Composition and structure of proteins. Higher levels of protein organization. The monomers of DNA molecules are

Structure, properties and biological functions of proteins.

Proteins are integral components of any living cell that provide and support its vital activity. Protein molecules are biopolymers built primarily from amino acids. In addition to amino acids, other organic and inorganic components can be included in the composition of protein molecules. Proteins contain 50-55% carbon, 20-24% oxygen, 7% hydrogen, 0.5-3% sulfur; some proteins may also contain phosphorus and various metals.

The huge structural diversity of proteins and a wide range of changes in their physicochemical properties allow these biopolymers to perform diverse and vital functions in a living organism. Several thousand different proteins function simultaneously in each plant cell. All biochemical reactions in the cell occur with the participation of catalytic proteins - enzymes. The structural basis of the biological membranes of the cytoplasm and intracellular organelles is also built with the participation of proteins. The protective function is performed by protein antibodies and stress proteins formed under the influence of stress factors. An important role in plant cells is played by regulatory and transport proteins that can reversibly change their conformation and thus actively participate in maintaining the vital activity of the plant as a self-regulating system.

Reserve proteins are deposited in seeds and other plant organs, which largely determine the nutritional, fodder and technological value of plant products. A lot of proteins accumulate in the grain of leguminous crops - 20-30%, in soybean and lupine - 30-40%, in oilseeds - 15-30%. The content of proteins in other plant products is, %: grains of cereal plants - 9-18; corn and rice - 6-10; potato tubers - 1.5-2; root crops - 1-1.5; vegetables, fruits and berries - 0.5-2; cauliflower - 2-3; Brussels sprouts and garlic -6-8; vegetative mass of bluegrass grasses - 5-15, legume grasses - 15-25 (the last two indicators are given per dry weight).

The first protein preparation was isolated from wheat flour in 1728 by J.B. Beccari and named gluten. In 1809-10. the first information about the elemental composition appeared, and in 1836 the first empirical formula of proteins was proposed. In the future, quite actively, many researchers studied the breakdown products of protein substances and more and more information appeared that the main products of the hydrolytic decomposition of proteins are amino acids. By 1899, 13 amino acids were already known, most of which were identified as products of protein hydrolysis.

A fundamental contribution to the development of the theory of the structure of proteins was made by the work of E. Fisher, who in 1901 suggested and then experimentally substantiated the position that protein molecules are built from amino acids, the residues of which are connected by peptide bonds. The polymers formed in this way are usually called polypeptides, and the doctrine of the construction of protein molecules from amino acids connected by peptide bonds is polypeptide theory of protein structure.

In the formation of a peptide bond, α-amino acids are involved, which interact with their amine and carboxyl groups, and water molecules are released. In diaminomonocarboxylic acids, only an amino group located in the α-position can form a peptide bond, and in monoaminodicarboxylic acids, a carboxyl group having an amino group in the α-position can form a peptide bond. Hydrocarbon radicals of amino acid residues connected by peptide bonds remain in the form of side radicals. So, for example, a tripeptide is formed from alanine, aspartic acid and lysine:

The name of the peptide is composed of the names of the amino acids that form it, while the amino acid having a free carboxyl group is written at the end of the formulation, while the other amino acids have the ending changed to "il" and they are listed in the name of the peptide in the order in which they are in structural formula of the resulting compound. Accordingly, the above tripeptide is named alanilasparagillisin.

X-ray diffraction analysis showed that the atomic groups of the peptide bond are located in the same plane, forming predominantly trance-configuration about the C-N bond, which largely has the character of a double bond, and rotation around this bond is highly limited.

In general, the spatial construction of a polypeptide chain can be represented as a sequence of flat structures formed by peptide bond elements that are connected through α-carbon atoms of amino acid radicals. Since the bonds at α-carbon atoms are not double, rotation of groups located in the plane of the peptide bond is possible around them.

If we change the order of the amino acids in the peptide, we will get several isomers. Most often, protein polypeptides can include 100-400 amino acid residues, which, when connected by peptide bonds in a certain order, can give a huge number of isomeric molecules capable of performing various biological functions. IN general view The structure of a polypeptide can be expressed by the following formula:

In this formula, amino acid residues are connected by -CO-NH- bonds, which are called peptide, and R 1 , R 2 , R 3 ... Rn - radicals of amino acid residues containing various groups of atoms and forming side branches in the polypeptide molecule.

At opposite ends of the polypeptide chain, there are free amine and free carboxyl groups, which determine the orientation of the polypeptide. The amino acid at the end of the polypeptide chain, which has a free amino group in the α-position, is called the N-terminal amino acid, and the amino acid at the opposite end of the polypeptide, which has a free carboxyl group not used to form a peptide bond, is called the C-terminal amino acid. The determination of the N- and C-terminal amino acids is important for elucidating the structure of a protein molecule, as it allows one to determine the number of polypeptide chains in it.

Most of the known proteins contain more than one polypeptide chain in a molecule and this differs significantly from conventional peptides that have one polypeptide chain and a lower molecular weight. However, it is rather difficult to draw a clear boundary between peptides and proteins; both of them have a well-defined spatial structure and perform their biochemical function. The main criteria should be considered the degree of polymerization of a molecule, which provides it with the necessary colloidal, osmotic, buffer and other properties characteristic of proteins, as well as the ability to form a certain spatial structure. The lowest degree of polymerization of known proteins is at least 50 amino acid residues per molecule. At the same time, some proteins are known, the molecules of which have more than a thousand amino acid residues.

Peptides in various organisms are very often synthesized using the same mechanisms as proteins, and are important metabolic intermediates, many of them perform regulatory functions and are physiologically active compounds. However, peptides are known, in the synthesis of which amino acids that are not part of proteins take part, they are able to form cyclic structures. These peptides include the antibiotics gramicidin, cyclosporine, thyrocidin, and toxin pallidum. Peptides that perform regulatory functions include many human and animal hormones (oxytocin, vasopressin, adrenocorticotropic hormone, and some others).

Of the plant peptides, glutathione is the most well studied, the structure of which was elucidated in 1945 by F. Hopkins. The glutathione molecule includes the residues of three amino acids - glutamic acid, cysteine ​​and glycine. Glycine and cysteine ​​are connected by a peptide bond, and cysteine ​​and glutamic acid are connected by a pseudopeptide (or isopeptide) bond, which is formed by the interaction of the amino group of cysteine ​​with the carboxyl group of glutamic acid, which does not have an amino group in the α-position and is usually found in protein polypeptides. lateral radical.

H 2 N-CH-CH 2 -CH 2 -CO-NH-CH-CO-NH-CH 2 -COOH

glutathione

The high biological activity of glutathione is due to its ability to participate in reduction reactions, since under the action of the enzyme it can easily remove hydrogen from the sulfhydryl group (-SH) and go into the reduced form, forming dimers linked by disulfide (-S-S-) bonds . Schematically, the formation of oxidized glutathione dimers can be represented as follows:

R-SH + HS-R ¾¾® R-S-S-R + enzyme - H 2

Glutathione is found in all plant cells and affects the activity of many enzymes that catalyze the transformation of proteins.

Given the high biological activity of many peptides, technologies for their chemical synthesis are being developed in order to obtain artificial hormones, antibiotics, and various medical preparations. As experiments show, by chemical synthesis it is possible to obtain polypeptide chains containing up to 100 amino acid residues. Particularly significant progress has been achieved as a result of a combination of chemical and enzymatic syntheses. For example, peptide fragments of the desired composition are isolated from natural polypeptides by partial hydrolysis, and then they are combined using chemical reactions or enzymatic synthesis, thus obtaining biologically active peptide preparations.

After the polypeptide theory of the structure of proteins was formulated and experimentally confirmed, the next step was to determine the structural formulas of proteins, showing the sequence of connecting amino acid residues in protein molecules. For the first time this was done by F. Senger in 1954, who applied new approaches to the chemical identification of terminal amino acids in various peptides, which can be obtained by partial hydrolysis of the polypeptides of the studied protein.

Comparison of the amino acid sequences of overlapping fragments of the polypeptide chains of the pancreatic hormone insulin allowed him to determine with a sufficiently high accuracy the sequence of the connection of amino acid residues in the molecule of this protein. As it turned out, the insulin molecule consists of two polypeptide chains, one of which contains 30 amino acid residues, the other - 21. Polypeptide chains in two positions are connected by disulfide bonds, which are formed by the interaction of sulfhydryl groups (-SH) of cysteine ​​radicals exactly the same mechanism as that of glutathione dimers. The position of these cysteine ​​residues in the insulin polypeptide chains is shown in Figure 5.

It should be taken into account that the numbering of amino acid residues in polypeptides is usually calculated in the direction from the N-terminal amino acid to the C-terminal one. In the short chain of insulin, another disulfide bond is formed between the cysteine ​​residues in the 6th and 11th positions. In a long chain, the N-terminal amino acid is phenylalanine, the C-terminal amino acid is alanine; in the short chain, the N-terminal amino acid is glycine, the C-terminal is asparagine. Thus, using the example of insulin, we see that a protein molecule can be built from more than one polypeptide and different polypeptide chains in a protein molecule can be connected by disulfide bonds due to cysteine ​​residues.

