Secondary structure is the way a polypeptide chain is arranged into an ordered structure. The secondary structure is determined by the primary structure. Since the primary structure is genetically determined, the formation of a secondary structure can occur when the polypeptide chain leaves the ribosome. The secondary structure is stabilized hydrogen bonds, which are formed between the NH and CO groups of peptide bonds.
Distinguish a-helix, b-structure and disordered conformation (clew).
Structure α-helices was proposed Pauling And Corey(1951). This is a type of protein secondary structure that looks like a regular helix (Fig. 2.2). An α-helix is a rod-shaped structure in which the peptide bonds are located inside the helix and the side chain amino acid radicals are located outside. The a-helix is stabilized by hydrogen bonds, which are parallel to the helix axis and occur between the first and fifth amino acid residues. Thus, in extended helical regions, each amino acid residue takes part in the formation of two hydrogen bonds.
Rice. 2.2. Structure of an α-helix.
There are 3.6 amino acid residues per turn of the helix, the helix pitch is 0.54 nm, and there are 0.15 nm per amino acid residue. The helix angle is 26°. The regularity period of an a-helix is 5 turns or 18 amino acid residues. The most common are right-handed a-helices, i.e. The spiral twists clockwise. The formation of an a-helix is prevented by proline, amino acids with charged and bulky radicals (electrostatic and mechanical obstacles).
Another spiral shape is present in collagen . In the mammalian body, collagen is the quantitatively predominant protein: it makes up 25% of the total protein. Collagen is present in various forms, primarily in connective tissue. It is a left-handed helix with a pitch of 0.96 nm and 3.3 residues per turn, flatter than the α-helix. Unlike the α-helix, the formation of hydrogen bridges is impossible here. Collagen has an unusual amino acid composition: 1/3 is glycine, approximately 10% proline, as well as hydroxyproline and hydroxylysine. The last two amino acids are formed after collagen biosynthesis by post-translational modification. In the structure of collagen, the gly-X-Y triplet is constantly repeated, with position X often occupied by proline, and position Y by hydroxylysine. There is good evidence that collagen is ubiquitously present as a right-handed triple helix twisted from three primary left-handed helices. In a triple helix, every third residue ends up in the center, where, for steric reasons, only glycine fits. The entire collagen molecule is about 300 nm long.
b-Structure(b-folded layer). It is found in globular proteins, as well as in some fibrillar proteins, for example, silk fibroin (Fig. 2.3).
Rice. 2.3. b-Structure
The structure has flat shape. The polypeptide chains are almost completely elongated, rather than tightly twisted, as in an a-helix. The planes of peptide bonds are located in space like uniform folds of a sheet of paper. It is stabilized by hydrogen bonds between the CO and NH groups of peptide bonds of adjacent polypeptide chains. If the polypeptide chains forming the b-structure go in the same direction (i.e. the C- and N-termini coincide) – parallel b-structure; if in the opposite - antiparallel b-structure. The side radicals of one layer are placed between the side radicals of another layer. If one polypeptide chain bends and runs parallel to itself, then this antiparallel b-cross structure. Hydrogen bonds in the b-cross structure are formed between the peptide groups of the loops of the polypeptide chain.
The content of a-helices in proteins studied to date is extremely variable. In some proteins, for example, myoglobin and hemoglobin, the a-helix underlies the structure and accounts for 75%, in lysozyme - 42%, in pepsin only 30%. Other proteins, for example, the digestive enzyme chymotrypsin, are practically devoid of an a-helical structure and a significant part of the polypeptide chain fits into layered b-structures. Supporting tissue proteins collagen (tendon and skin protein), fibroin (natural silk protein) have a b-configuration of polypeptide chains.
It has been proven that the formation of α-helices is facilitated by glu, ala, leu, and β-structures by met, val, ile; in places where the polypeptide chain bends - gly, pro, asn. It is believed that six clustered residues, four of which contribute to the formation of the helix, can be considered as the center of helicalization. From this center there is a growth of helices in both directions to a section - a tetrapeptide, consisting of residues that prevent the formation of these helices. During the formation of the β-structure, the role of primers is performed by three out of five amino acid residues that contribute to the formation of the β-structure.
