Characteristics, b-structure, b-bend. Supersecondary (supra-secondary) protein structures

22.07.2020

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1. Structural organization of proteins

Each protein is characterized by a specific amino acid sequence and individual spatial structure (conformation). Protein accounts for at least 50% of dry weight organic compounds animal cell. In the human body, there are up to 5 million. different types proteins. A protein molecule can consist of one or more chains containing from fifty to several hundred (sometimes more than a thousand) amino acid residues. Molecules containing less than fifty residues are referred to as peptides. Many molecules include cysteine residues, the disulfide bonds of which covalently link parts of one or more chains. In the native state, protein macromolecules have a specific conformation. The conformation characteristic of a given protein is determined by the sequence of amino acid residues and is stabilized by hydrogen bonds between the peptide and side groups of amino acid residues, as well as by electrostatic and hydrophobic interactions.

2. Primary protein structure: research methods

Structural features of the peptide bond.

A peptide bond is formed by the reaction of the amino group of one amino

acid and another carboxyl group with the release of a water molecule:

CH3-CH (NH2) -COOH + CH3- CH (NH2) -COOH> CH3-CH (NH2) -CONH- (CH3) CH-COOH + H2O

Amino acids linked by a peptide bond form a polypeptide chain. The peptide bond has a planar structure: the C, O, and N atoms are in sp2 hybridization; the N atom has a p-orbital with a lone pair of electrons; a p-p-conjugated system is formed, leading to a shortening of the C? N bond (0.132 nm) and restriction of rotation (the rotation barrier is ≈63 kJ / mol). The peptide bond has a predominantly trans-configuration relative to the plane of the peptide bond. This structure of the peptide bond affects the formation of the secondary and tertiary structure of the protein. The peptide bond is rigid, covalent, genetically determined. In structural formulas, it is depicted as a single bond, but in fact, this bond between carbon and nitrogen is partially double bond:

This is due to the different electronegativity of the C, N, and O atoms. Rotation around the peptide bond is impossible, all four atoms lie in the same plane, i.e. coplanar. Rotation of other bonds around the polypeptide backbone is quite free.

The primary structure was discovered by the professor of Kazan University A.Ya. Danilevsky in 1989. In 1913, E. Fischer synthesized the first peptides. The amino acid sequence for each protein is unique and genetically fixed

Rice. 1.2 Formation of a dipeptide

To determine the primary structure of a separate, chemically homogeneous polypeptide chain, the amino acid composition is determined by hydrolysis: the ratio of each of the twenty amino acids in a sample of a homogeneous polypeptide. Then proceed to determine the chemical nature of the terminal amino acids of the polypeptide chain containing one free NH2 group and one free COOH group.

To determine the nature of the N-terminal amino acid, a number of methods have been proposed, in particular, the Sanger method (for its development, F. Sanger was awarded the Nobel Prize in 1958). This method is based on a polypeptide arylation reaction with 2,4-dinitrofluorobenzene. The polypeptide solution is treated with 2,4-dinitrofluorobenzene, which interacts with the free β-amino group of the peptide. After acidic hydrolysis of the reaction product, only one amino acid is bound to the reagent in the form of 2,4-dinitrophenylamino acid. Unlike other amino acids, it is yellow in color. It is isolated from the hydrolyzate and identified by chromatography.

Enzymatic methods are often used to determine the C-terminal amino acid. Treatment of the polypeptide with carboxypeptidase, which breaks the peptide bond from the end of the peptide containing the free COOH group, results in the release of the C-terminal amino acid, the nature of which can be identified by chromatography. There are other methods for the determination of the C-terminal amino acid, in particular, the Akabori chemical method, based on the hydrazinolysis of the polypeptide. The next stage of work is associated with the determination of the amino acid sequence in the polypeptide. To do this, first carry out partial (chemical and enzymatic) hydrolysis of the polypeptide chain into short peptide fragments, the sequence of which can be accurately determined. After hydrolysis using electrophoresis and chromatography, peptide maps are drawn up. Then the sequence of amino acids in the selected peptides and the primary structure of the entire molecule are established.

Secondary structure of proteins: b - helix, its main characteristics, c - structure, c - bend. Role hydrogen bonds in the formation of the secondary structure .. Supersecondary (supra-secondary) structures of the protein.

Secondary structure? this is the spatial arrangement of the polypeptide chain in the form of a b-helix or b-folding, regardless of the types of side radicals and their conformation. L. Pauling and R. Corey proposed a model of the secondary structure of a protein in the form of a b-helix, in which hydrogen bonds are closed between each first and fourth amino acid, which allows you to preserve the native structure of the protein, perform the simplest functions, and protect against destruction. All peptide groups take part in the formation of hydrogen bonds, which ensures maximum stability, reduces hydrophilicity and increases the hydrophobicity of the protein molecule. b-helix is formed spontaneously and is the most stable conformation corresponding to the minimum of free energy.

The most common element of the secondary structure is the right b-helix (b R).

