acid residues.

Individual domains function as relatively autonomous units within protein molecules, making domain proteins structurally comparable to oligomeric proteins. However, unlike proteins with quaternary structure (oligomers), individual domain globules are formed by the same polypeptide chain and are therefore connected by intervening peptide segments ("hinge" regions). Interdomain bonds can be cleaved solely through the action of Proteolytic Enzymes.

Examples of domain proteins include Enzymes of the glycolytic glucose oxidation pathway — glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase (Fig. 2.13), in which distinct domains carry out different stages of a complex catalytic event.

Fig. 2.13. Domain organization of the enzyme phosphoglycerate kinase.

Concluding our examination of the molecular mechanisms underlying higher Levels of Protein structural organization, it must be emphasized that all highly ordered spatial conformations of protein molecules are strictly determined by the primary structure of the polypeptide chain—that is, the Amino Acid Sequence encoded by The Genetic Code of The Cell in which the specific protein is synthesized.

Secondary, tertiary, quaternary, and domain organizations of proteins are the result of spontaneous spatial folding driven toward achieving a thermodynamically stable state for the complex biophysical macromolecule (Fig. 2.14).

Fig. 2.14. Formation of higher levels of protein structural organization based on primary structure.