4 secondary structure of protein. Protein secondary structure and its spatial organization

And proteins are made up of a polypeptide chain, and a protein molecule can consist of one, two or several chains. However, physical, biological and Chemical properties biopolymers are determined not only by the general chemical structure, which may be “meaningless,” but also by the presence of other levels of organization of the protein molecule.

Determined by quantitative and qualitative amino acid composition. Peptide bonds are the basis of the primary structure. This hypothesis was first expressed in 1888 by A. Ya. Danilevsky, and later his assumptions were confirmed by the synthesis of peptides, which was carried out by E. Fischer. The structure of the protein molecule was studied in detail by A. Ya. Danilevsky and E. Fischer. According to this theory, protein molecules consist of large quantity amino acid residues that are connected by peptide bonds. A protein molecule can have one or more polypeptide chains.

When studying the primary structure of proteins, chemical agents and proteolytic enzymes are used. Thus, using the Edman method it is very convenient to identify terminal amino acids.

The secondary structure of a protein demonstrates the spatial configuration of the protein molecule. The following types of secondary structure are distinguished: alpha helical, beta helical, collagen helix. Scientists have found that the alpha helix is most characteristic of the structure of peptides.

The secondary structure of the protein is stabilized with the help of The latter arise between those connected to the electronegative nitrogen atom of one peptide bond, and the carbonyl oxygen atom of the fourth amino acid from it, and they are directed along the helix. Energy calculations show that the right-handed alpha helix, which is present in native proteins, is more efficient in polymerizing these amino acids.

Protein secondary structure: beta-sheet structure

The polypeptide chains in beta-sheets are fully extended. Beta folds are formed by the interaction of two peptide bonds. The indicated structure is characteristic of (keratin, fibroin, etc.). In particular, beta-keratin is characterized by a parallel arrangement of polypeptide chains, which are further stabilized by interchain disulfide bonds. In silk fibroin, adjacent polypeptide chains are antiparallel.

Protein secondary structure: collagen helix

The formation consists of three helical chains of tropocollagen, which has the shape of a rod. The helical chains twist and form a superhelix. The helix is stabilized by hydrogen bonds that arise between the hydrogen of the peptide amino groups of amino acid residues of one chain and the oxygen of the carbonyl group of amino acid residues of the other chain. The presented structure gives collagen high strength and elasticity.

Protein tertiary structure

Most proteins in their native state have a very compact structure, which is determined by the shape, size and polarity of amino acid radicals, as well as the sequence of amino acids.

Hydrophobic and ionic interactions, hydrogen bonds, etc. have a significant influence on the process of formation of the native conformation of a protein or its tertiary structure. Under the influence of these forces, a thermodynamically appropriate conformation of the protein molecule and its stabilization are achieved.

Quaternary structure

This type of molecular structure results from the association of several subunits into a single complex molecule. Each subunit includes primary, secondary and tertiary structures.