Following insulin, the amino acid sequences of various peptides and proteins were deciphered: oxytocin, vasopressin, RNA polymerase, pepsin, trypsin, lysozyme, cytochromes, hemoglobin, papain, and many other polyamino acid compounds. Already by 1975, there were 600 proteins with known amino acid sequences, by 1985 - more than 2500. At present, work on the analysis of amino acid sequences in proteins is almost completely automated, and the number of such proteins already significantly exceeds 20 thousand.

PRIMARY STRUCTURE OF PROTEINS. The sequence of amino acids in the polypeptide chains of a protein molecule is usually called primary structure of a protein. It is determined by the nucleotide sequence of a particular section of DNA that encodes a given polypeptide and is called a gene.

Substitution of even one amino acid in the structure of a protein can significantly change its function. Therefore, polypeptides can be considered as "fingerprints" of the genes encoding them and can be used to recognize genotypes, as well as to establish a genetic relationship between them. For example, in the short polypeptide chain of human insulin, positions 8, 9, and 10 contain the amino acid sequence Thr-Ser-Ile, in sheep insulin - Ala-Gly-Val, in cow insulin - Ala-Ser-Val, in dog insulin - Thr-Ser-Ile, that is, the same amino acid sequence as in humans, which indicates a smaller phylogenetic difference between these organisms.

In other studies related to the study of abnormal forms of hemoglobin, it was found that in many cases, the replacement of at least one amino acid in one of its polypeptide chains with another causes a violation physiological function of this protein, which leads to serious clinical consequences for the human body.

SECONDARY STRUCTURE OF PROTEINS. A polypeptide chain, including a sequence of amino acid residues characteristic of a given protein, forms a well-defined spatial structure, which is usually called conformation protein molecule.

The spatial structure of each individual section of the polypeptide chain is the secondary structure of the protein.

The formation of the secondary structure of protein molecules depends on the physicochemical parameters of amino acid residues and their sequence in the polypeptide chain. As already noted, the atomic groups of the peptide bond are located in the same plane, and each such planar structure is connected to the neighboring one through the α-carbon atoms of the amino acid radicals by covalent bonds, around which the planar structures of the peptide bonds can rotate. The angle of rotation for each of these bonds for each amino acid residue is quite definite, depending on the structure of the amino acid radical. If amino acid residues with similar rotation angles are grouped at a specific site of the polypeptide molecule along the indicated bonds, then the same type of secondary structure is formed.

In the stabilization of the secondary structure of the polypeptide, an important role is played by hydrogen bonds that occur between groups of peptide

bonds according to the following scheme: ═N-H.....O=C═

One of the varieties of the secondary structure of a protein is the α-helix, which was established in 1951 by L. Pauling and R. Corey by X-ray diffraction analysis. During the formation of the α-helix, a helical twisting of the polypeptide chain occurs, which is stabilized due to the formation of hydrogen bonds that occur in a certain order between the NH- and CO-groups of peptide bonds located in adjacent turns of the helix (Fig. 6). The NH group of the peptide bond of each amino acid residue is hydrogen bonded to the CO group of the peptide bond of another amino acid residue removed in the polypeptide chain from the first by 4 amino acid residues, counting backwards in the direction of the chain.

Hydrogen bonds are oriented along the axis of the helix, with oxygen atoms connected by a double bond to carbon atoms spiraling forward from carbon atoms, and hydrogen atoms connected to nitrogen atoms spiraling back from nitrogen atoms. Side radicals of amino acids are also oriented along the axis of the helix in the direction opposite to the direction of the polypeptide chain (the direction of the polypeptide chain is considered to be from the N-terminus to the C-terminus). No cavity is formed inside the α-helix, since the entire space is completely occupied by groupings of peptide bonds and α-carbon atoms. On the surface of the α-helix are side radicals of amino acids, which can interact both with each other and with environmental substances.

Most of the known proteins form an α-helix, in which the helical twisting of the polypeptide chain occurs in a clockwise direction. Calculations show that there are 3.6 amino acid residues per turn of the helix, and the course of the helix when the chain is extended by one amino acid residue is 0.15 nm. The diameter of the conditional cylindrical surface, on which the α-carbon atoms of amino acid radicals are located, is 1.01 nm ( rice. 7).

The spiral configuration of the secondary structure is the basis for fibrillar proteins, such as the protein of hair, wool, feathers, horns - keratin. However, the length of the helical sections of globular proteins is small and usually amounts to several turns (3-4 turns of the α-helix). Spiralization of the polypeptide chain occurs when the residues of α-alanine, leucine, phenylalanine, tyrosine, tryptophan, cysteine, methionine, histidine, asparagine, glutamine, and valine are grouped in a certain section of it.

Quite often in the structure of globular proteins there are bends and loops that turn the peptide chain at a certain angle. The most characteristic form of such a structure is the so-called b-bend, which rotates the peptide chain by 180˚. Typically, the b-fold includes 3-4 amino acid residues, the key of which is the glycine amino acid residue.

Proline amino acid residues cause a break in the resulting α-helix with a deviation from the axis of the helix by an angle of 20˚-30˚. This is explained by the fact that the nitrogen of proline, which is part of the structure of peptide groups, is not bound to the hydrogen atom and therefore does not form a hydrogen bond.

There are amino acids that, based on the structure of the radical, form another type of secondary structure (serine, isoleucine, threonine, lysine, arginine, aspartic and glutamic acids), it is called the b-structure. In the b-structure, hydrogen bonds are formed between CO- and NH-groups located in neighboring segments of the polypeptide chain, which have a parallel or opposite orientation; in accordance with this, b-structures are also called parallel or antiparallel.

In two neighboring chains forming the b-structure, half of the CO- and NH-groups participate in the formation of hydrogen bonds, which is associated with the alternation spatial arrangement amino acid radicals. Side radicals of neighboring amino acid residues are located in trance-position in relation to the peptide group, therefore, every second peptide group is involved in the formation of hydrogen bonds with the neighboring polypeptide chain. The remaining free CO and NH groups can form hydrogen bonds with similar groups of another chain on the opposite side, and it with the next peptide chain, etc. Thus, several peptide chains (2-10 ) up to 8 amino acid residues along each of the chains, and some even more.

The radicals of amino acid residues departing in opposite directions from each polypeptide chain form surfaces having a folded structure. The folds of these surfaces are determined

bond angles of α-carbon atoms of amino acid residues (Fig. 8). Very often, the surface of the b-structure twists at a certain angle, forming a super-secondary structure.

The secondary structure of polypeptides in the form of α-helix and b-structures refers to structures that periodically repeat their configurations in space, which is why they are called regular structures. However, in almost every protein molecule there are regions with a well-defined spatial configuration, but it is not repeated in other regions. Such types of protein secondary structure are called irregular structures.

Each protein, depending on the primary structure that determines the set and sequence of amino acid residues in its polypeptide chains, has well-defined groups of amino acids in separate parts of the molecule, which, depending on their physicochemical parameters, are capable of forming one or another type of secondary structure. Therefore, in a given protein, in accordance with the sequence of amino acids, a completely specific type of secondary structure is realized at each site.

Very few proteins are known that have the same secondary structure in all parts of the molecule. These proteins include keratin (structural protein of wool, feathers, horns) and collagen (tendon protein), which have an α-helix molecule configuration. Another example is silk proteins (fibroin) and canavallia seeds (concanavalin A), which predominantly form b-structures. The majority of proteins form a mixed type of secondary structure, including both α-helix, and b-structures, and irregular structures in specific regions of the molecule. For example, in the protein myoglobin, 79% of its constituent amino acid residues form a secondary structure in the form of an α-helix, 16% are in areas with an irregular structure, and 5% are involved in the formation of b-bends. In the plant protein papain, 28% of the secondary structure is represented by α-helices, 14% by b-structures, 17% by b-bends, and 41% by irregular structures.

Section of antiparallel b-structure

Plot of parallel b-structure

(arrows show directions of polypeptide chains)

Figure 9 shows a diagram of the possible formation of secondary structures in one of the regions of the polypeptide chain of the enzymatic protein glyceraldehyde phosphate dehydrogenase. As can be seen from the diagram, amino acid sequences 9 ® 22, 33 ® 45, 78 ® 81, 85 ® 88, 95 ® 98, 100 ® 112, 129 ® 133 form a helical secondary structure, while amino acid sequences 1®7, 26 ®32, 56®75, 90®94, 115®120, 126®128, 142® 147 form b-structures, other amino acid residues are involved in the formation of bends and irregular structures.

TERTIARY STRUCTURE OF PROTEINS. The arrangement in space of all atomic groups of a polypeptide chain is commonly called the tertiary structure of a protein molecule. For the first time, the concept of the tertiary structure of proteins was formulated in 1958 by D. Kendrew on the basis of X-ray diffraction analysis of the spatial configuration of the myoglobin protein, as a result of which it was possible to elucidate the three-dimensional structure of this protein.

