The protein molecule has four types of structural organization - primary, secondary, tertiary and quaternary.
Primary structure
A linear structure, which is a strictly defined genetically determined sequence of amino acid residues in a polypeptide chain. The main type of communication is peptide (the mechanism of formation and characteristics of the peptide bond are discussed above).
The polypeptide chain has significant flexibility and, as a result, acquires a certain spatial structure (conformation) within the chain interactions.
In proteins, there are two levels of conformation of peptide chains - secondary and tertiary structures.
Protein secondary structure
This is the arrangement of a polypeptide chain into an ordered structure due to the formation of hydrogen bonds between the atoms of the peptide groups of one polypeptide chain or adjacent chains.
During the formation of the secondary structure, hydrogen bonds are formed between the oxygen and hydrogen atoms of the peptide groups:
According to configuration, the secondary structure is divided into two types:
helical (α-helix)
layered (β-structure and cross-β-form).
α-Helix looks like a regular spiral. It is formed due to interpeptide hydrogen bonds within one polypeptide chain (Fig. 1).
Rice. 1. Scheme of α-helix formation
Main characteristics of the α-helix:
– hydrogen bonds are formed between the peptide groups of each first and fourth amino acid residue;
– the turns of the helix are regular, with 3.6 amino acid residues per turn;
– side radicals of amino acids do not participate in the formation of the α-helix;
– all peptide groups participate in the formation of a hydrogen bond, which determines the maximum stability of the α-helix;
– since all the oxygen and hydrogen atoms of the peptide groups are involved in the formation of hydrogen bonds, this leads to a decrease in the hydrophilicity of the α-helical regions;
– the α-helix is formed spontaneously and is the most stable conformation of the polypeptide chain, corresponding to the minimum free energy;
– proline and hydroxyproline prevent the formation of an α-helix – in the places where they are located, the regularity of the α-helix is disrupted and the polypeptide chain easily bends (breaks), since it is not held by a second hydrogen bond (Fig. 2).
Rice. 2. Violations of the regularity of the α-helix
The nitrogen atom of the α-imino group of proline during the formation of a peptide bond remains without a hydrogen atom, and therefore cannot participate in the formation of a hydrogen bond. There is a lot of proline and hydroxyproline in the polypeptide chain of collagen (see classification of simple proteins - collagen).
A high frequency of α-helix is characteristic of myoglobin and globin (a protein that is part of hemoglobin). Average globular(round or ellipsoidal) proteins have degree of spiralization 60–70%. Spiral areas alternate with chaotic tangles. As a result of protein denaturation, the helix → coil transitions increase. For spiralization(formation of α-helix) influence amino acid radicals that are part of the polypeptide chain, for example, negatively charged groups of glutamic acid radicals, located close to each other, they repel and prevent the formation of an α-helix (a coil is formed). For the same reason, closely located arginine and lysine, which have positively charged functional groups in the radicals, prevent the formation of an α-helix (see example protamines and histones).
The large size of amino acid radicals (for example, serine, threonine, leucine radicals) also prevent the formation of an α-helix.
Thus, the content of α-helices in proteins varies.
β-Structure (layered-folded) - has a slightly curved configuration of the polypeptide chain and is formed with the help of interpeptide hydrogen bonds within individual sections of one polypeptide chain or adjacent polypeptide chains. There are two types of β-structure:
– Toross-β-form(short β-structure) - represents limited layered regions formed by one polypeptide chain of a protein (Fig. 3).
Rice. 3. Cross-β form of a protein molecule
Most globular proteins include short β-structures (laminated regions). Their composition can be presented as follows: (αα), (αβ), (βα), (αβα), (βαβ).
– complete β structure. This type is characteristic of the entire polypeptide chain, which has an elongated shape and is held by interpeptide hydrogen bonds between adjacent parallel or antiparallel polypeptide chains (Fig. 4).
Rice. 4. Complete β-structure
In antiparallel structures, connections are more stable than in parallel ones.
Proteins with a regular β-structure are stronger and are poorly or not digested at all in the gastrointestinal tract.
The formation of a secondary structure (α-helix or β-structure) is determined by the sequence of amino acid residues in the polypeptide chain (i.e., the primary structure of the protein) and, therefore, is genetically determined. Amino acids such as methionine, valine, isoleucine and aspartic acid favor the formation of the β-structure.
Proteins with a complete β structure have fibrillar(thread-like) form. The complete β-structure is found in the proteins of supporting tissues (tendons, skin, bones, cartilage, etc.), in keratin (protein of hair and wool) (for the characteristics of individual proteins, see the section “Proteins of food raw materials”).