The peptide chains of proteins are organized into a secondary structure stabilized by hydrogen bonds. The oxygen atom of each peptide group forms a hydrogen bond with N.H. -group corresponding to the peptide bond. In this case, the following structures are formed: a-helix, b-structure and b-bend.a-Spiral. One of the most thermodynamically favorable structures is the right-handed α-helix. a-helix, representing a stable structure in which each carbonyl group forms a hydrogen bond with the fourth along the chain N.H. - in a group. In an α-helix, there are 3.6 amino acid residues per turn, the pitch of the helix is approximately 0.54 nm, and the distance between residues is 0.15 nm. L -Amino acids can form only right-handed α-helices, with the side radicals located on both sides of the axis and facing outward. In the a-helix, the possibility of forming hydrogen bonds is fully used, so it is not capable, unlike b -structures form hydrogen bonds with other elements of the secondary structure. When an α-helix is formed, the side chains of amino acids can move closer together, forming hydrophobic or hydrophilic compact sites. These sites play a significant role in the formation of the three-dimensional conformation of the protein macromolecule, as they are used for packing α-helices in the spatial structure of the protein.Spiral ball. The content of a-helices in proteins is not the same and is an individual feature of each protein macromolecule. Some proteins, such as myoglobin, have an α-helix as the basis of their structure; others, such as chymotrypsin, do not have α-helical regions. On average, globular proteins have a degree of helicalization of the order of 60-70%. Spiralized sections alternate with chaotic coils, and as a result of denaturation, the helix-coil transitions increase. The helicalization of a polypeptide chain depends on the amino acid residues that form it. Thus, the negatively charged groups of glutamic acid located in close proximity to each other experience strong mutual repulsion, which prevents the formation of the corresponding hydrogen bonds in the α-helix. For the same reason, chain helicalization is hindered due to the repulsion of closely located positively charged chemical groups of lysine or arginine. The large size of amino acid radicals is also the reason why the helicalization of the polypeptide chain is difficult (serine, threonine, leucine). The most frequently interfering factor in the formation of an α-helix is the amino acid proline. In addition, proline does not form an intrachain hydrogen bond due to the absence of a hydrogen atom at the nitrogen atom. Thus, in all cases when proline is found in the polypeptide chain, the α-helical structure is disrupted and a coil or ( b - bend). b-Structure. Unlike the a-helix b -the structure is formed due to cross-chain hydrogen bonds between adjacent sections of the polypeptide chain, since there are no intrachain contacts. If these sections are directed in one direction, then such a structure is called parallel, but if in the opposite direction, then antiparallel. The polypeptide chain in the b-structure is highly elongated and does not have a spiral, but rather a zigzag shape. The distance between adjacent amino acid residues along the axis is 0.35 nm, i.e. three times greater than in an a-helix, the number of residues per turn is 2.In case of parallel arrangement b -hydrogen bond structures are less strong compared to those with antiparallel arrangement of amino acid residues. Unlike the α-helix, which is saturated with hydrogen bonds, each section of the polypeptide chain in b -structure is open to the formation of additional hydrogen bonds. The above applies to both parallel and antiparallel b -structure, however, in the antiparallel structure the connections are more stable. In a segment of the polypeptide chain that forms b -structure, contains from three to seven amino acid residues, and itself b -structure consists of 2-6 chains, although their number can be greater. b -The structure has a folded shape, depending on the corresponding a-carbon atoms. Its surface can be flat and left-handed so that the angle between individual sections of the chain is 20-25 degrees.b-Bending. Globular proteins have a spherical shape largely due to the fact that the polypeptide chain is characterized by the presence of loops, zigzags, hairpins, and the direction of the chain can change even by 180°. In the latter case, a b-bend occurs.This bend is shaped like a hairpin and is stabilized by a single hydrogen bond. The factor preventing its formation may be large side radicals, and therefore the inclusion of the smallest amino acid residue, glycine, is quite often observed. This configuration always appears on the surface of the protein globule, and therefore the B-bend takes part in the interaction with other polypeptide chains.Supersecondary structures. Supersecondary structures of proteins were first postulated and then discovered by L. Pauling and R. Corey. An example is a supercoiled α-helix, in which two α-helices are twisted into a left-handed superhelix. However, more often superhelical structures include both a-helices and b-pleated sheets. Their composition can be presented as follows: (aa), (a b ), (b a) and (b X b ). The last option consists of two parallel folded sheets, between which there is a statistical ball ( b C b ). The relationship between secondary and supersecondary structures has a high degree of variability and depends on the individual characteristics of a particular protein macromolecule.Domains -more complex levels of organization of the secondary structure. They are isolated globular sections connected to each other by short so-called hinge sections of the polypeptide chain. D. Birktoft was one of the first to describe the domain organization of chymotrypsin, noting the presence of two domains in this protein.

Secondary structure is the way a polypeptide chain is arranged into an ordered structure. The secondary structure is determined by the primary structure. Since the primary structure is genetically determined, the formation of a secondary structure can occur when the polypeptide chain leaves the ribosome. The secondary structure is stabilized hydrogen bonds, which are formed between the NH and CO groups of peptide bonds.

Distinguish a-helix, b-structure and disordered conformation (clew).

Structure α-helices was proposed Pauling And Corey(1951). This is a type of protein secondary structure that looks like a regular helix (Fig. 2.2). An α-helix is a rod-shaped structure in which the peptide bonds are located inside the helix and the side chain amino acid radicals are located outside. The a-helix is stabilized by hydrogen bonds, which are parallel to the helix axis and occur between the first and fifth amino acid residues. Thus, in extended helical regions, each amino acid residue takes part in the formation of two hydrogen bonds.

Rice. 2.2. Structure of an α-helix.

There are 3.6 amino acid residues per turn of the helix, the helix pitch is 0.54 nm, and there are 0.15 nm per amino acid residue. The helix angle is 26°. The regularity period of an a-helix is 5 turns or 18 amino acid residues. The most common are right-handed a-helices, i.e. The spiral twists clockwise. The formation of an a-helix is prevented by proline, amino acids with charged and bulky radicals (electrostatic and mechanical obstacles).

