The peptide bond is covalent in its chemical nature and gives high strength to the primary structure of the protein molecule. Being a repeating element of the polypeptide chain and having specific structural features, the peptide bond affects not only the form of the primary structure, but also the higher levels of organization of the polypeptide chain.
A great contribution to the study of the structure of the protein molecule was made by L. Pauling and R. Corey. Drawing attention to the fact that the protein molecule has the most peptide bonds, they were the first to conduct painstaking X-ray diffraction studies of this bond. We studied the bond lengths, the angles at which the atoms are located, the direction of the arrangement of atoms relative to the bond. Based on the research, the following main characteristics of the peptide bond were established.
1. Four atoms of the peptide bond (C, O, N, H) and two attached
a-carbon atoms lie in the same plane. The R and H groups of a-carbon atoms lie outside this plane.
2. O and H atoms of the peptide bond and two a-carbon atoms, as well as R-groups, have a trans orientation relative to the peptide bond.
3. The C–N bond length of 1.32 Å is intermediate between the length of a double covalent bond (1.21 Å) and a single covalent bond (1.47 Å). Hence it follows that the C–N bond has a partially unsaturated character. This creates the prerequisites for the implementation of tautomeric rearrangements at the site of the double bond with the formation of the enol form, i.e. the peptide bond may exist in the keto-enol form.
Rotation around the –C=N– bond is difficult, and all atoms in the peptide group have a planar trans configuration. The cis configuration is energetically less favorable and occurs only in some cyclic peptides. Each planar peptide fragment contains two bonds to rotatable a-carbon atoms.
There is a very close relationship between the primary structure of a protein and its function in a given organism. In order for a protein to perform its characteristic function, a completely specific sequence of amino acids is required in the polypeptide chain of this protein. This specific amino acid sequence, qualitative and quantitative composition is genetically fixed (DNA → RNA → protein). Each protein is characterized by a certain sequence of amino acids, the replacement of at least one amino acid in the protein leads not only to structural rearrangements, but also to changes in physicochemical properties and biological functions. The existing primary structure predetermines the subsequent (secondary, tertiary, quaternary) structures. For example, the erythrocytes of healthy people contain a protein - hemoglobin with a certain sequence of amino acids. A small part of people have a congenital anomaly in the structure of hemoglobin: their erythrocytes contain hemoglobin, which in one position instead of glutamic acid (charged, polar) contains the amino acid valine (hydrophobic, non-polar). Such hemoglobin significantly differs in physicochemical and biological properties from normal. The appearance of a hydrophobic amino acid leads to the appearance of a “sticky” hydrophobic contact (erythrocytes do not move well in blood vessels), to a change in the shape of an erythrocyte (from biconcave to crescent-shaped), as well as to a deterioration in oxygen transfer, etc. Children born with this anomaly die in early childhood from sickle cell anemia.
Comprehensive evidence in favor of the assertion that biological activity is determined by the amino acid sequence was obtained after artificial synthesis of the enzyme ribonuclease (Merrifield). The synthesized polypeptide with the same amino acid sequence as the natural enzyme had the same enzymatic activity.
Studies of recent decades have shown that the primary structure is fixed genetically, i.e. the sequence of amino acids in the polypeptide chain is determined by the genetic code of DNA, and, in turn, determines the secondary, tertiary and quaternary structures of the protein molecule and its general conformation. The first protein whose primary structure was established was the protein hormone insulin (contains 51 amino acids). This was done in 1953 by Frederick Sanger. To date, the primary structure of more than ten thousand proteins has been deciphered, but this is a very small number, given that there are about 10 12 proteins in nature. As a result of free rotation, polypeptide chains are able to twist (fold) into various structures.
secondary structure. The secondary structure of a protein molecule is understood as a way of laying a polypeptide chain in space. The secondary structure of a protein molecule is formed as a result of one or another type of free rotation around the bonds connecting a-carbon atoms in a polypeptide chain. As a result of this free rotation, polypeptide chains are able to twist (fold) in space into various structures.
Three main types of structure have been found in natural polypeptide chains:
- a-helix;
- β-structure (folded sheet);
- statistical tangle.
The most probable type of structure of globular proteins is considered to be α-helix Twisting occurs clockwise (right helix), which is due to the L-amino acid composition of natural proteins. The driving force in the emergence α-helices is the ability of amino acids to form hydrogen bonds. R-groups of amino acids are directed outward from the central axis a-helices. >С=О and >N–Н dipoles of adjacent peptide bonds are optimally oriented for dipole interaction, resulting in the formation of an extensive system of intramolecular cooperative hydrogen bonds stabilizing the a-helix.
Helix pitch (one full turn) 5.4Å includes 3.6 amino acid residues.