In the course of further research, it was found that non-covalent interactions between the radicals of amino acid residues located on the surface of secondary structures, as well as disulfide bonds resulting from the interaction of sulfhydryl groups, play an important role in the construction of the tertiary structure of a protein.

(-SH) cysteine ​​amino acid residues. When forming a tertiary structure, three types of non-covalent interactions are realized: the formation of hydrogen bonds, electrostatic and hydrophobic interactions.

Hydrogen bonds link functional groups together.

side chains of amino acid residues:

R-OH....O=C-R R-O....H-N-R R-C=O....H-N-R

OH H H NH 2 H

The saturation of a protein molecule with hydrogen bonds is very high - at least 90% of their possible formation. Important for the stabilization of the tertiary structure of proteins are also hydrogen bonds, which form groups of polypeptides with water molecules that form the liquid phase of the protein solution.

Electrostatic interaction forces arise between the charged groups of amino acid residues:

R-COO‾...H 3 N⁺-R

The formation of a compact spatial structure is largely facilitated by hydrophobic interactions between non-polar groups of side radicals of amino acids that make up the polypeptide chain. As a result of hydrophobic interactions, water molecules are repelled from the surface of hydrophobic groups and the latter approach each other, as a result of which the polypeptide chain is coiled in the form of a globule. In this case, most of the hydrophobic radicals are inside the globule and thus protected from contact with water molecules, while hydrophilic radicals, on the contrary, are on the surface of the protein globule, they form hydrogen bonds with water molecules and stabilize the spatial structure of the protein.

Amino acids with hydrophobic radicals include glycine, leucine, isoleucine, valine, alanine, phenylalanine, cysteine, methionine. Hydrophilic radicals have amino acid residues of threonine, serine, tryptophan, tyrosine, asparagine and aspartic acid, glutamine and glutamic acid, lysine, histidine.

The spatial structure of the polypeptide formed as a result of hydrophobic interactions has a rather dense packing, as a result of which it is very often called the hydrophobic core of the protein molecule. Around the nucleus, a shell of hydrophilic amino acid residues is formed, which can also include hydrophobic radicals that form hydrophobic outlets on the surface of the protein globule. Due to the formation of such structures, the specificity of the interaction of a protein molecule with environmental substances is ensured. The composition of the hydrophilic shell surrounding the hydrophobic core also includes water molecules linked by hydrogen bonds to the polar groups of the protein molecule.

In many proteins, an important factor in the stabilization of the tertiary structure is disulfide bonds, which are formed during the interaction of cysteine ​​residues according to the same mechanism as in the formation of glutathione dimers. However, the formation of disulfide bonds is not a prerequisite for the stability of the tertiary structure of a protein, since quite a few proteins are known that form a stable spatial structure only due to non-covalent interactions.

During the formation of the tertiary structure of a protein, not one, but two or more hydrophobic nuclei may arise, including rather large segments of the same polypeptide chain. Between these nuclei, depressions and cavities are formed, which are essential for the functioning of the protein.

The tertiary structure of polypeptides is made up of elements of the secondary structure. So, in the composition of a number of proteins, the tertiary structure is represented only by α-helices, which are located in space in the form of parallel sections. At the same time, proteins are known that are built mainly from b-structures folded in space at a certain angle. However, in many proteins, the spatial configuration of the molecule is formed in the form of mixed structures, including certain combinations of α-helices and b-structures. In this case, quite often the inner part of the polypeptide molecule is represented by b-structures, which are surrounded by α-helices on the surface.

Figure 10 shows the tertiary structure of the enzyme proteins triose phosphate isomerase and lysozyme. In the triose phosphate isomerase molecule, b-layers are presented in the central part, which are surrounded by α-helices. In lysozyme, part of the tertiary structure (in the upper part of the figure) is formed in the form of b-structures, and the other part (in the lower part of the figure) is represented by α-helices.

For naturally occurring proteins, a strict correspondence has been established between the primary and tertiary structures of polypeptides. The sequence of amino acid residues in the polypeptide chain determines its spatial configuration. This principle is confirmed in experiments on the construction of amino acid sequences of polypeptides capable of forming a spatial structure of a given type.

QUATERNARY STRUCTURE OF PROTEINS. Many proteins are complex molecules formed by the non-covalent interaction of two or more polypeptides, each of which has its own tertiary structure. Such proteins are usually called oligomers, and the polypeptides that form them are called polypeptide subunits of the protein. The method of joint packaging and placement in space of polypeptide subunits of oligomeric proteins is called the quaternary structure of the protein.

For the first time, the quaternary structure of a protein was established by X-ray diffraction analysis when studying the spatial configuration.

tions of hemoglobin molecules (Peruts M., 1959). In these studies, it was determined that the hemoglobin molecule consists of four subunits: two α-polypeptide chains of 141 amino acid residues each and two b-chains of 146 amino acid residues each. Hemoglobin subunits are placed in space symmetrically, occupying the tops of the tetrahedral structure (Fig. 11).

In the hemoglobin molecule, there is a stronger interaction between different subunits and a relatively weaker relationship between similar subunits, as a result of which quite stable dimers of different subunits (ab) are formed, from which the structure of a tetrameric molecule is already formed due to weaker interactions. This order of interaction of hemoglobin subunits leads to the formation of completely the same type of a 2 b molecules, while other combinations of subunits are unstable.

If the nature of the interaction between all subunits of an oligomeric protein is the same, then molecules with a different set of polypeptides may arise. For example, in a tetramer whose molecules are formed from two types of subunits A and B, oligomers of the following composition are formed: A 4 , A 3 B, A 2 B 2 , AB 3 , AB 4 . All of them are structurally similar proteins that perform the same function in the body. Molecules of an oligomeric protein built from different polypeptide subunits and performing the same biological function are commonly called multiple molecular forms, or isoforms, of a given protein.

The connection of polypeptide subunits into oligomeric molecules occurs due to non-covalent interactions. An important role is played by hydrogen bonds, which are formed between overlapping elements of b-structures that make up protein subunits, as well as as a result of the interaction of amino acid radicals having groups:

COOH, -OH, \u003d NH, -NH 2.

When considering the tertiary structure of proteins, it was shown that the surface shell surrounding the hydrophobic core also contains many hydrophobic amino acid radicals, which, as a result of the approach of the surfaces of the tertiary structures of the two subunits, enter into hydrophobic interactions, which makes a significant contribution to the formation of the quaternary structure proteins. Moreover, in some proteins, hydrophobic interactions are the main factors in the formation of their quaternary structure. For example, a number of regulatory proteins have characteristic sequences of amino acid residues in which the hydrophobic leucine radical occurs with a certain frequency (in the same position every 2 turns of the α-helix). As a result of the interaction of two subunits, the hydrophobic combination of their helical configurations occurs and the formation of a double helix connecting these subunits into one molecule occurs. This type of hydrophobic interaction between protein polypeptides is called "leucine loops".

Important factors in the formation of the quaternary structure of proteins

are electrostatic interactions between charged groups of neighboring subunits, represented by radicals of dicarboxylic (aspartic and glutamic acids) and diaminomonocarboxylic (lysine, arginine) acids. Thus, as a result of the combined action of all these factors, a sufficiently stable spatial structure of the oligomeric protein molecule is formed.

Most often, the quaternary structure of proteins is represented by dimers, trimers, tetramers and hexamers, although proteins containing 8, 12, 24 or more subunits in a molecule are known. The biological role of the quaternary structure of proteins is that by combining relatively small structural elements, it is possible to form more complex structures that provide the protein with greater lability, the ability to perform a specific biological function, and the possibility of combining several functionally active centers in one spatial structure.

CONFORMATION OF PROTEIN MOLECULES

In the cells of a living organism at a certain temperature, pH and concentration of the physiological environment, protein molecules form the most thermodynamically stable spatial structure under these conditions, which ensures that the protein performs its biological function. This spatial structure is called native conformation-tion protein molecule.

When physiological conditions change, protein molecules can reversibly change their native conformation, and their biological activity also changes. Reversible changes in the native conformation of proteins (restructuring of their spatial structure) are important for the regulation of enzymatic activity, the transport of ions and metabolites through membranes, and the regulation of cell membrane permeability.

As mentioned earlier, the formation of the spatial structure of proteins is determined by the genetically determined sequence of the connection of amino acid residues in polypeptide chains. Therefore, the native conformation of a protein depends on its primary structure. But at the same time, the formation of a native protein conformation requires the entire set of factors of the internal physiological environment of a given cell (a certain pH, the presence of certain ions and other cofactors).

The construction of the spatial structure of a protein molecule occurs during its synthesis as the polypeptide chain is elongated, which probably predetermines the sequence of interaction of groups during the formation of the secondary and tertiary structure of the synthesized polypeptide. Special experiments have shown that the protein molecule contains amino acid residues that are active initiators of non-covalent interactions that facilitate the formation of intermediate structures during the transition of the protein to the native conformation.

Specialized proteins are involved in the correct construction of the spatial structure of protein molecules - chaperones. Especially many of these proteins are synthesized under stressful conditions. They form complexes with polypeptide chains, preventing their aggregation during the formation of secondary and tertiary structures. One of the regions of the chaperone protein non-covalently binds to the unfolded polypeptide chain, and the other attaches ATP. Upon hydrolysis of ATP, the chaperone passes into another conformational state and its complex with the polypeptide that forms the spatial structure disintegrates.