The peptide chain bends helically here. Each turn has 3.6 amino acid residues, the pitch of the screw, i.e. the minimum distance between two equivalent points is 0.54 nm; b-helix is stabilized by almost linear hydrogen bonds between NH-group and CO-group of the fourth amino acid residue. Thus, in extended helical regions, each amino acid residue takes part in the formation of two hydrogen bonds. Non-polar or amphiphilic b-helices with 5-6 turns often provide anchoring of proteins in biological membranes (transmembrane helices). The left b-helix (bL), mirror-symmetric with respect to the b R-helix, is extremely rare in nature, although it is energetically possible. The twisting of the protein polypeptide chain into a helical structure occurs due to the interaction between the oxygen of the carbonyl group of the i-th amino acid residue and the hydrogen of the amido group (i + 4) - amino acid residue through the formation of hydrogen bonds:

Rice. 1.3 (a) Nitrogen atoms are shown in blue, oxygen atoms - in red. Orange depicts hydrogen bonds formed between the corresponding nitrogen and oxygen atoms. Nitrogen atoms are depicted in blue spirals. And orange shows the hydrogen bonds formed between the oxygen and nitrogen atoms corresponding to the rule

Figure 1.3 (b) Secondary structure of the protein: alpha helix

Another form of helix is present in collagen, an essential component of connective tissue. This is the left helix of collagen with a step of 0.96 nm and, with a remainder of 3.3 in each turn, is flatter compared to the b-helix. Unlike the b-helix, the formation of hydrogen bridges is impossible here. The structure is stabilized by twisting three peptide chains into a right triple helix. Along with β-helices, β-structures and β-bending are also involved in the formation of the secondary structure of the protein. In contrast to the condensed b-helix, the b-layers are almost completely elongated and can be located both parallel and antiparallel. In folded structures, transverse interchain hydrogen bonds are also formed. If the chains are oriented in opposite directions, the structure is called an antiparallel folded sheet (wb); if the chains are oriented in one direction, the structure is called a parallel folded sheet (bn). In folded structures, the b-C atoms are located at the bends, and the side chains are oriented almost perpendicular to the median plane of the sheet, alternately up and down.

The wb-folded structure with almost linear H-bridges turns out to be energetically preferable. In stretched folded sheets, individual chains are most often not parallel, but somewhat curved relative to each other.

Rice. 1.4 Beta-fold protein structure

In addition to the regular ones, there are also irregular secondary structures in the polypeptide chains, i.e. standard structures that do not form long periodic systems. These are B-bends, they are called so because they often pull together the tops of adjacent B-strands in antiparallel B-hairpins). The bends usually include about half of the residues that have not fallen into the regular structures of proteins.

Super secondary structure? this is a higher level of organization of a protein molecule, represented by an ensemble of interacting secondary structures:

1.b-spiral? two antiparallel areas that interact with hydrophobic complementary surfaces (according to the "trough-protrusion" principle);

2. supercoiling of the b-helix;

3.vhv? two parallel sections in the chain;

4. in-zigzag.

There are various ways of folding the protein chain:

Fig. 1.5 Methods of laying the protein chain

A domain is a compact globular structural unit within a polypeptide chain. Domains can perform different functions and undergo folding into independent compact globular structural units connected by flexible regions within the protein molecule.

Rice. 1.6 Motives for laying the protein chain and ornaments on Indian and Greek vases. Above: meander motif; middle: Greek key motif; below: zigzag motif - "lightning".

3.Secondary structure of proteins: conformations of the polypeptide chain

To understand the structure of the protein, it is necessary to consider the possible conformations of the polypeptide chain. They are determined, first of all, by the flat structure of the peptide bond -CO - NH-. The structural parameters of peptide units, established as a result of X-ray diffraction studies of peptides and related compounds, are presented in Table.

Table 1. Structural parameters of peptide units: bond lengths and angles between them X and Y -atoms with which carbon is bound both in the main chain and in the attachment of radicals.

A fully extended chain (without deformation of bond angles and changes in bond lengths) has a trans conformation with zero rotation angles; however, this conformation is not the most stable. Imine atoms groups N-H form hydrogen bonds with oxygen atoms of carbonyl groups. Finding the most stable conformation requires minimizing its total energy, including the energy of intramolecular hydrogen bonds.

Pauling and Corey determined the most stable conformations of the polypeptide chain based on the data of X-ray structural studies and consideration of the complete packing of chains with the maximum number of hydrogen bonds. There are three such conformations: first, the already known b-helix. It is characterized by a rotation around the axis by 54 nm.

Hydrogen bonds are formed between the C = O group of this group and the N-H group of the fourth preceding unit. Such bonds are realized between all amino acid residues, with the exception of prolyl (Pro), which does not contain an N-H group. B-spiral can be both right and left. In the first case, the angles = 132 ?? and = 123 ?? , in the second = 228 ?? and = 237 ?? respectively.

The second and third conformations with the maximum saturation of hydrogen bonds are parallel and antiparallel B-forms. This is not a single chain conformation, but a set of chains that form a layered structure. Chains in this shape do not have a flat trans structure. In a parallel form, the angles are 61? and 239? respectively, in antiparallel - 380? and 325 ?.