Figure 2 - Structure and parameters of the a-helix of the protein
Each protein is characterized by a certain degree of helicalization of its polypeptide chain.
The spiral structure can be disturbed by two factors:
1) in the presence of a proline residue in the chain, the cyclic structure of which introduces a kink in the polypeptide chain - there is no –NH 2 group, therefore the formation of an intrachain hydrogen bond is impossible;
2) if in the polypeptide chain there are many amino acid residues in a row that have a positive charge (lysine, arginine) or a negative charge (glutamic, aspartic acids), in this case, the strong mutual repulsion of like-charged groups (-COO - or -NH 3 +) significantly exceeds stabilizing effect of hydrogen bonds in a-helices.
Another type of polypeptide chain configuration found in hair, silk, muscle and other fibrillar proteins is called β structures or folded sheet. The folded sheet structure is also stabilized by hydrogen bonds between the same dipoles –NH...... O=C<. Однако в этом случае возникает совершенно иная структура, при которой остов полипептидной цепи вытянут таким образом, что имеет зигзагообразную структуру. Складчатые участки полипептидной цепи проявляют кооперативные свойства, т.е. стремятся расположиться рядом в белковой молекуле, и формируют параллельные
identically directed polypeptide chains or antiparallel,
which are strengthened by hydrogen bonds between these chains. Such structures are called b-folded sheets (Figure 2).
Figure 3 - b-structure of polypeptide chains
a-Helix and folded sheets are ordered structures, they have a regular arrangement of amino acid residues in space. Some sections of the polypeptide chain do not have any regular periodic spatial organization, they are designated as random or statistical tangle.
All these structures arise spontaneously and automatically due to the fact that a given polypeptide has a specific amino acid sequence that is genetically predetermined. a-helices and b-structures determine a certain ability of proteins to perform specific biological functions. So, the a-helical structure (a-keratin) is well adapted to form external protective structures - feathers, hair, horns, hooves. The b-structure contributes to the formation of flexible and inextensible silk and cobwebs, and the conformation of the collagen protein provides the high tensile strength required for tendons. The presence of only a-helices or b-structures is typical for filamentous (fibrillar) proteins. In the composition of globular (spherical) proteins, the content of a-helices and b-structures and structureless regions varies greatly. For example: insulin spiralized 60%, ribonuclease enzyme - 57%, chicken egg protein lysozyme - 40%.
Tertiary structure. Under the tertiary structure understand the way of laying the polypeptide chain in space in a certain volume.
The tertiary structure of proteins is formed by additional folding of the peptide chain containing a-helix, b-structures and random coil regions. The tertiary structure of a protein is formed completely automatically, spontaneously and completely predetermined by the primary structure and is directly related to the shape of the protein molecule, which can be different: from spherical to threadlike. The shape of a protein molecule is characterized by such an indicator as the degree of asymmetry (the ratio of the long axis to the short one). At fibrillar or filamentous proteins, the degree of asymmetry is greater than 80. When the degree of asymmetry is less than 80, proteins are classified as globular. Most of them have a degree of asymmetry of 3-5, i.e. the tertiary structure is characterized by a fairly dense packing of the polypeptide chain, approaching the shape of a ball.
During the formation of globular proteins, non-polar hydrophobic radicals of amino acids are grouped inside the protein molecule, while polar radicals are oriented towards water. At some point, the thermodynamically most favorable stable conformation of the molecule, the globule, arises. In this form, the protein molecule is characterized by a minimum free energy. The conformation of the resulting globule is influenced by such factors as the pH of the solution, the ionic strength of the solution, as well as the interaction of protein molecules with other substances.
The main driving force in the emergence of a three-dimensional structure is the interaction of amino acid radicals with water molecules.
fibrillar proteins. When forming a tertiary structure, they do not form globules - their polypeptide chains do not fold, but remain elongated in the form of linear chains, grouping into fibril fibers.
Drawing – The structure of a collagen fibril (fragment).
Recently, evidence has appeared that the process of formation of the tertiary structure is not automatic, but is regulated and controlled by special molecular mechanisms. This process involves specific proteins - chaperones. Their main functions are the ability to prevent the formation of non-specific (chaotic) random coils from the polypeptide chain, and to ensure their delivery (transport) to subcellular targets, creating conditions for the completion of the folding of the protein molecule.
Stabilization of the tertiary structure is ensured by non-covalent interactions between the atomic groups of side radicals.