Other proteins are also known - catalysts for the formation of the spatial structure of polypeptides. So, in the cells of higher organisms, an enzyme was found protein disulfide isomerase, catalyzing the correct formation of disulfide bonds during the formation of the tertiary structure of polypeptides. It is a dimeric protein containing cysteine ​​amino acid residues in the active center.

In the construction of the native conformation of a protein, the rate-limiting step may be the transition of groups of peptide bonds from cis- V trance-configuration. Passes especially slowly cis-trance-isomerization of peptide bond groups formed by the imino group of proline. To accelerate such transformations in the cells of organisms, there is a special enzyme shed-cis-trance-isomerase.

The characteristic features of the spatial configuration of homologous protein molecules that perform the same function in different organisms are determined by the presence of the same amino acid residues in key positions that strongly affect the conformation of the molecule, while different amino acid residues can be located in other positions. But they have a weaker effect on the conformation of the molecule.

Very characteristic structure have membrane proteins, which, as a rule, contain transmembrane fragments in the form of α-helices; extramembrane polypeptides depart from them, providing communication with the environment physiological environment. Transmembrane polypeptide fragments can also be formed in the form of b-structures. The main functions of membrane proteins are the transport of molecules and ions through the membrane, intercellular interactions, the formation of ion channels, the transmission of external signals to the cell, etc.

Under the influence of strong factors (high temperature, extreme pH values, the presence of heavy metal cations, the use of organic solvents and detergents), the system of hydrogen bonds, electrostatic and hydrophobic interactions in protein molecules can be disordered, which causes a significant change in their secondary and tertiary structure, leading to the loss of the native conformation. At the same time, the protein can no longer perform its biological function. An irreversible change in the spatial structure of protein molecules, which is accompanied by the loss of their native properties, is called denaturation proteins.

A good example of denaturation is the thermal denaturation of proteins. With an increase in temperature, the amplitude of atomic vibrations increases, which leads to the breaking of hydrogen bonds and the weakening of electrostatic interactions in protein molecules, resulting in irreversible coagulation and precipitation of proteins from solution. Most proteins undergo denaturation at 70–80˚C. However, some proteins are characterized by a rather high thermal stability. For example, the enzymes of thermophilic bacteria retain their catalytic activity at a temperature of 80˚C.

Substances are known that stabilize the native structure of protein molecules, and their presence in solution increases the temperature of protein denaturation. These substances include water-soluble salts containing calcium cations (Ca 2+).

Protein denaturation can occur in highly acidic or strongly alkaline environments. In a strongly acidic medium, the dissociation of carboxyl groups of amino acid radicals of dicarboxylic acids is almost completely suppressed, and the charge of a protein molecule is determined by the positive charges of diaminomonocarboxylic acid radicals, the mutual repulsion of which causes the breaking of hydrogen bonds and the weakening of electrostatic interactions that stabilize the tertiary structure of the molecule. As a result, proteins lose their native conformation and undergo coagulation (precipitation).

In a strongly alkaline environment (pH>11), the positive charge of the radicals of diaminomonocarboxylic acids is lost and the charge of the protein molecule is determined by the negative charges of the carboxyl groups of dicarboxylic amino acids, the mutual repulsion of which causes the rupture of hydrogen bonds and the weakening of electrostatic interactions in the molecule, as a result of which a significant change in the spatial structure and denaturation of the protein.

Heavy metal cations, trichloroacetic, perchloric, tungstic and some other acids, which form insoluble salts with proteins, have a strong denaturing effect.

Some organic solvents (alcohol, acetone, formamide) are able to interact with hydrophobic radicals of amino acid residues of proteins and with water molecules, causing weakening of hydrophobic interactions and breaking of hydrogen bonds that stabilize the tertiary structure of polypeptides, resulting in denaturation of protein molecules.

It has been established that the denaturation of proteins in a solution or in a wet state occurs much easier and faster than in a dried state, and this is used in the development of technologies for drying biological material and various plant products (grains, pasta, vegetables and fruits). Information about protein denaturation is also taken into account when baking bread and confectionery, preparing canned food and other food products.

Squirrels- natural polypeptides with a huge molecular weight. They are part of all living organisms and perform various biological functions.

The structure of the protein.

Proteins have 4 levels of structure:

• primary structure of a protein- linear sequence of amino acids in the polypeptide chain, folded in space:

• protein secondary structure- conformation of the polypeptide chain, because twisting in space due to hydrogen bonds between NH And SO groups. There are 2 installation methods: α -spiral and β - structure.

• protein tertiary structure is a three-dimensional representation of a swirling α - spiral or β -structures in space:

This structure is formed by disulfide bridges -S-S- between cysteine ​​residues. Oppositely charged ions participate in the formation of such a structure.

• quaternary protein structure formed by the interaction between different polypeptide chains:

Protein synthesis.

The synthesis is based on the solid-phase method, in which the first amino acid is fixed on a polymer carrier, and new amino acids are sequentially sutured to it. The polymer is then separated from the polypeptide chain.

The physical properties of the protein.

The physical properties of the protein are determined by the structure, so the proteins are divided into globular(soluble in water) and fibrillar(insoluble in water).

Chemical properties of proteins.

1. Protein denaturation(destruction of the secondary and tertiary structure with the preservation of the primary). An example of denaturation is the curdling of egg whites when eggs are boiled.

2. Protein hydrolysis- irreversible destruction of the primary structure in an acidic or alkaline solution with the formation of amino acids. So you can install quantitative composition proteins.

3. Qualitative reactions:

Biuret reaction- interaction of the peptide bond and salts of copper (II) in an alkaline solution. At the end of the reaction, the solution turns purple.

xantoprotein reaction- when reacted with nitric acid, a yellow color is observed.

The biological significance of protein.

1. Proteins are a building material; muscles, bones, and tissues are built from it.

2. Proteins - receptors. They transmit and receive signals from neighboring cells from the environment.

3. Proteins play an important role in the body's immune system.

4. Proteins perform transport functions and carry molecules or ions to the place of synthesis or accumulation. (Hemoglobin carries oxygen to tissues.)

5. Proteins - catalysts - enzymes. These are very powerful selective catalysts that speed up reactions millions of times.

There are a number of amino acids that cannot be synthesized in the body - irreplaceable, they are obtained only with food: tizine, phenylalanine, methinine, valine, leucine, tryptophan, isoleucine, threonine.

These are biopolymers whose monomers are amino acids.

Amino acids are low molecular weight organic compounds containing carboxyl (-COOH) and amine (-NH 2) groups that are bonded to the same carbon atom. A side chain is attached to the carbon atom - a radical that gives each amino acid certain properties.

Most amino acids have one carboxyl group and one amino group; these amino acids are called neutral. There are, however, also basic amino acids- with more than one amino group, as well as acidic amino acids- with more than one carboxyl group.

About 200 amino acids are known to occur in living organisms, but only 20 of them are part of proteins. These are the so-called main or proteinogenic amino acids.

Depending on the radical, the basic amino acids are divided into 3 groups:

1. Non-polar (alanine, methionine, valine, proline, leucine, isoleucine, tryptophan, phenylalanine);
2. Polar uncharged (asparagine, glutamine, serine, glycine, tyrosine, threonine, cysteine);
3. Charged (arginine, histidine, lysine - positive; aspartic and glutamic acid - negative).

The side chains of amino acids (radical) can be hydrophobic and hydrophilic and give proteins the corresponding properties.

In plants, all the necessary amino acids are synthesized from the primary products of photosynthesis. Man and animals are not able to synthesize a number of proteinogenic amino acids and must receive them ready-made with food. Such amino acids are called essential. These include lysine, valine, leucine, isoleucine, threonine, phenylalanine, tryptophan, methionine; arginine and histidine are indispensable for children.

In a solution, amino acids can act as both acids and bases, that is, they are amphoteric compounds. The carboxyl group (-COOH) is able to donate a proton, functioning as an acid, and the amine (-NH2) group can accept a proton, thus exhibiting the properties of a base.

The amino group of one amino acid can react with the carboxyl group of another amino acid. The resulting molecule is dipeptide, and the -CO-NH- bond is called a peptide bond.

At one end of the dipeptide molecule is a free amino group, and at the other end is a free carboxyl group. Due to this, the dipeptide can attach other amino acids to itself, forming oligopeptides. If many amino acids (more than 10) are combined in this way, then polypeptide.

Peptides play an important role in the body. Many aligopeptides are hormones. These are oxytocin, vasopressin, thyroliberin, thyrotropin, etc. Oligopeptides also include bradykidin (pain peptide) and some opiates (“natural drugs” of a person) that perform the function of pain relief. Taking drugs destroys the opiate system of the body, so the addict without a dose of drugs experiences 1 severe pain- "withdrawal", which is normally removed by opiates.

Oligopeptides include some antibiotics (eg gramicidin S).