The possibility of beta-form formation in a separate polypeptide chain is also very important. These are the so-called cross-beta forms. In places of bends, the angles of turns have values that differ from those inherent in ordered sections.

Rice. 1.7 Regular Secondary Structures - Alpha Helix, Parallel Beta List, Antiparallel Beta List

Thus, hydrogen bonds stabilize the conformations of the polypeptide chain in solution. The presence of a secondary structure with periodicity means that the chain is similar to a crystal: the alpha-helix is similar to a one-dimensional crystal, the beta-form is like a two-dimensional crystal.

Rice. 1.8 Auxiliary interactions: hydrogen bonds

The alpha and beta forms in particular are not the only ones. For example, fibrillar proteins have different conformations.

Let us now consider the dependences of the energies of the polypeptide chain on the angles of internal rotation - the so-called steric maps, similar to geodesics.

The conformational energy of the chain is determined by the weak interaction of valence unbonded atoms. As a consequence flat structure of the peptide group, the angles of rotation of the i-th unit are practically independent of the angles of rotation of adjacent units. And if the angles of rotation of the ith link vary in the range of values not prohibited by the overlapping of atoms of the peptide groups connected by bonds of the ith and (i + 1) th links, and if the angles (i + 1) vary simultaneously, then there is no such a combination of these four angles, at which steric interaction of the i-th and (i + 2) -th links is possible. Thus, the polypeptide chain has a limited cooperativity, the close interactions in it are limited by the close neighbors. This allows us to consider separately the conformational energies for individual conformational residues. The steric map for a given residue essentially depends on the nature of its radical R.

It can be assumed that interactions in a given pair of peptide groups characterize the amino acid residue connecting these groups. Ramachardan studied the Glycyl-L-alanine dipeptide and obtained a conformational (steric map for alanine).

Rice. 1.9 Two-dimensional probability density distribution over torsion angles.

The most frequently visited areas are darker in color. For amino acid residues, two-dimensional distributions over torsion angles w, q,? Among the possible variants of two-dimensional distributions, special attention is usually paid to the section at the angles w, c.

Rice. 2.1 Ramachandran map for amino acid residue.

Conformations that can be achieved with any amtic acid residue are shown in dark gray. Most amino acids can colonize the light gray areas. White indicates forbidden conformations, which, however, may occur in some protein structures.

The calculation was carried out on the basis of the simplest assumption about atoms as hard spheres with van der Waals radii determined from data on interatomic distances in molecular crystals. The table lists these distances, most often observed in crystals, and the minimum distances observed in only a few cases.

Table 2. Contact distances between atoms in polypeptides

A pair of atoms	Typical distance, nm	Minimum distance, nm	A pair of atoms	Typical distance, nm	Minimum Distance, nm

4. Tertiary structure of proteins. Types of non-covalent bonds that stabilize the tertiary structure. The role of S - S - bridges in the formation of the tertiary structure of some proteins

Tertiary structure is understood as the spatial arrangement of the polypeptide chain (the way the chain is folded in a certain volume). Non-covalent bonds play the main role in stabilizing the spatial structure. These include hydrogen bonds, electrostatic interactions of charged groups, intermolecular van der Waals forces, interactions of non-polar side radicals of amino acids (hydrophobic interactions), and dipole-dipole interactions. In addition, disulfide bonds (S-S bridges) play an important role in the formation of the tertiary structure:

Rice. 2.2 (a) Formation of disulfide bonds

Rice. 2.2 (b) Formation of disulfide bonds

Disulfide bonds are formed during the oxidation of cysteine residues close in the spatial structure of the protein to cystine residues. It is believed that disulfide bonds, often multiple, are especially important for the stabilization of small proteins, in which an extensive system of non-covalent interactions cannot occur.

Tertiary structure is a unique for each protein location in the space of the polypeptide chain, depending on the number and alternation of amino acids, i.e. predetermined by the primary structure of the protein. The configuration of protein molecules can be fibrillar and globular. The tertiary structure of many proteins is composed of several compact globules called domains. Domains are usually connected with thin bridges.

Tertiary structure of proteins. Hemoglobin and myoglobin: conformational rearrangements. It is known that the native, three-dimensional structure of a protein is established as a result of the action of a number of energetic and entropic factors. The characteristic times of many intramolecular changes, including enzymatic processes in thousandths of a second, depend on pH, temperature and ionic composition of the medium. Thus, changes in ionic homeostasis can directly affect structural changes in cellular proteins and, accordingly, their function and activity. Let us consider, as an example, the conformational rearrangements of oxygen-carrying proteins, hemoglobin and myoglobin. The structure of these proteins, which are in crystalline form, has been studied in detail by X-ray diffraction analysis. The space between the alpha-helical regions, including the cavity of the active center of the heme group inside the protein molecules, is filled with hydrophobic side chains of amino acids, and in the surrounding aquatic environment many polar protein chains protrude. The hemoglobin molecule consists of four subunits (two b and two c), forming a regular tetramer. Water molecules localized in the area of contacts of the subunits form salt bridges and additionally stabilize the tetramer. Iron can be in a high- and low-spin state, depending on how the d-orbital is filled with electrons, which is determined by Hund's rule. In this regard, the filling of the outer d-orbitals of ferrous and trivalent iron ions with electrons is characteristic of free ions or ions in the composition of compounds with an ionic bond. The situation changes when iron atoms are in a complex, where they are bound to ligand atoms by a covalent bond and are part of the heme. It should be emphasized that the spin state of the central atom in the complex is determined by the nature of the ligand environment: symmetry, the strength of ligand binding in the complex, etc. Because of this, changes in the ligand environment can lead to changes in the spin state of the metal ion, which in turn can cause changes in the conformation of the protein to which the metal ion is bound. Changes in the spin state of iron ions induced by the addition of substrates and temperature changes have been demonstrated for a number of hemoproteins. The transition of the iron ion from the low-spin state to the high-spin state increases the diameter of the ion and leads to its withdrawal from the heme plane, which causes conformational changes in the nearest protein “environment”.

