The peptide bond is covalent in its chemical nature and imparts 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 shape of the primary structure, but also the higher levels of organization of the polypeptide chain.
L. Pauling and R. Corey made a great contribution to the study of the structure of the protein molecule. Noticing that the protein molecule contains the most peptide bonds, they were the first to conduct painstaking X-ray studies of this bond. We studied the bond lengths, the angles at which the atoms are located, and the direction of the 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. The O and H atoms of the peptide bond and the two a-carbon atoms, as well as the R-groups, have a trans orientation relative to the peptide bond.
3. The C–N bond length, equal to 1.32 Å, is intermediate between the length of a double covalent bond (1.21 Å) and a single covalent bond (1.47 Å). It follows that the C–N bond is partially unsaturated. This creates the prerequisites for tautomeric rearrangements to occur at the double bond with the formation of the enol form, i.e. the peptide bond can exist in the keto-enol form.
Rotation around the –C=N– bond is difficult and all atoms included in the peptide group have a planar trans configuration. The cis configuration is energetically less favorable and is found only in some cyclic peptides. Each planar peptide fragment contains two bonds with a-carbon atoms capable of rotation.
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 inherent function, a very specific sequence of amino acids is required in the polypeptide chain of this protein. This specific sequence of amino acids, qualitative and quantitative composition is fixed genetically (DNA→RNA→protein). Each protein is characterized by a specific sequence of amino acids; replacing at least one amino acid in a protein leads not only to structural rearrangements, but also to changes in physicochemical properties and biological functions. The existing primary structure predetermines subsequent (secondary, tertiary, quaternary) structures. For example, the red blood cells of healthy people contain a protein called hemoglobin with a certain sequence of amino acids. A small proportion of people have a congenital abnormality in the structure of hemoglobin: their red blood cells contain hemoglobin, which in one position contains the amino acid valine (hydrophobic, non-polar) instead of glutamic acid (charged, polar). Such hemoglobin differs significantly in physicochemical and biological properties from normal. The appearance of a hydrophobic amino acid leads to the appearance of a “sticky” hydrophobic contact (red blood cells do not move well in blood vessels), to a change in the shape of the red blood cell (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 statement that biological activity is determined by the amino acid sequence was obtained after the artificial synthesis of the enzyme ribonuclease (Merrifield). A synthesized polypeptide with the same amino acid sequence as the natural enzyme had the same enzymatic activity.
Research in recent decades has shown that the primary structure is fixed genetically, i.e. the sequence of amino acids in a 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, considering 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 refers to the way the polypeptide chain is arranged 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 the 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 are 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-hand spiral), 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. Amino acid R groups point outward from the central axis a-helices. dipoles >C=O and >N–H of neighboring peptide bonds are oriented optimally for dipole interaction, thereby forming an extensive system of intramolecular cooperative hydrogen bonds that stabilize the a-helix.
The helix pitch (one full turn) of 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 helicity of its polypeptide chain
The spiral structure can be disrupted by two factors:
1) the presence of a proline residue in the chain, the cyclic structure of which introduces a break in the polypeptide chain - there is no –NH 2 group, therefore the formation of an intrachain hydrogen bond is impossible;
2) if in a 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 similarly charged groups (–COO– or –NH 3 +) significantly exceeds stabilizing influence 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
polypeptide chains that are identically directed or antiparallel,
which are strengthened due to 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 regions of the polypeptide chain do not have any regular periodic spatial organization; they are designated as disordered or statistical tangle.
All these structures arise spontaneously and automatically due to the fact that a given polypeptide has a certain amino acid sequence, which is genetically predetermined. a-helices and b-structures determine a certain ability of proteins to perform specific biological functions. Thus, the a-helical structure (a-keratin) is well adapted to form external protective structures - feathers, hair, horns, hooves. The b-structure promotes the formation of flexible and inextensible silk and web threads, and the collagen protein conformation provides the high tensile strength required for tendons. The presence of only a-helices or b-structures is characteristic of 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 is spiralized 60%, ribonuclease enzyme - 57%, chicken egg protein lysozyme - 40%.