Many hormones (insulin, adrenocorticotropic hormone, etc.), antibiotics (eg, gramicidin A), toxins (eg, diphtheria toxin) are polypeptides.

Proteins are polypeptides, the molecule of which includes from 50 to several thousand amino acids with a molecular weight of over 10,000.

Each protein has its own special spatial structure in a certain environment. When characterizing the spatial (three-dimensional) structure, four levels of organization of protein molecules are distinguished.

Primary Structure- the sequence of amino acids in the polypeptide chain. The primary structure is specific for each protein and is determined by genetic information, i.e. depends on the sequence of nucleotides in the region of the DNA molecule that encodes a given protein. All properties and functions of proteins depend on the primary structure. The replacement of a single amino acid in the composition of protein molecules or a change in their location usually entails a change in the function of the protein. Since proteins contain 20 types of amino acids, the number of options for their combinations in the floor and the peptide chain is truly unlimited, which provides a huge number of types of proteins in living cells.

In living cells, protein molecules or their individual sections are not an elongated chain, but twisted into a spiral resembling an extended spring (this is the so-called α-helix) or folded into a folded layer (β-layer). secondary structure arises as a result of the formation of hydrogen bonds between the -CO - and -NH 2 groups of two peptide bonds within one polypeptide chain (helical configuration) or between two polypeptide chains (folded layers).

The keratin protein has a fully α-helical configuration. It is a structural protein of hair, wool, nails, claws, beak, feathers and horns. The spiral secondary structure is characteristic, in addition to keratin, for such fibrillar (filamentous) proteins as myosin, fibrinogen, collagen.

In most proteins, the helical and non-helical sections of the polypeptide chain fold into a three-dimensional formation spherical shape- globule (characteristic of globular proteins). A globule of a particular configuration is tertiary structure squirrel. The tertiary structure is stabilized by ionic, hydrogen bonds, covalent disulfide bonds (which are formed between the sulfur atoms that make up cysteine), as well as hydrophobic interactions. The hydrophobic interactions are the most important in the formation of the tertiary structure; At the same time, the protein folds in such a way that its hydrophobic side chains are hidden inside the molecule, that is, they are protected from contact with water, and the hydrophilic side chains, on the contrary, are exposed to the outside.

Many proteins with a particularly complex structure consist of several polypeptide chains held together in a molecule due to hydrophobic interactions, as well as with the help of hydrogen and ionic bonds - there is quaternary structure. Such a structure is present, for example, in the globular protein of hemoglobin. Its molecule consists of four separate polypeptide subunits (protomers) located in the tertiary structure, and a non-protein part - heme. Only in such a structure is hemoglobin able to perform its transport function.

Under the influence of various chemical and physical factors (treatment with alcohol, acetone, acids, alkalis, high temperature, irradiation, high pressure etc.) there is a change in the tertiary and quaternary structure of the protein due to the breaking of hydrogen and ionic bonds. The process of disrupting the native (natural) structure of a protein is called denaturation. In this case, a decrease in protein solubility, a change in the shape and size of molecules, a loss of enzymatic activity, etc. are observed. The process of denaturation is sometimes reversible, i.e., the return normal conditions environment may be accompanied by spontaneous restoration of the natural structure of the protein. This process is called renaturation. It follows that all the features of the structure and functioning of a protein macromolecule are determined by its primary structure.

By chemical composition distinguish between simple and complex proteins. TO simple proteins are made up of only amino acids, difficult- containing the protein part and non-protein (prostatic) - metal ions, carbohydrates, lipids, etc. Simple proteins are blood serum albumin, immunoglobulin (antibodies), fibrin, some enzymes (trypsin), etc. Complex proteins are all proteolipids and glycoproteins, hemoglobin , most enzymes, etc.

Functions of proteins

Structural.

Proteins are part of cell membranes and cell organelles. The walls of blood vessels, cartilage, tendons, hair, nails, claws in higher animals consist mainly of proteins.

Catalytic (enzymatic).

Protein enzymes catalyze all chemical reactions in the body. They provide for the breakdown of nutrients in the digestive tract, carbon fixation during photosynthesis, matrix synthesis reactions, etc.

Transport.

Proteins are able to attach and carry various substances. Blood albumins transport fatty acids, globulins - metal ions and hormones. Hemoglobin carries oxygen and carbon dioxide.

Protein molecules that make up the plasma membrane take part in the transport of substances into and out of the cell.

Protective.

It is carried out by immunoglobulins (antibodies) of the blood, which provide the immune defense of the body. Fibrinogen and thrombin are involved in blood clotting and prevent bleeding.

Contractile.

It is provided by the movement relative to each other of the filaments of actin and myosin proteins in muscles and inside cells. The sliding of microtubules, built from the protein tubulin, is explained by the movement of cilia and flagella.

Regulatory.

Many hormones are oligopeptides or proteins, for example: insulin, glucagon, adenocorticotropic hormone, etc.

Receptor.

Some proteins embedded in the cell membrane are able to change their structure to act external environment. This is how signals are received from the external environment and information is transmitted to the cell. An example would be phytochrome- a photosensitive protein that regulates the photoperiodic response of plants, and opsin - component rhodopsin, a pigment found in the cells of the retina.

Proteins were isolated as a separate class of biological molecules in the 18th century as a result of the work of the French chemist Antoine Fourcroix and other scientists, in which the property of proteins to coagulate (denature) under the influence of heat or acids was noted. Proteins such as albumin ("egg white"), fibrin (a protein from the blood), and gluten from wheat grains were researched at the time. Dutch chemist Gerrit Mulder analyzed the composition of proteins and hypothesized that almost all proteins have a similar empirical formula. The term "protein" for similar molecules was proposed in 1838 by the Swedish chemist Jakob Berzelius. Mulder also identified the degradation products of proteins - amino acids, and for one of them (leucine), with a small margin of error, determined the molecular weight - 131 daltons. In 1836 Mulder proposed the first model of the chemical structure of proteins. Based on the theory of radicals, he formulated the concept of the minimum structural unit of protein composition, C 16 H 24 N 4 O 5, which was called "protein", and the theory - "protein theory". As new data on proteins accumulated, the theory began to be repeatedly criticized, but until the end of the 1850s, despite the criticism, it was still considered generally accepted.

By the end of the 19th century, most of the amino acids that make up proteins were investigated. In 1894, the German physiologist Albrecht Kossel put forward the theory that amino acids are the basic building blocks of proteins. At the beginning of the 20th century, the German chemist Emil Fischer experimentally proved that proteins consist of amino acid residues connected by peptide bonds. He also carried out the first analysis of the amino acid sequence of a protein and explained the phenomenon of proteolysis.

However, the central role of proteins in organisms was not recognized until 1926, when the American chemist James Sumner (later Nobel laureate) showed that the enzyme urease is a protein.

The difficulty of isolating pure proteins made it difficult to study them. Therefore, the first studies were carried out using those polypeptides that could be purified in in large numbers, that is, blood proteins, chicken eggs, various toxins, as well as digestive / metabolic enzymes released after slaughtering livestock. In the late 1950s, the company Armor Hot Dog Co. was able to purify a kilogram of bovine pancreatic ribonuclease A, which has become an experimental object for many scientists.

The idea that the secondary structure of proteins is the result of the formation of hydrogen bonds between amino acids was proposed by William Astbury in 1933, but Linus Pauling is considered the first scientist to successfully predict the secondary structure of proteins. Later, Walter Kauzman, relying on the work of Kai Linderström-Lang, made a significant contribution to understanding the laws of formation of the tertiary structure of proteins and the role of hydrophobic interactions in this process. In 1949, Fred Sanger determined the amino acid sequence of insulin, demonstrating in this way that proteins are linear polymers of amino acids, and not their branched (as in some sugars) chains, colloids or cyclols. The first protein structures based on single-atom X-ray diffraction were obtained in the 1960s and by NMR in the 1980s. In 2006, the Protein Data Bank contained about 40,000 protein structures.

In the 21st century, the study of proteins has moved to a qualitatively new level, when not only individual purified proteins are studied, but also the simultaneous change in the number and post-translational modifications of a large number of proteins of individual cells, tissues or organisms. This area of ​​biochemistry is called proteomics. With the help of bioinformatics methods, it became possible not only to process X-ray structural analysis data, but also to predict the structure of a protein based on its amino acid sequence. Currently, cryoelectron microscopy of large protein complexes and the prediction of small proteins and domains of large proteins using computer programs are approaching the resolution of structures at the atomic level in accuracy.

Properties

The size of a protein can be measured in the number of amino acids or in daltons (molecular weight), more often due to the relatively large size of the molecule in derived units - kilodaltons (kDa). Yeast proteins, on average, consist of 466 amino acids and have a molecular weight of 53 kDa. The largest protein currently known, titin, is a component of muscle sarcomeres; molecular mass its various isoforms range from 3000 to 3700 kDa, it consists of 38,138 amino acids (in the human muscle solius).