In the high-spin state, the bivalent iron ion has a coordination number of 5 and is located outside the heme plane at a distance of 0.05-0.07 nm. It is coordinatively bound to four atoms of the nitrogen-pyrrole groups of the planar-porphyrin ring, and in the 5th position interacts with the N atom of the imidazole ring of histidine ... Oxygenation and the formation of an oxygen-iron bond do not change the valence of the iron atom, but transfer it from a high-spin state to a low-spin state, increasing the number of ligands in the coordination sphere to 6. In the 6th position, iron is coordinated with oxygen or other ligands.

Rice. 2.3 (a) Simplified diagram of the structure of hemoglobin

The attachment of oxygen induces a number of conformational changes in the hemoglobin molecule. The binding of oxygen with the transfer of the iron atom to the low-spin state is accompanied by a simultaneous displacement of iron by 0.07 nm to the plane of the heme group. This displacement is transmitted through histidine, and the helix is pulled along with it towards the heme to the center of the molecule, pushing out the tyrosine residue from the cavity, then there is a gradual rupture of salt bridges between the b-subunits and their displacement along the contact area. The distance between the heme and the β-subunits increases, while between the heme and the β-subunits, on the contrary, it decreases. In this case, the central cavity of the heme is compressed. The rupture of four salt bridges out of six during oxygenation of the first two b-subunits promotes the rupture of the other two bridges and, therefore, facilitates the connection of the following oxygen molecules with the remaining subunits, increasing their affinity for oxygen by several hundred times. This is the cooperative nature of the addition of oxygen to hemoglobin, in which the beginning of oxygenation of the latter facilitates the binding of other oxygen molecules.

The use of laser radiation with an absorption wavelength in the range of the B-band of porphyrin and near it makes it possible to record the RRC spectra of protoporphyrins in whole cells (erythrocytes). In these spectra, lines lying in the region of 1000-1650 / cm, which are due to in-plane vibrations of C-C bonds, dominate. and C-N and deformation fluctuations CH... Some of them are influenced by chemical transformations with the iron atom and can be used to study the structure of the macrocycle. When the oxidation state of the iron atom changes from trivalent to bivalent, a decrease in the frequency of skeletal vibrations of porphyrin is observed. The position of this and other characteristic bands of the RR spectrum reflects the population of the p-orbitals of the porphyrin with electrons. With its increase, the bonds in porphyrin become weaker, which is reflected in a decrease in the vibration frequency. The population of these orbitals increases due to the reverse transition of electrons from the p-orbitals of the iron atom. Since the process is more pronounced for ferrous iron, the bands characterizing the oxidation state are shifted to the region of lower frequencies for heme with just such iron. With this approach, any effect (including a change in the oxidation state of iron atoms) that causes changes in the distribution of electrons in porphyrin can affect the frequency of the corresponding characteristic lines. This frequency changes greatly, for example, if an axial ligand with a p-orbital can interact with the porphyrin orbitals through the dp-electrons of the iron atom. The axial p-electron donor leads to an additional transition of the dp-electrons of the iron atom to the p-orbital of the porphyrin and causes a decrease in the frequency of the bands characterizing the oxidation state to atypical values.

Rice. 2.3 (b) Model of the tertiary structure of the myoglobin molecule (according to J. Kendrew). Structural domains are denoted in Latin letters, gems are denoted in red.

Figure 1.7 (c) oxygen saturation of myoglobin and hemoglobin

When the protein globule coagulates, a significant part (at least half) of the hydrophobic radicals of amino acid residues is hidden from contact with the water surrounding the protein. The formation of a kind of intramolecular "hydrophobic nuclei" occurs. They are especially represented by bulky residues of leucine, isoleucine, phenylalanine, valine.

With the appearance of a tertiary structure, a protein acquires new properties - biological. In particular, the manifestation of catalytic properties is associated with the presence of a tertiary structure in the protein. Conversely, heating proteins, leading to the destruction of the tertiary structure (denaturation), also leads to the loss of biological properties.