Another spiral shape is present in collagen . In the mammalian body, collagen is the quantitatively predominant protein: it makes up 25% of the total protein. Collagen is present in various forms, primarily in connective tissue. It is a left-handed helix with a pitch of 0.96 nm and 3.3 residues per turn, flatter than the α-helix. Unlike the α-helix, the formation of hydrogen bridges is impossible here. Collagen has an unusual amino acid composition: 1/3 is glycine, approximately 10% proline, as well as hydroxyproline and hydroxylysine. The last two amino acids are formed after collagen biosynthesis by post-translational modification. In the structure of collagen, the gly-X-Y triplet is constantly repeated, with position X often occupied by proline, and position Y by hydroxylysine. There is good evidence that collagen is ubiquitously present as a right-handed triple helix twisted from three primary left-handed helices. In a triple helix, every third residue ends up in the center, where, for steric reasons, only glycine fits. The entire collagen molecule is about 300 nm long.

b-Structure(b-folded layer). It is found in globular proteins, as well as in some fibrillar proteins, for example, silk fibroin (Fig. 2.3).

Rice. 2.3. b-Structure

The structure has flat shape. The polypeptide chains are almost completely elongated, rather than tightly twisted, as in an a-helix. The planes of peptide bonds are located in space like uniform folds of a sheet of paper. It is stabilized by hydrogen bonds between the CO and NH groups of peptide bonds of neighboring polypeptide chains. If the polypeptide chains forming the b-structure go in the same direction (i.e. the C- and N-termini coincide) – parallel b-structure; if in the opposite - antiparallel b-structure. The side radicals of one layer are placed between the side radicals of another layer. If one polypeptide chain bends and runs parallel to itself, then this antiparallel b-cross structure. Hydrogen bonds in the b-cross structure are formed between the peptide groups of the loops of the polypeptide chain.

The content of a-helices in proteins studied to date is extremely variable. In some proteins, for example, myoglobin and hemoglobin, the a-helix underlies the structure and accounts for 75%, in lysozyme - 42%, in pepsin only 30%. Other proteins, for example, the digestive enzyme chymotrypsin, are practically devoid of an a-helical structure and a significant part of the polypeptide chain fits into layered b-structures. Supporting tissue proteins collagen (tendon and skin protein), fibroin (natural silk protein) have a b-configuration of polypeptide chains.

It has been proven that the formation of α-helices is facilitated by glu, ala, leu, and β-structures by met, val, ile; in places where the polypeptide chain bends - gly, pro, asn. It is believed that six clustered residues, four of which contribute to the formation of the helix, can be considered as the center of helicalization. From this center there is a growth of helices in both directions to a section - a tetrapeptide, consisting of residues that prevent the formation of these helices. During the formation of the β-structure, the role of primers is performed by three out of five amino acid residues that contribute to the formation of the β-structure.

In most structural proteins, one of the secondary structures predominates, which is determined by their amino acid composition. A structural protein constructed primarily in the form of an α-helix is α-keratin. Animal hair (fur), feathers, quills, claws and hooves are composed primarily of keratin. As a component of intermediate filaments, keratin (cytokeratin) is an essential component of the cytoskeleton. In keratins, most of the peptide chain is folded into a right-handed α-helix. Two peptide chains form a single left super spiral. Supercoiled keratin dimers combine into tetramers, which aggregate to form protofibrils with a diameter of 3 nm. Finally, eight protofibrils form microfibrils with a diameter of 10 nm.

Hair is built from the same fibrils. Thus, in a single wool fiber with a diameter of 20 microns, millions of fibrils are intertwined. Individual keratin chains are cross-linked by numerous disulfide bonds, which gives them additional strength. During perm, the following processes occur: first, disulfide bridges are destroyed by reduction with thiols, and then, to give the hair the required shape, it is dried by heating. At the same time, due to oxidation by air oxygen, new disulfide bridges are formed, which retain the shape of the hairstyle.

Silk is obtained from the cocoons of silkworm caterpillars ( Bombyx mori) and related species. The main protein of silk, fibroin, has the structure of an antiparallel folded layer, and the layers themselves are located parallel to each other, forming numerous layers. Since in folded structures the side chains of amino acid residues are oriented vertically up and down, only compact groups can fit in the spaces between the individual layers. In fact, fibroin consists of 80% glycine, alanine and serine, i.e. three amino acids characterized by minimal side chain sizes. The fibroin molecule contains a typical repeating fragment (gli-ala-gli-ala-gli-ser)n.

Disordered conformation. Regions of a protein molecule that do not belong to helical or folded structures are called disordered.

Suprasecondary structure. Alpha-helical and beta structural regions in proteins can interact with each other and with each other, forming assemblies. The supra-secondary structures found in native proteins are energetically the most preferable. These include a supercoiled α-helix, in which two α-helices are twisted relative to each other, forming a left-handed superhelix (bacteriorhodopsin, hemerythrin); alternating α-helical and β-structural fragments of the polypeptide chain (for example, Rossmann's βαβαβ link, found in the NAD + -binding region of dehydrogenase enzyme molecules); the antiparallel three-stranded β structure (βββ) is called β-zigzag and is found in a number of microbial, protozoan, and vertebrate enzymes.