Proteins vary in their degree of solubility in water, but most proteins are soluble in it. Insolubles include, for example, keratin (the protein that makes up hair, mammalian hair, bird feathers, etc.) and fibroin, which is part of silk and cobwebs. Proteins are also divided into hydrophilic and hydrophobic. Hydrophilic include most of the proteins of the cytoplasm, nucleus and intercellular substance, including insoluble keratin and fibroin. Hydrophobic include most of the proteins that make up the biological membranes of integral membrane proteins that interact with hydrophobic membrane lipids (these proteins usually also have small hydrophilic regions).

Denaturation

Irreversible denaturation of chicken egg protein under the influence of high temperature

As a general rule, proteins retain structure and hence physico-chemical properties, such as solubility under conditions such as temperature and to which a given organism is adapted. Changing these conditions, such as heating or treating the protein with acid or alkali, results in the loss of the quaternary, tertiary, and secondary structures of the protein. The loss of a native structure by a protein (or other biopolymer) is called denaturation. Denaturation can be complete or partial, reversible or irreversible. The most famous case of irreversible protein denaturation in everyday life is the preparation of a chicken egg, when, under the influence of high temperature, the water-soluble transparent protein ovalbumin becomes dense, insoluble and opaque. Denaturation is in some cases reversible, as in the case of precipitation (precipitation) of water-soluble proteins with ammonium salts, and is used as a way to purify them.

Simple and complex proteins

In addition to peptide chains, many proteins also contain non-amino acid fragments; according to this criterion, proteins are classified into two groups. large groups- simple and complex proteins (proteins). Simple proteins contain only amino acid chains, complex proteins also contain non-amino acid fragments. These fragments of non-protein nature in the composition of complex proteins are called "prosthetic groups". Depending on the chemical nature of the prosthetic groups, the following classes are distinguished among complex proteins:

• Glycoproteins containing covalently linked carbohydrate residues as a prosthetic group and their subclass, proteoglycans, with mucopolysaccharide prosthetic groups. The hydroxyl groups of serine or threonine are usually involved in the formation of bonds with carbohydrate residues. Most of the extracellular proteins, in particular, immunoglobulins, are glycoproteins. In proteoglycans, the carbohydrate part is ~95%; they are the main component of the extracellular matrix.
• Lipoproteins containing non - covalently linked lipids as the prosthetic part . Lipoproteins formed by proteins-apolipoproteins with lipids binding to them and perform the function of lipid transport.
• Metalloproteins containing non-heme coordinated metal ions. Among metalloproteins there are proteins that perform storage and transport functions (for example, iron-containing ferritin and transferrin) and enzymes (for example, zinc-containing carbonic anhydrase and various superoxide dismutases containing copper, manganese, iron and other metal ions as active centers)
• Nucleoproteins containing non-covalently linked DNA or RNA, in particular the chromatin that makes up chromosomes, is a nucleoprotein.
• Phosphoproteins containing covalently linked phosphoric acid residues as a prosthetic group. The hydroxyl groups of serine or threonine are involved in the formation of an ester bond with phosphate; phosphoproteins are, in particular, milk casein.
• Chromoproteins are the collective name for complex proteins with colored prosthetic groups of various chemical nature. These include many proteins with a metal-containing porphyrin prosthetic group that perform various functions - hemoproteins (proteins containing heme - hemoglobin, cytochromes, etc. as a prosthetic group), chlorophylls; flavoproteins with a flavin group, etc.

protein structure

• Tertiary structure- the spatial structure of the polypeptide chain (a set of spatial coordinates of the atoms that make up the protein). Structurally, it consists of secondary structure elements stabilized by various types of interactions, in which hydrophobic interactions play an important role. In the stabilization of the tertiary structure take part:
  • covalent bonds (between two cysteine ​​residues - disulfide bridges);
  • ionic bonds between oppositely charged side groups of amino acid residues;
  • hydrogen bonds;
  • hydrophilic-hydrophobic interactions. When interacting with surrounding water molecules, the protein molecule “tends” to curl up so that the non-polar side groups of amino acids are isolated from aqueous solution; polar hydrophilic side groups appear on the surface of the molecule.

• Quaternary structure (or subunit, domain) - the mutual arrangement of several polypeptide chains as part of a single protein complex. Protein molecules that make up a protein with a quaternary structure are formed separately on ribosomes and only after the end of synthesis form a common supramolecular structure. A protein with a quaternary structure can contain both identical and different polypeptide chains. The same types of interactions take part in the stabilization of the quaternary structure as in the stabilization of the tertiary. Supramolecular protein complexes can consist of dozens of molecules.

Protein environment

Different ways of depicting the three-dimensional structure of a protein using the enzyme triose phosphate isomerase as an example. On the left - a "rod" model, with the image of all atoms and the bonds between them; elements are shown in colors. Structural motifs, α-helices and β-sheets are depicted in the middle. On the right is the contact surface of the protein, built taking into account the van der Waals radii of atoms; the colors show the features of the activity of the sites

By general type protein structures can be divided into three groups:

Formation and maintenance of protein structure in living organisms

The ability of proteins to restore the correct three-dimensional structure after denaturation made it possible to put forward the hypothesis that all information about the final structure of a protein is contained in its amino acid sequence. It is now a generally accepted theory that, as a result of evolution, the stable conformation of a protein has minimal free energy compared to other possible conformations of that polypeptide.

Nevertheless, there is a group of proteins in cells whose function is to ensure the restoration of the protein structure after damage, as well as the creation and dissociation of protein complexes. These proteins are called chaperones. The concentration of many chaperones in the cell increases with a sharp increase in ambient temperature, so they belong to the Hsp group (eng. heat shock proteins- heat shock proteins). The importance of the normal functioning of chaperones for the functioning of the body can be illustrated by the example of the α-crystallin chaperone, which is part of the human eye lens. Mutations in this protein lead to clouding of the lens due to protein aggregation and, as a result, cataracts.

Protein synthesis

Chemical synthesis

Short proteins can be synthesized chemically using a group of methods that use organic synthesis - for example, chemical ligation. Most chemical synthesis methods proceed in the C-terminal to N-terminal direction, as opposed to biosynthesis. Thus, it is possible to synthesize a short immunogenic peptide (epitope), which is used to obtain antibodies by injection into animals, or to obtain hybridomas; chemical synthesis is also used to produce inhibitors of certain enzymes. Chemical synthesis allows the introduction of artificial, that is, amino acids not found in ordinary proteins - for example, attaching fluorescent labels to the side chains of amino acids. However, chemical methods of synthesis are inefficient when proteins are longer than 300 amino acids; in addition, artificial proteins may have an incorrect tertiary structure, and there are no post-translational modifications in the amino acids of artificial proteins.

Biosynthesis of proteins

Universal way: ribosomal synthesis

Proteins are synthesized by living organisms from amino acids based on information encoded in genes. Each protein consists of a unique sequence of amino acids, which is determined by the nucleotide sequence of the gene that codes for this protein. The genetic code is made up of three-letter "words" called codons; each codon is responsible for attaching one amino acid to the protein: for example, the combination AUG corresponds to methionine. Since DNA consists of four types of nucleotides, the total number of possible codons is 64; and since 20 amino acids are used in proteins, many amino acids are specified by more than one codon. Protein-coding genes are first transcribed into messenger RNA (mRNA) nucleotide sequence by RNA polymerase proteins.

The process of protein synthesis based on an mRNA molecule is called translation. During the initial stage of protein biosynthesis, initiation, the methionine codon is usually recognized as a small subunit of the ribosome, to which methionine transfer RNA (tRNA) is attached using protein initiation factors. After recognition of the start codon, the large subunit joins the small subunit and the second stage of translation begins - elongation. With each movement of the ribosome from the 5" to the 3" end of the mRNA, one codon is read through the formation of hydrogen bonds between the three nucleotides (codon) of the mRNA and the complementary anticodon of the transfer RNA to which the corresponding amino acid is attached. The synthesis of the peptide bond is catalyzed by ribosomal RNA (rRNA), which forms the peptidyl transferase center of the ribosome. Ribosomal RNA catalyzes the formation of a peptide bond between the last amino acid of the growing peptide and the amino acid attached to the tRNA, positioning the nitrogen and carbon atoms in a position favorable for the reaction. Aminoacyl-tRNA synthetase enzymes attach amino acids to their tRNAs. The third and final stage of translation, termination, occurs when the ribosome reaches the stop codon, after which the protein termination factors hydrolyze the last tRNA from the protein, stopping its synthesis. Thus, in ribosomes, proteins are always synthesized from the N- to the C-terminus.

Nonribosomal synthesis

Post-translational modification of proteins

After translation is completed and the protein is released from the ribosome, the amino acids in the polypeptide chain undergo various chemical modifications. Examples of post-translational modification are:

• attachment of various functional groups (acetyl-, methyl- and phosphate groups);
• addition of lipids and hydrocarbons;
• change of standard amino acids to non-standard ones (formation of citrulline);
• formation of structural changes (formation of disulfide bridges between cysteines);
• removal of a part of the protein both at the beginning (signal sequence) and in some cases in the middle (insulin);
• addition of small proteins that affect protein degradation (sumoylation and ubiquitination).