5. Quaternary structure of proteins. The number and types of subunits, interactions between subunits, stabilizing the quaternary structure. Functional significance of the quaternary structure of proteins

Quaternary structure? it is a supramolecular formation, consisting of two or more polypeptide chains linked together non-covalently, but by hydrogen bonds, electrostatic, dipole-dipole and hydrophobic interactions between amino acid residues on the surface. An example is the hemoglobin molecule, the tobacco mosaic virus (2130 subunits).

Each of the proteins participating in the tertiary structure during the formation of the quaternary structure is called a subunit or protomer. The resulting molecule is called an oligomer or multimer. Oligomeric proteins are often built from an even number of protomers with the same or different molecular weights. In the formation of the quaternary structure of the protein, the same bonds are involved as in the formation of the tertiary structure, with the exception of covalent bonds.

The combination of protein molecules of a tertiary structure without the appearance of new biological properties is called an aggregated state. Both the quaternary structure and the aggregated state can be reversibly destroyed using detergents, in particular sodium dodecyl sulfate or non-ionic detergents such as Triton. Very often, to destroy the quaternary structure, the protein under study is heated at 100 ° C in the presence of 1% 2-mercaptoethanol and 2% sodium dodecyl sulfate. Under such conditions, -S-S-bonds between Cys residues are restored, which in some cases retain subunits of the quaternary structure. The subunits that form the quaternary structure of the protein can be different both in structure and in functional properties (heteromers). This allows you to combine several interrelated functions in one structure, to create a polyfunctional molecule. For example, in protein kinase, the stoichiometry of the worm structure of which corresponds to the formula C2R2, the C subunit is responsible for enzymatic activity, carrying out the transfer of a phosphate residue from ATP to protein; the R subunit is regulatory. In the absence of cyclic AMP, the latter is bound to the C-subunit and inhibits it. When a complex is formed with cAMP, the quaternary structure breaks down and the C-subunits are capable of phosphorylating protein substrates. In homomeric proteins, the subunits are the same.

The overwhelming majority of proteins with a quaternary structure are dimers, tetramers, and hexamers; the latter are found in proteins with a molecular weight greater than 100 kDa.

A characteristic feature of proteins with a quaternary structure is their ability to self-assemble. The interaction of protomers is carried out with high specificity, due to the formation of ten weak bonds between the contact surfaces of the subunits, therefore, errors in the formation of the quaternary structure of proteins are excluded. Almost all enzyme proteins have a quaternary structure and consist, as a rule, of an even number of protomers (two, four, six, eight). The quaternary structure of a protein implies such a combination of proteins of the tertiary structure, in which new biological properties appear that are not characteristic of a protein in a tertiary structure. In particular, such effects as cooperative and allosteric are characteristic only for proteins with a quaternary structure. The quaternary structure is the last level in the organization of a protein molecule, and it is not necessary - up to half of the known proteins do not have it.

Literature

protein biophysics polypeptide

1. Biochemistry and molecular biology. Version 1.0 [Electronic resource]: lecture notes / N.М. Titova, A.A. Savchenko, T.N. Zamay and others - Electron. Dan. (10 Mb). - Krasnoyarsk: IPK SFU, 2008.

2 Revin V.V. Biophysics: Textbook / V.V. Revin, G.V. Maximov, O.R. Coles; Edited by prof. A.B. Rubina.-Saransk: Publishing house of Mordov. University, 2002. 156 s.

3. M.V. Volkenstein. Biophysics M .: Nauka, 1988.-592 p.

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α-Helix

This structure is a right-handed spiral formed by hydrogen links between peptide groups 1st and 4th, 4th and 7th, 7th and 10th and so on amino acid residues.

Spiral formation is prevented proline and hydroxyproline, which, due to their cyclic structure, cause a chain break, i. e. its forced bending as, for example, in collagen.

The helix turn height is 0.54 nm and corresponds to the height of 3.6 amino acid residues, 5 full turns correspond to 18 amino acids and occupy 2.7 nm.

β-pleated layer

In this method of folding, the protein molecule lies like a "snake", distant segments of the chain are close to each other. As a result, peptide groups of previously removed amino acids of the protein chain are able to interact using hydrogen bonds.

Secondary structure Is the spatial arrangement of the polypeptide chain in the form of an α-helix or β-folding, regardless of the types of side radicals and their conformation.

L. Pauling and R. Corey proposed a model of the secondary structure of a protein in the form of an α-helix, in which hydrogen bonds are closed between each first and fourth amino acid, which allows you to preserve the native structure of the protein, perform the simplest functions, and protect against destruction. All peptide groups take part in the formation of hydrogen bonds, which ensures maximum stability, reduces hydrophilicity and increases the hydrophobicity of the protein molecule. The α-helix forms spontaneously and is the most stable conformation corresponding to the minimum free energy.