However, not all fibrillar proteins have only β structure. For example, α-keratin and paramyosin (protein of the obturator muscle of the mollusk), tropomyosin (protein of skeletal muscles) are fibrillar proteins and their secondary structure is α-helix.
For every protein, in addition to the primary one, there is also a certain secondary structure. Usually a protein molecule resembles an extended spring.
This is the so-called a-helix, stabilized by many hydrogen bonds that arise between CO and NH groups located nearby. Hydrogen atom of NH group one amino acid forms such a bond with the oxygen atom of the CO group of another amino acid, separated from the first by four amino acid residues.
Thus amino acid 1 turns out to be connected to amino acid 5, amino acid 2 to amino acid 6, etc. X-ray structural analysis shows that there are 3.6 amino acid residues per turn of the helix.
Fully a-helical conformation and, therefore, keratin protein has a fibrillar structure. It's structural protein hair, wool, nails, beak, feathers and horns, which is also part of the skin of vertebrates.
Hardness and keratin stretchability vary depending on the number of disulfide bridges between adjacent polypeptide chains (the degree of cross-linking of the chains).
Theoretically, all CO and NH groups can participate in the formation hydrogen bonds, so the α-helix is a very stable and therefore very common conformation. Sections of the α-helix in the molecule resemble rigid rods. However, most proteins exist in a globular form, which also contains regions (3-layers (see below) and regions with an irregular structure.
This is explained by the fact that education hydrogen bonds a number of factors hinder this: the presence of certain amino acid residues in the polypeptide chain, the presence of disulfide bridges between different sections of the same chain, and, finally, the fact that the amino acid proline is generally incapable of forming hydrogen bonds.
Beta Layer, or folded layer is another type of secondary structure. The silk protein fibroin, secreted by the silk-secreting glands of silkworm caterpillars when curling cocoons, is represented entirely in this form. Fibroin consists of a number of polypeptide chains that are more elongated than chains with an alpha conformation. spirals.
These chains are laid in parallel, but neighboring chains are opposite in direction to each other (antiparallel). They are connected to each other using hydrogen bonds, arising between the C=0- and NH-groups of neighboring chains. In this case, all NH and C=0 groups also take part in the formation of hydrogen bonds, i.e. the structure is also very stable.
This conformation of polypeptide chains is called beta conformation, and the structure as a whole is a folded layer. It has high tensile strength and cannot be stretched, but this organization of polypeptide chains makes silk very flexible. In globular proteins, the polypeptide chain can fold on itself, and then at these points of the globule regions appear that have the structure of a folded layer.
Another method of organizing polypeptide chains we find in the fibrillar protein collagen. This is also a structural protein that, like keratin and fibroin, has high tensile strength. Collagen has three polypeptide chains twisted together, like strands in a rope, forming a triple helix. Each polypeptide chain of this complex helix, called tropocollagen, contains about 1000 amino acid residues. An individual polypeptide chain is free coiled spiral(but not a-helix;).
Three chains held together hydrogen bonds. Fibrils are formed from many triple helices arranged parallel to each other and held together by covalent bonds between adjacent chains. They in turn combine into fibers. The structure of collagen is thus formed in stages - at several levels - similar to the structure of cellulose. Collagen also cannot be stretched, and this property is essential for the function it performs, for example, in tendons, bones and other types of connective tissue.
Squirrels, existing only in a fully coiled form, like keratin and collagen, are an exception among other proteins.
The name “squirrels” comes from the ability of many of them to turn white when heated. The name "proteins" comes from the Greek word for "first", indicating their importance in the body. The higher the level of organization of living beings, the more diverse the composition of proteins.
Proteins are formed from amino acids, which are linked together by covalent bonds. peptide bond: between the carboxyl group of one amino acid and the amino group of another. When two amino acids interact, a dipeptide is formed (from the residues of two amino acids, from the Greek. peptos– cooked). Replacement, exclusion or rearrangement of amino acids in a polypeptide chain causes the emergence of new proteins. For example, when replacing only one amino acid (glutamine with valine), a serious disease occurs - sickle cell anemia, when red blood cells have a different shape and cannot perform their main functions (oxygen transport). When a peptide bond is formed, a water molecule is split off. Depending on the number of amino acid residues, they are distinguished:
– oligopeptides (di-, tri-, tetrapeptides, etc.) – contain up to 20 amino acid residues;
– polypeptides – from 20 to 50 amino acid residues;
– squirrels – over 50, sometimes thousands of amino acid residues
Based on their physicochemical properties, proteins are distinguished between hydrophilic and hydrophobic.