Figure 4 - Types of bonds that stabilize the tertiary structure of the protein
A) electrostatic forces attraction between radicals carrying oppositely charged ionic groups (ion-ion interactions), for example, a negatively charged carboxyl group (- COO -) of aspartic acid and (NH 3 +) a positively charged e-amino group of a lysine residue.
b) hydrogen bonds between the functional groups of side radicals. For example, between the OH group of tyrosine and the carboxyl oxygen of aspartic acid
V) hydrophobic interactions due to van der Waals forces between non-polar amino acid radicals. (For example, groups
-CH 3 - alanine, valine, etc.
G) dipole-dipole interactions
e) disulfide bonds(–S–S–) between cysteine residues. This bond is very strong and is not present in all proteins. This connection plays an important role in the protein substances of grain and flour, because. affects the quality of gluten, the structural and mechanical properties of the dough and, accordingly, the quality of the finished product - bread, etc.
A protein globule is not an absolutely rigid structure: within certain limits, reversible movements of parts of the peptide chain relative to each other are possible with the breaking of a small number of weak bonds and the formation of new ones. The molecule, as it were, breathes, pulsates in its different parts. These pulsations do not disturb the basic conformation plan of the molecule, just as thermal vibrations of atoms in a crystal do not change the structure of the crystal unless the temperature is so high that melting occurs.
Only after a protein molecule acquires a natural, native tertiary structure does it show its specific functional activity: catalytic, hormonal, antigenic, etc. It is during the formation of the tertiary structure that the formation of active centers of enzymes, centers responsible for the incorporation of the protein into the multienzyme complex, centers responsible for the self-assembly of supramolecular structures takes place. Therefore, any impact (thermal, physical, mechanical, chemical) that leads to the destruction of this native conformation of the protein (breaking bonds) is accompanied by a partial or complete loss of its biological properties by the protein.
The study of the complete chemical structures of some proteins has shown that in their tertiary structure zones are revealed where the hydrophobic radicals of amino acids are concentrated, and the polypeptide chain is actually wrapped around the hydrophobic core. Moreover, in some cases, two or even three hydrophobic nuclei are isolated in a protein molecule, resulting in a 2 or 3 nuclear structure. This type of molecular structure is characteristic of many proteins with a catalytic function (ribonuclease, lysozyme, etc.). A separate part or region of a protein molecule that has a certain degree of structural and functional autonomy is called a domain. Some enzymes, for example, have distinct substrate-binding and coenzyme-binding domains.
Biologically, fibrillar proteins play a very important role in the anatomy and physiology of animals. In vertebrates, these proteins account for 1/3 of their total content. An example of fibrillar proteins is silk protein - fibroin, which consists of several antiparallel chains with a folded sheet structure. Protein a-keratin contains from 3-7 chains. Collagen has a complex structure in which 3 identical left-handed chains are twisted together to form a right-handed triple helix. This triple helix is stabilized by numerous intermolecular hydrogen bonds. The presence of amino acids such as hydroxyproline and hydroxylysine also contributes to the formation of hydrogen bonds that stabilize the triple helix structure. All fibrillar proteins are poorly soluble or completely insoluble in water, since they contain many amino acids containing hydrophobic, water-insoluble R-groups of isoleucine, phenylalanine, valine, alanine, methionine. After special processing, insoluble and indigestible collagen is converted into a gelatin-soluble mixture of polypeptides, which is then used in the food industry.
Globular proteins. They perform a variety of biological functions. They perform a transport function, i.e. carry nutrients, inorganic ions, lipids, etc. Hormones, as well as components of membranes and ribosomes, belong to the same class of proteins. All enzymes are also globular proteins.
Quaternary structure. Proteins containing two or more polypeptide chains are called oligomeric proteins, they are characterized by the presence of a quaternary structure.
Figure - Schemes of tertiary (a) and quaternary (b) protein structures
In oligomeric proteins, each of the polypeptide chains is characterized by its primary, secondary and tertiary structure, and is called a subunit or protomer. The polypeptide chains (protomers) in such proteins can be either the same or different. Oligomeric proteins are called homogeneous if their protomers are the same and heterogeneous if their protomers are different. For example, the hemoglobin protein consists of 4 chains: two -a and two -b protomers. The a-amylase enzyme consists of 2 identical polypeptide chains. Quaternary structure is understood as the arrangement of polypeptide chains (protomers) relative to each other, i.e. way of their joint stacking and packaging. In this case, the protomers interact with each other not by any part of their surface, but by a certain area (contact surface). The contact surfaces have such an arrangement of atomic groups between which hydrogen, ionic, hydrophobic bonds arise. In addition, the geometry of the protomers also contributes to their connection. Protomers fit together like a key to a lock. Such surfaces are called complementary. Each protomer interacts with the other at multiple points, making it impossible to link to other polypeptide chains or proteins. Such complementary interactions of molecules underlie all biochemical processes in the body.