In this case, the type of modification can be both universal (the addition of chains consisting of ubiquitin monomers serves as a signal for the degradation of this protein by the proteasome) and specific for this protein. At the same time, the same protein can undergo numerous modifications. Thus, histones (proteins that make up chromatin in eukaryotes) under different conditions can undergo up to 150 different modifications.

Functions of proteins in the body

Like other biological macromolecules (polysaccharides, lipids) and nucleic acids, proteins are essential components of all living organisms, they are involved in most of the life processes of the cell. Proteins carry out metabolism and energy transformations. Proteins are part of cellular structures - organelles, secreted into the extracellular space for the exchange of signals between cells, hydrolysis of food and the formation of intercellular substance.

It should be noted that the classification of proteins according to their function is rather arbitrary, because in eukaryotes the same protein can perform several functions. A well-studied example of such multifunctionality is lysyl-tRNA synthetase, an enzyme from the class of aminoacyl-tRNA synthetases, which not only attaches lysine to tRNA, but also regulates the transcription of several genes. Proteins perform many functions due to their enzymatic activity. So, the enzymes are the motor protein myosin, the regulatory proteins of protein kinase, the transport protein sodium-potassium adenosine triphosphatase, etc.

catalytic function

The most well-known role of proteins in the body is the catalysis of various chemical reactions. Enzymes are a group of proteins with specific catalytic properties, that is, each enzyme catalyzes one or more similar reactions. Enzymes catalyze the reactions of splitting complex molecules (catabolism) and their synthesis (anabolism), as well as DNA replication and repair and RNA template synthesis. Several thousand enzymes are known; among them, such as, for example, pepsin break down proteins in the process of digestion. In the process of post-translational modification, some enzymes add or remove chemical groups on other proteins. About 4,000 protein-catalyzed reactions are known. The acceleration of the reaction as a result of enzymatic catalysis is sometimes enormous: for example, the reaction catalyzed by the enzyme orotate carboxylase proceeds 10 17 times faster than the non-catalyzed one (78 million years without the enzyme, 18 milliseconds with the participation of the enzyme). Molecules that attach to an enzyme and change as a result of the reaction are called substrates.

Although enzymes are usually composed of hundreds of amino acids, only a small fraction of them interact with the substrate, and even fewer - an average of 3-4 amino acids, often located far apart in the primary amino acid sequence - are directly involved in catalysis. The part of the enzyme that attaches the substrate and contains the catalytic amino acids is called the active site of the enzyme.

structural function

Protective function

There are several types of protective functions of proteins:

Regulatory function

Many processes inside cells are regulated by protein molecules, which serve neither as a source of energy nor building material for the cell. These proteins regulate transcription, translation, splicing, as well as the activity of other proteins, etc. The regulatory function of proteins is carried out either due to enzymatic activity (for example, protein kinase), or due to specific binding to other molecules, as a rule, affecting the interaction with these molecules enzymes.

Hormones are carried in the blood. Most animal hormones are proteins or peptides. The binding of the hormone to the receptor is a signal that triggers a response in the cell. Hormones regulate the concentration of substances in the blood and cells, growth, reproduction and other processes. An example of such proteins is insulin, which regulates the concentration of glucose in the blood.

Cells interact with each other using signal proteins transmitted through the intercellular substance. Such proteins include, for example, cytokines and growth factors.

transport function

Spare (reserve) function of proteins

These proteins include the so-called reserve proteins, which are stored as a source of energy and matter in plant seeds and animal eggs; proteins of the tertiary egg shells (ovalbumins) and the main milk protein (casein) also perform a mainly nutritional function. A number of other proteins are used in the body as a source of amino acids, which in turn are precursors of biologically active substances that regulate metabolic processes.

Receptor function

Protein receptors can either be located in the cytoplasm or integrated into the cell membrane. One part of the receptor molecule perceives a signal, which is most often a chemical substance, and in some cases - light, mechanical action (for example, stretching), and other stimuli. When a signal is applied to a certain part of the molecule - the receptor protein - its conformational changes occur. As a result, the conformation of another part of the molecule, which transmits the signal to other cellular components, changes. There are several signaling mechanisms. Some receptors catalyze a particular chemical reaction; others serve as ion channels that open or close when a signal is applied; still others specifically bind intracellular messenger molecules. In membrane receptors, the part of the molecule that binds to the signal molecule is located on the cell surface, and the signal-transmitting domain is inside.

Motor (motor) function

Amino acids that cannot be synthesized by animals are called essential. Key enzymes in biosynthetic pathways, such as aspartate kinase, which catalyzes the first step in the formation of lysine, methionine, and threonine from aspartate, are absent in animals.

Animals mainly obtain amino acids from the proteins in their food. Proteins are broken down during digestion, which usually begins with the denaturation of the protein by placing it in an acidic environment and hydrolyzing it with enzymes called proteases. Some of the amino acids obtained from digestion are used to synthesize the body's proteins, while the rest are converted to glucose through the process of gluconeogenesis or used in the Krebs cycle. The use of protein as an energy source is especially important in fasting conditions, when the body's own proteins, especially muscles, serve as an energy source. Amino acids are also an important source of nitrogen in the nutrition of the body.

There are no single norms for human consumption of proteins. The microflora of the large intestine synthesizes amino acids that are not taken into account when compiling protein norms.

Protein Biophysics

The physical properties of proteins are very complex. In favor of the hypothesis of a protein as an ordered “crystal-like system” - an “aperiodic crystal” - is evidenced by X-ray diffraction analysis data (up to a resolution of 1 angstrom), high packing density, cooperativity of the denaturation process and other facts.

In favor of another hypothesis, the liquid-like properties of proteins in the processes of intraglobular movements (a model of limited hopping or continuous diffusion) are evidenced by experiments on neutron scattering, Mössbauer spectroscopy and Rayleigh scattering of Mössbauer radiation.

Study Methods

A number of methods are used to determine the amount of protein in a sample:

• Spectrophotometric method

see also

Notes

1. From a chemical point of view, all proteins are polypeptides. However, short, less than 30 amino acids in length, polypeptides, especially chemically synthesized ones, cannot be called proteins.
2. Muirhead H., Perutz M. Structure of hemoglobin. A three-dimensional Fourier synthesis of reduced human hemoglobin at 5.5 A resolution // Nature: magazine. - 1963. - T. 199. - No. 4894. - S. 633-638.
3. Kendrew J., Bodo G., Dintzis H., Parrish R., Wyckoff H., Phillips D. A three-dimensional model of the myoglobin molecule obtained by x-ray analysis // Nature: magazine. - 1958. - T. 181. - No. 4610. - S. 662-666.
4. Leicester, Henry."Berzelius, Johns Jacob". Dictionary of Scientific Biography 2. New York: Charles Scribner's Sons. 90-97 (1980). ISBN 0-684-10114-9
5. Yu. A. Ovchinnikov. Bioorganic chemistry. - Enlightenment, 1987.
6. Proteins // Chemical Encyclopedia. - Soviet Encyclopedia, 1988.
7. N. H. Barton, D. E. G. Briggs, J. A. Eisen."Evolution", Cold Spring Harbor Laboratory Press, 2007 - P. 38. ISBN 978-0-87969-684-9
8. Nobel lecture by F. Sanger
9. Fulton A, Isaacs W. (1991). "Titin, a huge, elastic sarcomeric protein with a probable role in morphogenesis". Bioessays 13 (4): 157-161. PMID 1859393.
10. EC 3.4.23.1 - pepsin A
11. S J Singer. The Structure and Insertion of Integral Proteins in Membranes. Annual Review of Cell Biology. Volume 6, Page 247-296. 1990
12. Strayer L. Biochemistry in 3 volumes. - M.: Mir, 1984
13. Selenocysteine ​​is an example of a non-standard amino acid.
14. B. Lewin. Genes. - M ., 1987. - 544 p.
15. Lehninger A. Fundamentals of biochemistry, in 3 volumes. - M.: Mir, 1985.
16. Lecture 2
17. http://pdbdev.sdsc.edu:48346/pdb/molecules/pdb50_6.html
18. Anfinsen C. (1973). "Principles that Govern the Folding of Protein Chains". Science 181 : 223-229. Nobel lecture. The author, together with Stanford Moore and William Stein, received Nobel Prize in Chemistry for "the study of ribonuclease, especially the relationship between the amino acid sequence of [an enzyme] and [its] biologically active conformation."
19. Ellis RJ, van der Vies SM. (1991). "Molecular chaperones". Annu. Rev. Biochem. 60 : 321-347.

But life on our planet originated from a coacervate droplet. It was also a protein molecule. That is, the conclusion follows that it is these chemical compounds that are the basis of all life that exists today. But what are protein structures? What role do they play in the body and people's lives today? What types of proteins are there? Let's try to figure it out.

Proteins: a general concept

From the point of view, the molecule of the substance under consideration is a sequence of amino acids interconnected by peptide bonds.

Each amino acid has two functional groups:

• carboxyl -COOH;
• an amino group -NH 2 .

It is between them that the formation of bonds in different molecules occurs. Thus, the peptide bond has the form -CO-NH. A protein molecule may contain hundreds or thousands of such groups, it will depend on the specific substance. The types of proteins are very diverse. Among them there are those that contain essential amino acids for the body, which means they must enter the body with food products. There are varieties that perform important functions in the cell membrane and its cytoplasm. Biological catalysts are also isolated - enzymes, which are also protein molecules. They are widely used in human life, and not only participate in the biochemical processes of living beings.