There are four levels of organization of the protein molecule - equivalent spatial structures (configurations, conformation) proteins: primary, secondary, tertiary and quaternary.
Primary the structure of proteins is the simplest. It has the form of a polypeptide chain, where amino acids are linked to each other by a strong peptide bond. Determined by the qualitative and quantitative composition of amino acids and their sequence.
Secondary structure of proteins
Secondary the structure is formed predominantly by hydrogen bonds that were formed between the hydrogen atoms of the NH group of one helix curl and the oxygen atoms of the CO group of the other and are directed along the spiral or between parallel folds of the protein molecule. The protein molecule is partially or entirely twisted into an α-helix or forms a β-sheet structure. For example, keratin proteins form an α-helix. They are part of hooves, horns, hair, feathers, nails, and claws. The proteins that make up silk have a β-sheet. Amino acid radicals (R-groups) remain outside the helix. Hydrogen bonds are much weaker than covalent bonds, but with a significant number of them they form a fairly strong structure.
Functioning in the form of a twisted spiral is characteristic of some fibrillar proteins - myosin, actin, fibrinogen, collagen, etc.
Protein tertiary structure
Tertiary protein structure. This structure is constant and unique for each protein. It is determined by the size, polarity of R-groups, shape and sequence of amino acid residues. The polypeptide helix is twisted and folded in a certain way. The formation of the tertiary structure of a protein leads to the formation of a special configuration of the protein - globules (from Latin globulus - ball). Its formation is determined by different types of non-covalent interactions: hydrophobic, hydrogen, ionic. Disulfide bridges appear between cysteine amino acid residues.
Hydrophobic bonds are weak bonds between non-polar side chains that result from the mutual repulsion of solvent molecules. In this case, the protein twists so that the hydrophobic side chains are immersed deep inside the molecule and protect it from interaction with water, while the hydrophilic side chains are located outside.
Most proteins have a tertiary structure - globulins, albumins, etc.
Quaternary protein structure
Quaternary protein structure. Formed as a result of the combination of individual polypeptide chains. Together they form a functional unit. There are different types of bonds: hydrophobic, hydrogen, electrostatic, ionic.
Electrostatic bonds occur between electronegative and electropositive radicals of amino acid residues.
Some proteins are characterized by a globular arrangement of subunits - this is globular proteins. Globular proteins easily dissolve in water or salt solutions. Over 1000 known enzymes belong to globular proteins. Globular proteins include some hormones, antibodies, and transport proteins. For example, the complex molecule of hemoglobin (red blood cell protein) is a globular protein and consists of four globin macromolecules: two α-chains and two β-chains, each of which is connected to heme, which contains iron.
Other proteins are characterized by association into helical structures - this is fibrillar (from Latin fibrilla - fiber) proteins. Several (3 to 7) α-helices are twisted together, like fibers in a cable. Fibrillar proteins are insoluble in water.
Proteins are divided into simple and complex.
Simple proteins (proteins)
Simple proteins (proteins) consist only of amino acid residues. Simple proteins include globulins, albumins, glutelins, prolamins, protamines, pistons. Albumins (for example, serum albumin) are soluble in water, globulins (for example, antibodies) are insoluble in water, but soluble in aqueous solutions of certain salts (sodium chloride, etc.).
Complex proteins (proteids)
Complex proteins (proteids) include, in addition to amino acid residues, compounds of a different nature, which are called prosthetic group. For example, metalloproteins are proteins containing non-heme iron or linked by metal atoms (most enzymes), nucleoproteins are proteins connected to nucleic acids (chromosomes, etc.), phosphoproteins are proteins that contain phosphoric acid residues (egg proteins yolk, etc.), glycoproteins - proteins combined with carbohydrates (some hormones, antibodies, etc.), chromoproteins - proteins containing pigments (myoglobin, etc.), lipoproteins - proteins containing lipids (included in the composition of membranes).
Regular protein secondary structures
Secondary structures are distinguished by a regular, periodic shape (conformation) of the main chain, with a variety of conformations of side groups.
Secondary structure of RNA
Examples of secondary structures include the stem-loop and pseudoknot.