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.

Notes

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The role of proteins in the body is extremely large. Moreover, a substance can bear such a name only after it acquires a predetermined structure. Until this moment, it is a polypeptide, just an amino acid chain that cannot perform its intended functions. IN general view the spatial structure of proteins (primary, secondary, tertiary and domain) is their three-dimensional structure. Moreover, the most important for the body are secondary, tertiary and domain structures.

Prerequisites for studying protein structure

Among the methods for studying the structure chemical substances X-ray crystallography plays a special role. Through it, you can obtain information about the sequence of atoms in molecular compounds and their spatial organization. Simply put, an X-ray can be taken for a single molecule, which became possible in the 30s of the 20th century.

It was then that researchers discovered that many proteins not only have a linear structure, but can also be located in helices, coils and domains. And as a result of a lot of scientific experiments, it turned out that the secondary structure of a protein is the final form for structural proteins and an intermediate form for enzymes and immunoglobulins. This means that substances that ultimately have a tertiary or quaternary structure, at the stage of their “maturation,” must also go through the stage of spiral formation characteristic of the secondary structure.

Formation of secondary protein structure

As soon as the synthesis of the polypeptide on ribosomes in the rough network of the cell endoplasm is completed, the secondary structure of the protein begins to form. The polypeptide itself is a long molecule that takes up a lot of space and is inconvenient for transport and performing its intended functions. Therefore, in order to reduce its size and give it special properties, a secondary structure is developed. This occurs through the formation of alpha helices and beta sheets. In this way, a protein of secondary structure is obtained, which in the future will either turn into tertiary and quaternary, or will be used in this form.

Secondary structure organization

As numerous studies have shown, the secondary structure of a protein is either an alpha helix, or a beta sheet, or an alternation of regions with these elements. Moreover, the secondary structure is a method of twisting and helical formation of a protein molecule. This is a chaotic process that occurs due to hydrogen bonds that arise between the polar regions of amino acid residues in the polypeptide.

Alpha helix secondary structure

Since only L-amino acids participate in the biosynthesis of polypeptides, the formation of the secondary structure of the protein begins with twisting the helix clockwise (to the right). There are strictly 3.6 amino acid residues per helical turn, and the distance along the helical axis is 0.54 nm. This general properties for the secondary structure of the protein, which do not depend on the type of amino acids involved in the synthesis.

It has been determined that not the entire polypeptide chain is completely helical. Its structure contains linear sections. In particular, the pepsin protein molecule is only 30% helical, lysozyme - 42%, and hemoglobin - 75%. This means that the secondary structure of the protein is not strictly a helix, but a combination of its sections with linear or layered ones.

Beta layer secondary structure

The second type of structural organization of a substance is a beta layer, which is two or more strands of a polypeptide connected by a hydrogen bond. The latter occurs between free CO NH2 groups. In this way, mainly structural (muscle) proteins are connected.

The structure of proteins of this type is as follows: one strand of the polypeptide with the designation of the terminal sections A-B is parallel to the other. The only caveat is that the second molecule is located antiparallel and is designated as BA. This forms a beta layer, which can consist of any number of polypeptide chains connected by multiple hydrogen bonds.

Hydrogen bond

The secondary structure of a protein is a bond based on multiple polar interactions of atoms with different electronegativity indices. Four elements have the greatest ability to form such a bond: fluorine, oxygen, nitrogen and hydrogen. Proteins contain everything except fluoride. Therefore, a hydrogen bond can and does form, making it possible to connect polypeptide chains into beta layers and alpha helices.

It is easiest to explain the occurrence of a hydrogen bond using the example of water, which is a dipole. Oxygen carries a strong negative charge, and due to its high O-H polarization hydrogen bonds are considered positive. In this state, molecules are present in a certain environment. Moreover, many of them touch and collide. Then oxygen from the first water molecule attracts hydrogen from the other. And so on down the chain.

Similar processes occur in proteins: the electronegative oxygen of a peptide bond attracts hydrogen from any part of another amino acid residue, forming a hydrogen bond. This is a weak polar conjugation, which requires about 6.3 kJ of energy to break.

By comparison, the weakest covalent bond in proteins requires 84 kJ of energy to break. The strongest covalent bond will require 8400 kJ. However, the number of hydrogen bonds in a protein molecule is so huge that their total energy allows the molecule to exist in aggressive conditions and maintain its spatial structure. This is why proteins exist. The structure of this type of protein provides the strength needed for the functioning of muscles, bones and ligaments. The importance of the secondary structure of proteins for the body is so enormous.