The molecular weight of the compounds under consideration can vary from several tens to millions. After all, the number of monomer units in a large polypeptide chain is unlimited and depends on the type of a particular substance. Protein in its pure form, in its native conformation, can be seen when examining a chicken egg in a light yellow, transparent, dense colloidal mass, inside of which the yolk is located - this is the desired substance. The same can be said about fat-free cottage cheese. This product is also almost pure protein in its natural form.

However, not all compounds under consideration have the same spatial structure. In total, four organizations of the molecule are distinguished. Species determine its properties and speak of the complexity of the structure. It is also known that more spatially entangled molecules undergo extensive processing in humans and animals.

Types of protein structures

There are four of them in total. Let's take a look at what each of them is.

1. Primary. Represents the usual linear sequence of amino acids connected by peptide bonds. There are no spatial twists, no spiralization. The number of links included in the polypeptide can reach several thousand. Types of proteins with a similar structure are glycylalanine, insulin, histones, elastin, and others.
2. Secondary. It consists of two polypeptide chains that are twisted in the form of a spiral and oriented towards each other by formed turns. In this case, hydrogen bonds form between them, holding them together. This is how a single protein molecule is formed. The types of proteins of this type are as follows: lysozyme, pepsin and others.
3. Tertiary conformation. It is a densely packed and compactly coiled secondary structure. Here, other types of interaction appear, in addition to hydrogen bonds - this is the van der Waals interaction and the forces of electrostatic attraction, hydrophilic-hydrophobic contact. Examples of structures are albumin, fibroin, silk protein, and others.
4. Quaternary. The most complex structure, which is several polypeptide chains twisted into a spiral, rolled into a ball and united all together into a globule. Examples such as insulin, ferritin, hemoglobin, collagen illustrate just such a protein conformation.

If we consider all the given structures of molecules in detail from a chemical point of view, then the analysis will take a long time. Indeed, in fact, the higher the configuration, the more complex and intricate its structure, the more types of interactions are observed in the molecule.

Denaturation of protein molecules

One of the most important chemical properties of polypeptides is their ability to break down under the influence of certain conditions or chemical agents. For example, various types of protein denaturation are widespread. What is this process? It consists in the destruction of the native structure of the protein. That is, if initially the molecule had a tertiary structure, then after the action of special agents it will collapse. However, the sequence of amino acid residues remains unchanged in the molecule. Denatured proteins quickly lose their physical and chemical properties.

What reagents can lead to the process of conformation destruction? There are several.

1. Temperature. When heated, there is a gradual destruction of the quaternary, tertiary, secondary structure of the molecule. Visually, this can be observed, for example, when frying an ordinary chicken egg. The resulting "protein" is the primary structure of the albumin polypeptide that was in the raw product.
2. Radiation.
3. Action by strong chemical agents: acids, alkalis, salts of heavy metals, solvents (for example, alcohols, ethers, benzene and others).

This process is sometimes also called the melting of the molecule. The types of protein denaturation depend on the agent under whose action it occurred. Moreover, in some cases, the reverse process takes place. This is renaturation. Not all proteins are able to restore their structure back, but a significant part of them can do this. So, chemists from Australia and America carried out the renaturation of a boiled chicken egg using some reagents and a centrifugation method.

This process is important for living organisms in the synthesis of polypeptide chains by ribosomes and rRNA in cells.

Hydrolysis of a protein molecule

Along with denaturation, proteins are characterized by another chemical property - hydrolysis. This is also the destruction of the native conformation, but not to the primary structure, but completely to individual amino acids. An important part of digestion is protein hydrolysis. The types of hydrolysis of polypeptides are as follows.

1. Chemical. Based on the action of acids or alkalis.
2. Biological or enzymatic.

However, the essence of the process remains unchanged and does not depend on what types of protein hydrolysis take place. As a result, amino acids are formed, which are transported to all cells, organs and tissues. Their further transformation consists in the participation of the synthesis of new polypeptides, already those that are necessary for a particular organism.

In industry, the process of hydrolysis of protein molecules is used just to obtain the desired amino acids.

Functions of proteins in the body

Various types of proteins, carbohydrates, fats are vital components for the normal functioning of any cell. And that means the whole organism as a whole. Therefore, their role is largely explained a high degree significance and ubiquity within living beings. There are several main functions of polypeptide molecules.

1. catalytic. It is carried out by enzymes that have a protein structure. We'll talk about them later.
2. Structural. The types of proteins and their functions in the body primarily affect the structure of the cell itself, its shape. In addition, polypeptides that perform this role form hair, nails, mollusc shells, and bird feathers. They are also a certain armature in the body of the cell. Cartilage is also made up of these types of proteins. Examples: tubulin, keratin, actin and others.
3. Regulatory. This function is manifested in the participation of polypeptides in such processes as: transcription, translation, cell cycle, splicing, mRNA reading, and others. In all of them, they play an important role as a regulator.
4. Signal. This function is performed by proteins located on the cell membrane. They transmit different signals from one unit to another, and this leads to communication between tissues. Examples: cytokines, insulin, growth factors and others.
5. Transport. Some types of proteins and their functions that they perform are simply vital. This happens, for example, with the protein hemoglobin. It transports oxygen from cell to cell in the blood. For a person it is irreplaceable.
6. Spare or reserve. Such polypeptides accumulate in plants and animal eggs as a source of additional nutrition and energy. An example is globulins.
7. Motor. A very important function, especially for the simplest organisms and bacteria. After all, they are able to move only with the help of flagella or cilia. And these organelles, by their nature, are nothing more than proteins. Examples of such polypeptides are the following: myosin, actin, kinesin and others.

Obviously, the functions of proteins in the human body and other living beings are very numerous and important. This once again confirms that without the compounds we are considering, life on our planet is impossible.

Protective function of proteins

Polypeptides can protect against various influences: chemical, physical, biological. For example, if the body is in danger in the form of a virus or bacteria of a foreign nature, then immunoglobulins (antibodies) enter into battle with them, performing a protective role.

If we talk about physical effects, then fibrin and fibrinogen, which are involved in blood coagulation, play an important role here.

Food proteins

The types of dietary protein are as follows:

• complete - those that contain all the amino acids necessary for the body;
• incomplete - those in which there is an incomplete amino acid composition.

However, both are important for the human body. Especially the first group. Each person, especially during periods of intensive development (childhood and adolescence) and puberty, must maintain a constant level of proteins in himself. After all, we have already considered the functions that these amazing molecules perform, and we know that practically not a single process, not a single biochemical reaction within us can do without the participation of polypeptides.

That is why it is necessary to consume every day daily allowance proteins found in the following foods:

• egg;
• milk;
• cottage cheese;
• meat and fish;
• beans;
• beans;
• peanut;
• wheat;
• oats;
• lentils and others.

If one consumes 0.6 g of the polypeptide per kg of weight per day, then a person will never lack these compounds. If for a long time the body does not receive the necessary proteins, then a disease occurs, which has the name of amino acid starvation. This leads to severe metabolic disorders and, as a result, many other ailments.

Proteins in a cell

Inside the smallest structural unit of all living things - cells - there are also proteins. Moreover, they perform almost all of the above functions there. First of all, the cytoskeleton of the cell is formed, consisting of microtubules, microfilaments. It serves to maintain shape, as well as for transport inside between organelles. Various ions and compounds move along protein molecules, as along channels or rails.

The role of proteins immersed in the membrane and located on its surface is also important. Here they perform both receptor and signal functions, take part in the construction of the membrane itself. They stand guard, which means they play a protective role. What types of proteins in the cell can be attributed to this group? There are many examples, here are a few.

1. actin and myosin.
2. Elastin.
3. Keratin.
4. Collagen.
5. Tubulin.
6. Hemoglobin.
7. Insulin.
8. Transcobalamin.
9. Transferrin.
10. Albumen.

In total, there are several hundred different ones that constantly move inside each cell.

Types of proteins in the body

Of course, they have a huge variety. If you try to somehow divide all existing proteins into groups, then you can get something like this classification.

In general, many features can be taken as a basis for classifying proteins found in the body. One does not yet exist.

Enzymes

Biological catalysts of protein nature, which significantly accelerate all ongoing biochemical processes. Normal exchange is impossible without these compounds. All processes of synthesis and decay, assembly of molecules and their replication, translation and transcription, and others are carried out under the influence of a specific type of enzyme. Examples of these molecules are:

• oxidoreductases;
• transferases;
• catalase;
• hydrolases;
• isomerases;
• lyases and others.

Today, enzymes are used in everyday life. So, in the production of washing powders, so-called enzymes are often used - these are biological catalysts. They improve the quality of washing, subject to the specified temperature regime. Easily binds to dirt particles and removes them from the surface of fabrics.

However, due to their protein nature, enzymes do not tolerate too hot water or proximity to alkaline or acidic drugs. Indeed, in this case, the process of denaturation will occur.