Secondary structures in mRNA serve to regulate translation. For example, the insertion of the unusual amino acids selenomethionine and pyrrolysine into proteins depends on a stem-loop located in the 3" untranslated region. Pseudoknots serve for programmed changes in the reading frame of genes.
see also
- Quaternary structure
Notes
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See what “Secondary structure of proteins” is in other dictionaries:
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Secondary structure is a way of folding a polypeptide chain into an ordered structure due to the formation of hydrogen bonds between peptide groups of the same chain or adjacent polypeptide chains. According to their configuration, secondary structures are divided into helical (α-helix) and layered-folded (β-structure and cross-β-form).
α-Helix. This is a type of secondary protein structure that looks like a regular helix, formed due to interpeptide hydrogen bonds within one polypeptide chain. The model of the structure of the α-helix (Fig. 2), which takes into account all the properties of the peptide bond, was proposed by Pauling and Corey. Main features of the α-helix:
· helical configuration of the polypeptide chain having helical symmetry;
· formation of hydrogen bonds between the peptide groups of each first and fourth amino acid residue;
Regularity of spiral turns;
· equivalence of all amino acid residues in the α-helix, regardless of the structure of their side radicals;
· side radicals of amino acids do not participate in the formation of the α-helix.
Externally, the α-helix looks like a slightly stretched spiral of an electric stove. The regularity of hydrogen bonds between the first and fourth peptide groups determines the regularity of the turns of the polypeptide chain. The height of one turn, or the pitch of the α-helix, is 0.54 nm; it includes 3.6 amino acid residues, i.e., each amino acid residue moves along the axis (the height of one amino acid residue) by 0.15 nm (0.54:3.6 = 0.15 nm), which allows us to talk about equivalence of all amino acid residues in the α-helix. The regularity period of an α-helix is 5 turns or 18 amino acid residues; the length of one period is 2.7 nm. Rice. 3. Pauling-Corey a-helix model
β-Structure. This is a type of secondary structure that has a slightly curved configuration of the polypeptide chain and is formed by interpeptide hydrogen bonds within individual sections of one polypeptide chain or adjacent polypeptide chains. It is also called a layered-fold structure. There are varieties of β-structures. The limited layered regions formed by one polypeptide chain of a protein are called cross-β form (short β structure). Hydrogen bonds in the cross-β form are formed between the peptide groups of the loops of the polypeptide chain. Another type - the complete β-structure - is characteristic of the entire polypeptide chain, which has an elongated shape and is held by interpeptide hydrogen bonds between adjacent parallel polypeptide chains (Fig. 3). This structure resembles the bellows of an accordion. Moreover, variants of β-structures are possible: they can be formed by parallel chains (the N-terminal ends of the polypeptide chains are directed in the same direction) and antiparallel (the N-terminal ends are directed in different directions). The side radicals of one layer are placed between the side radicals of another layer.
In proteins, transitions from α-structures to β-structures and back are possible due to the rearrangement of hydrogen bonds. Instead of regular interpeptide hydrogen bonds along the chain (thanks to which the polypeptide chain is twisted into a spiral), the helical sections unwind and hydrogen bonds close between the elongated fragments of the polypeptide chains. This transition is found in keratin, the protein of hair. When washing hair with alkaline detergents, the helical structure of β-keratin is easily destroyed and it turns into α-keratin (curly hair straightens).
The destruction of regular secondary structures of proteins (α-helices and β-structures), by analogy with the melting of a crystal, is called the “melting” of polypeptides. In this case, hydrogen bonds are broken, and the polypeptide chains take the form of a random tangle. Consequently, the stability of secondary structures is determined by interpeptide hydrogen bonds. Other types of bonds take almost no part in this, with the exception of disulfide bonds along the polypeptide chain at the locations of cysteine residues. Short peptides are closed into cycles due to disulfide bonds. Many proteins contain both α-helical regions and β-structures. There are almost no natural proteins consisting of 100% α-helix (the exception is paramyosin, a muscle protein that is 96-100% α-helix), while synthetic polypeptides have 100% helix.
Other proteins have varying degrees of coiling. A high frequency of α-helical structures is observed in paramyosin, myoglobin, and hemoglobin. In contrast, in trypsin, a ribonuclease, a significant part of the polypeptide chain is folded into layered β-structures. Proteins of supporting tissues: keratin (protein of hair, wool), collagen (protein of tendons, skin), fibroin (protein of natural silk) have a β-configuration of polypeptide chains. The different degrees of helicity of the polypeptide chains of proteins indicate that, obviously, there are forces that partially disrupt the helicity or “break” the regular folding of the polypeptide chain. The reason for this is a more compact folding of the protein polypeptide chain in a certain volume, i.e., into a tertiary structure.