The most common element of the secondary structure is the right α-helix (α R). The peptide chain bends helically here. Each turn has 3.6 amino acid residues, the pitch of the screw, i.e. the minimum distance between two equivalent points is 0.54 nm; The α-helix is stabilized by almost linear hydrogen bonds between the NH-group and the CO-group of the fourth amino acid residue. Thus, in extended helical regions, each amino acid residue takes part in the formation of two hydrogen bonds. Non-polar or amphiphilic α-helices with 5-6 turns often provide anchoring of proteins in biological membranes (transmembrane helices). The left α-helix (α L), mirror-symmetric with respect to the α R-helix, is extremely rare in nature, although it is energetically possible. The twisting of the protein polypeptide chain into a helical structure occurs due to the interaction between the oxygen of the carbonyl group of the i-th amino acid residue and the hydrogen of the amido group (i + 4) - amino acid residue through the formation of hydrogen bonds (Figure 6.1).

Rice. 6.1. Protein secondary structure: α-helix

Along with α-helices, β-structures and β-bending are also involved in the formation of the secondary structure of the protein.

In contrast to the condensed α-helix, the β-layers are almost completely elongated and can be located both parallel and antiparallel (Fig. 6.2).

Figure 6.2. Parallel (a) and antiparallel (b) arrangement of β-layers

In the folded structures, transverse interchain hydrogen bonds are also formed (Figure 6.3). If the chains are oriented in opposite directions, the structure is called an antiparallel folded sheet (β α); if the chains are oriented in one direction, the structure is called a parallel folded sheet (β n). In folded structures, α-С-atoms are located at the bends, and the side chains are oriented almost perpendicular to the median plane of the sheet, alternately up and down. The β α -fold structure with almost linear H-bridges turns out to be energetically preferable. In stretched folded sheets, individual chains are most often not parallel, but somewhat curved relative to each other.

Figure 6.3. β-fold structure

In addition to the regular ones, there are also irregular secondary structures in the polypeptide chains, i.e. standard structures that do not form long periodic systems. These are β-bends, they are called so because they often pull together the tops of neighboring β-strands in antiparallel β-hairpins). The bends usually include about half of the residues that have not fallen into the regular structures of proteins.

Super secondary structure Is more high level organization of a protein molecule, represented by an ensemble of interacting secondary structures.

Secondary structure Is the spatial arrangement of the polypeptide chain in the form of an α-helix or β-folding, regardless of the types of side radicals and their conformation.

Rice. 6.1. Protein secondary structure: α-helix

Along with α-helices, β-structures and β-bending are also involved in the formation of the secondary structure of the protein.

In contrast to the condensed α-helix, the β-layers are almost completely elongated and can be located both parallel and antiparallel (Fig. 6.2).

Figure 6.2. Parallel (a) and antiparallel (b) arrangement of β-layers

In the folded structures, transverse interchain hydrogen bonds are also formed (Figure 6.3). If the chains are oriented in opposite directions, the structure is called an antiparallel folded sheet (β α); if the chains are oriented in one direction, the structure is called a parallel folded sheet (β n). In folded structures, the α-C atoms are located at the bends, and the side chains are oriented almost perpendicular to the median plane of the sheet, alternately up and down. The β α -fold structure with almost linear H-bridges turns out to be energetically preferable. In stretched folded sheets, individual chains are most often not parallel, but somewhat curved relative to each other.

Figure 6.3. β-fold structure

In addition to the regular ones, there are also irregular secondary structures in the polypeptide chains, i.e. standard structures that do not form long periodic systems. These are β-bends, they are called so because they often pull together the tops of adjacent β-strands in antiparallel β-hairpins). The bends usually include about half of the residues that have not fallen into the regular structures of proteins.

Super secondary structure Is a higher level of organization of a protein molecule, represented by an ensemble of interacting secondary structures:

1. α-helix - two antiparallel regions that interact with hydrophobic complementary surfaces (according to the "trough-protrusion" principle);

2. supercoiling of the α-helix;

3. βхβ - two parallel sections of the β-chain;

4. β-zigzag.

There are various ways of folding the protein chain (Fig. 6.5). Figure 6.5 is taken from the cover of the 1977 Nature magazine (v.268, no. 5620), where an article by J. Richardson on the motives of protein chain folding was published.

Domain- a compact globular structural unit within a polypeptide chain. Domains can perform different functions and undergo folding into independent compact globular structural units connected by flexible regions within the protein molecule.

Primary structure- a certain sequence of nucleotides in the chain. Formed by phosphodiester bonds. The beginning of the chain is the 5 "-end (at its end there is a phosphate residue), the end, the end of the chain, is designated as the 3" (OH) -end.

As a rule, nitrogenous bases are not involved in the formation of the chain itself, but hydrogen bonds between complementary nitrogenous bases play an important role in the formation of the secondary structure of NC:

2 hydrogen bonds are formed between adenine and uracil in RNA or adenine and thymine in DNA,

· Between guanine and cytosine - 3.

The NC is characterized by a linear rather than a branched structure. In addition to the primary and secondary structure, most NCs are characterized by a tertiary structure - for example, DNA, tRNA, and rRNA.

RNA (ribonucleic acids). RNA is contained in the cytoplasm (90%) and the nucleus. By structure and function, RNA is divided into 4 types:

1) tRNA (transport),

2) rRNA (ribosomal),

3) mRNA (matrix),

4) nRNA (nuclear).