Tertiary structure. Tertiary structure refers to the way a polypeptide chain is arranged in space in a certain volume.
The tertiary structure of proteins is formed by additional folding of the peptide chain containing an 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 filamentous. 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). U fibrillar or filamentous proteins, the degree of asymmetry is greater than 80. With a degree of asymmetry 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, nonpolar hydrophobic amino acid radicals are grouped within the protein molecule, while polar radicals are oriented toward water. At some point, the thermodynamically most favorable stable conformation of the molecule, a globule, appears. In this form, the protein molecule is characterized by minimal free energy. The conformation of the resulting globule is influenced by factors such 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. During the formation of the 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 – Structure of collagen fibril (fragment).
Recently, evidence has emerged that the process of tertiary structure formation 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 nonspecific (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 due to non-covalent interactions between the atomic groups of side radicals.
Figure 4 - Types of bonds that stabilize the tertiary structure of a protein
A) electrostatic forces attraction between radicals carrying oppositely charged ionic groups (ion-ion interactions), for example, the negatively charged carboxyl group (– COO –) of aspartic acid and (NH 3 +) the positively charged e-amino group of a lysine residue.
b) hydrogen bonds between functional groups of side radicals. For example, between the OH group of tyrosine and the carboxylic oxygen of aspartic acid
V) hydrophobic interactions are caused by van der Waals forces between non-polar amino acid radicals. (For example, in groups
–CH 3 – alanine, valine, etc.
G) dipole-dipole interactions
d) 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 influences 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 seems to breathe, pulsate in its different parts. These pulsations do not disrupt the basic conformation plan of the molecule, just as thermal vibrations of atoms in a crystal do not change the structure of the crystal if the temperature is not so high that melting occurs.
Only after a protein molecule acquires a natural, native tertiary structure does it exhibit 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 occurs, centers responsible for the integration of proteins into the multienzyme complex, centers responsible for the self-assembly of supramolecular structures. Therefore, any influences (thermal, physical, mechanical, chemical) leading to the destruction of this native conformation of the protein (breaking bonds) are accompanied by partial or complete loss of the protein’s biological properties.
The study of the complete chemical structures of some proteins has shown that in their tertiary structure zones are identified where hydrophobic amino acid radicals are concentrated, and the polypeptide chain is actually wrapped around the hydrophobic core. Moreover, in some cases, two or even three hydrophobic nuclei are separated in a protein molecule, resulting in a 2- or 3-nuclear structure. This type of molecular structure is characteristic of many proteins that have 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. A number of enzymes, for example, have separate substrate-binding and coenzyme-binding domains.
Biologically, fibrillar proteins play a very important role related to the anatomy and physiology of animals. In vertebrates, these proteins account for 1/3 of their total content. An example of fibrillar proteins is the 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 levorotatory chains are twisted together to form a dextrorotatory 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 structure of the triple helix. All fibrillar proteins are poorly soluble or completely insoluble in water, since they contain many amino acids containing hydrophobic, water-insoluble R-groups isoleucine, phenylalanine, valine, alanine, methionine. After special processing, insoluble and indigestible collagen is converted into a gelatin-soluble polypeptide mixture, which is then used in the food industry.
Globular proteins. Perform a variety of biological functions. They perform a transport function, i.e. transport 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 protein hemoglobin consists of 4 chains: two -a and two -b protomers. The enzyme a-amylase consists of 2 identical polypeptide chains. Quaternary structure refers to the arrangement of polypeptide chains (protomers) relative to each other, i.e. the method of their joint stacking and packaging. In this case, protomers interact with each other not with any part of their surface, but with a certain area (contact surface). Contact surfaces have such an arrangement of atomic groups between which hydrogen, ionic, and hydrophobic bonds arise. In addition, the geometry of the protomers also favors 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 connection with other polypeptide chains or proteins impossible. Such complementary interactions of molecules underlie all biochemical processes in the body.