Matrix RNAs. They account for no more than 5% of the total RNA of the cell. Synthesized in the nucleus. This process is called transcription. It is a copy of a gene of one of the DNA strands. During protein biosynthesis (this process is called translation) it enters the cytoplasm and binds to the ribosome, where protein biosynthesis takes place. The mRNA contains information about the primary structure of the protein (the sequence of amino acids in the chain), i.e. the sequence of nucleotides in mRNA completely corresponds to the sequence of amino acid residues in the protein. The 3 nucleotides encoding 1 amino acid are called a codon.

Properties of the genetic code. The collection of codons makes up the genetic code. There are 64 codons in the code, 61 are sense codons (they correspond to a certain amino acid), 3 are nonsense codons. They do not correspond to any amino acid. These codons are called termination codons, as they signal the completion of protein synthesis.

6 properties of the genetic code:

1) tripletness(each amino acid in a protein is encoded as a sequence of 3 nucleotides),

2) versatility(the same for all types of cells - bacterial, animal and plant),

3) unambiguity(1 codon corresponds only to 1 amino acid),

4) degeneracy(1 amino acid can be encoded by several codons; only 2 amino acids - methionine and tryptophan each have 1 codon, the rest - 2 or more),

5) continuity(genetic information is read by 3 codons in the 5 "®3" direction without interruption),

6) collinearity(correspondence of the sequence of nucleotides in mRNA to the sequence of amino acid residues in the protein).

Primary structure of mRNA

A polynucleotide chain in which 3 main regions are distinguished:

1) pretranslated,

2) broadcast,

3) post-broadcast.

The pre-translated area contains 2 sections:

a) CEP-site - performs a protective function (ensures the preservation of genetic information);

b) AG-region - the place of attachment to the ribosome during protein biosynthesis.

The translated region contains genetic information about the structure of one or more proteins.

The post-translated region is represented by a sequence of nucleotides containing adenine (from 50 to 250 nucleotides), therefore it is called a poly-A region. This part of the mRNA has 2 functions:

a) protective,

b) serves as a "ticket" during protein biosynthesis, since after a single use several nucleotides are cleaved from the mRNA from the poly-A region. Its length determines the frequency of use of mRNA in protein biosynthesis. If mRNA is used only once, then it does not have a poly-A region, and its 3 "end is terminated by 1 or more hairpins. These hairpins are called fragments of instability.

As a rule, messenger RNA has no secondary and tertiary structure (at least nothing is known about this).

Transport RNAs. Make up 12-15% of all RNA in the cell. The number of nucleotides in the chain is 75-90.

Primary structure- polynucleotide chain.

Secondary structure- to designate it, R. Holly's model is used, which is called a "clover leaf", has 4 loops and 4 shoulders:

Acceptor site - the place of attachment of an amino acid, has the same CCA sequence in all tRNAs

Legend:

I - acceptor arm, 7 base pairs,

II - dihydrouridyl arm (3-4 pairs of nucleotides) and dihydrouridyl loop (D-loop),

III - pseudouridyl arm (5 base pairs) and pseudouridyl loop (Tψ-loop),

IV - anticodon arm (5 base pairs),

V - anti-codon loop,

VI - additional loop.

Hinge functions:

anti-codon loop - recognizes the mRNA codon,
D-loop - for interaction with an enzyme during protein biosynthesis,
TY-loop - for temporary attachment to the ribosome during protein biosynthesis,
an additional loop is used to balance the secondary structure of tRNA.

Tertiary structure- in prokaryotes in the form of a spindle (the D-shoulder and TY-shoulder roll around and form a spindle), in eukaryotes in the form of an inverted letter L.

The biological role of tRNA:

1) transport (delivers the amino acid to the site of protein synthesis, to the ribosome),

2) adapter (recognizes the mRNA codon), translates the cipher of the nucleotide sequence in the mRNA into the sequence of amino acids in the protein.

Ribosomal RNA, ribosomes. They account for up to 80% of the total RNA of the cell. Form a "skeleton", or the backbone of the ribosomes. Ribosomes are nucleoprotein complexes consisting of a large amount of rRNA and proteins. These are "factories" for protein biosynthesis in the cell.

Primary structure rRNA - polynucleotide chain.

According to the molecular weight and the number of nucleotides in the chain, 3 types of rRNA are distinguished:

high molecular weight (about 3000 nucleotides);
medium molecular weight (up to 500 nucleotides);
low molecular weight (less than 100 nucleotides).

To characterize various rRNAs and ribosomes, it is customary to use not the molecular weight and the number of nucleotides, but sedimentation coefficient (this is the settling rate in the ultracentrifuge). The sedimentation coefficient is expressed in swedberg (S),

1 S = 10-13 seconds.

For example, one of the high molecular weight will have a sedimentation coefficient of 23 S, medium and low molecular weight, respectively, 16 and 5 S.

Secondary structure of rRNA- partial spiralization due to hydrogen bonds between complementary nitrogenous bases, the formation of hairpins and loops.

Tertiary structure rRNA - more compact packing and overlapping of hairpins in the form of a V- or U-shape.

Ribosomes consist of 2 subunits - small and large.

In prokaryotes, the small subunit will have a sedimentation coefficient of 30 S, the large one - 50 S, and the entire ribosome - 70 S; in eukaryotes, respectively, 40, 60, and 80 S.

Composition, structure and biological role of DNA. In viruses, as well as in mitochondria, 1-stranded DNA, in other cells - 2-stranded, in prokaryotes - 2-stranded circular.

DNA composition- a strict ratio of nitrogenous bases in 2 DNA strands is observed, which are determined by the Chargaf Rules.

Chargaf's rules:

The number of complementary nitrogenous bases is equal to (A = T, G = C).
The molar fraction of purines is equal to the molar fraction of pyrimidines (A + G = T + C).
The number of 6-keto bases is equal to the number of 6-amino bases.
The ratio G + C / A + T is the coefficient of species specificity. For animal and plant cells< 1, у микроорганизмов колеблется от 0,45 до 2,57.

In microorganisms, the HC-type predominates, the AT-type is characteristic of vertebrates, invertebrates, and plant cells.

Primary structure - 2 polynucleotide, antiparallel chains (see the primary structure of the NC).

Secondary structure- is represented by a 2-chain spiral, inside of which the complementary nitrogenous bases are stacked in the form of “stacks of coins”. The secondary structure is held by two types of bonds:

hydrogen - they act horizontally, between complementary nitrogenous bases (between A and T 2 bonds, between G and C - 3),
forces of hydrophobic interaction - these bonds arise between substituents of nitrogenous bases and act vertically.

Secondary structure characterized by:

the number of nucleotides in the helix,
spiral diameter, spiral pitch,
the distance between the planes formed by a pair of complementary bases.

There are 6 known conformations of the secondary structure, which are designated by capital letters of the Latin alphabet: A, B, C, D, E and Z. A, B and Z conformations are typical for cells, the rest are for cell-free systems (for example, in a test tube). These conformations differ in basic parameters; mutual transition is possible. The conformation state largely depends on:

the physiological state of the cell,
pH of the medium,
the ionic strength of the solution,
actions of various regulatory proteins, etc.

For example, V- DNA confomation takes place during cell division and DNA duplication, A-conformation - during transcription. The Z-structure is left-handed, the rest are right-handed. The Z-structure can also be found in the cell at the DNA regions where the G-C dinucleotide sequences are repeated.

For the first time, the secondary structure was mathematically calculated and modeled by Watson and Crick (1953), for which they received Nobel Prize... As it turned out later, the model presented by them corresponds to B-conformations.

Its main parameters:

10 nucleotides per turn,
helix diameter 2 nm,
helix pitch 3.4 nm,
distance between the planes of the bases 0.34 nm,
right-handed.

During the formation of the secondary structure, 2 types of grooves are formed - large and small (respectively, 2.2 and 1.2 nm wide). Greater grooves play an important role in the functioning of DNA, since regulatory proteins that have zinc fingers as a domain are attached to them.

Tertiary structure- in prokaryotes, the supercoil, in eukaryotes, including humans, has several levels of packing:

nucleosomal,
fibrillar (or solenoid),
chromatin fiber,
looped (or domain),
superdomain (it is this level that can be seen in an electron microscope in the form of a transverse striation).

Nucleosomal. The nucleosome (opened in 1974) is a disk-shaped particle, 11 nm in diameter, which consists of a histone octamer, around which double-stranded DNA makes 2 incomplete turns (1.75 turns).

Histones are low molecular weight proteins, each containing 105-135 amino acid residues, in histone H1 - 220 amino acid residues, up to 30% are lys and arg.

The histone octamer is called the cortex. It consists of a central tetramer H32-H42 and two dimers H2A-H2B. These 2 dimers stabilize the structure and firmly bind 2 DNA half-turns. The distance between nucleosomes is called a linker, which can contain up to 80 nucleotides. Histone H1 prevents the unwinding of DNA around the core and ensures a decrease in the distance between nucleosomes, i.e., it participates in the formation of fibrilla (2nd level of folding of the tertiary structure).

When the fibril is twisted, chromatin fiber(3rd level), while one turn usually contains 6 g nucleosomes, the diameter of such a structure increases to 30 nm.

In interphase chromosomes, chromatin fibers are organized in domains, or loops, consisting of 35-150 thousand base pairs and anchored on the intranuclear matrix. DNA-binding proteins are involved in the formation of loops.

Superdomain level form up to 100 loops, in these regions of the chromosome in an electron microscope condensed densely packed DNA regions are clearly visible.

Thanks to this packing, the DNA is compactly packed. Its length is reduced by a factor of 10,000. As a result of packaging, DNA binds to histones and other proteins, forming a nucleoprotein complex in the form of chromatin.

The biological role of DNA:

storage and transmission of genetic information,
control of cell division and functioning,
genetic control of programmed cell death.

Chromatin contains DNA (30% of the total mass of chromatin), RNA (10%) and proteins (histone and non-histone).

Sample options test work on this topic

Characteristics, b-structure, b-bend. Supersecondary (supra-secondary) protein structures