In most structural proteins, one of the secondary structures predominates, which is determined by their amino acid composition. A structural protein constructed primarily in the form of an α-helix is α-keratin. Animal hair (fur), feathers, quills, claws and hooves are composed primarily of keratin. As a component of intermediate filaments, keratin (cytokeratin) is an essential component of the cytoskeleton. In keratins, most of the peptide chain is folded into a right-handed α-helix. Two peptide chains form a single left super spiral. Supercoiled keratin dimers combine into tetramers, which aggregate to form protofibrils with a diameter of 3 nm. Finally, eight protofibrils form microfibrils with a diameter of 10 nm.
Hair is built from the same fibrils. Thus, in a single wool fiber with a diameter of 20 microns, millions of fibrils are intertwined. Individual keratin chains are cross-linked by numerous disulfide bonds, which gives them additional strength. During perm, the following processes occur: first, disulfide bridges are destroyed by reduction with thiols, and then, to give the hair the required shape, it is dried by heating. At the same time, due to oxidation by air oxygen, new disulfide bridges are formed, which retain the shape of the hairstyle.
Silk is obtained from the cocoons of silkworm caterpillars ( Bombyx mori) and related species. The main protein of silk, fibroin, has the structure of an antiparallel folded layer, and the layers themselves are located parallel to each other, forming numerous layers. Since in folded structures the side chains of amino acid residues are oriented vertically up and down, only compact groups can fit in the spaces between the individual layers. In fact, fibroin consists of 80% glycine, alanine and serine, i.e. three amino acids characterized by minimal side chain sizes. The fibroin molecule contains a typical repeating fragment (gli-ala-gli-ala-gli-ser)n.
Disordered conformation. Regions of a protein molecule that do not belong to helical or folded structures are called disordered.
Suprasecondary structure. Alpha helical and beta structural regions in proteins can interact with each other and with each other, forming assemblies. The supra-secondary structures found in native proteins are energetically the most preferable. These include a supercoiled α-helix, in which two α-helices are twisted relative to each other, forming a left-handed superhelix (bacteriorhodopsin, hemerythrin); alternating α-helical and β-structural fragments of the polypeptide chain (for example, Rossmann's βαβαβ link, found in the NAD + -binding region of dehydrogenase enzyme molecules); the antiparallel three-stranded β structure (βββ) is called β-zigzag and is found in a number of microbial, protozoan, and vertebrate enzymes.
The name “squirrels” comes from the ability of many of them to turn white when heated. The name "proteins" comes from the Greek word for "first", indicating their importance in the body. The higher the level of organization of living beings, the more diverse the composition of proteins.
Proteins are formed from amino acids, which are linked together by covalent bonds. peptide bond: between the carboxyl group of one amino acid and the amino group of another. When two amino acids interact, a dipeptide is formed (from the residues of two amino acids, from the Greek. peptos– cooked). Replacement, exclusion or rearrangement of amino acids in a polypeptide chain causes the emergence of new proteins. For example, when replacing only one amino acid (glutamine with valine), a serious disease occurs - sickle cell anemia, when red blood cells have a different shape and cannot perform their main functions (oxygen transport). When a peptide bond is formed, a water molecule is split off. Depending on the number of amino acid residues, they are distinguished:
– oligopeptides (di-, tri-, tetrapeptides, etc.) – contain up to 20 amino acid residues;
– polypeptides – from 20 to 50 amino acid residues;
– squirrels – over 50, sometimes thousands of amino acid residues
Based on their physicochemical properties, proteins are distinguished between hydrophilic and hydrophobic.
There are four levels of organization of the protein molecule - equivalent spatial structures (configurations, conformation) proteins: primary, secondary, tertiary and quaternary.
Primary the structure of proteins is the simplest. It has the form of a polypeptide chain, where amino acids are linked to each other by a strong peptide bond. Determined by the qualitative and quantitative composition of amino acids and their sequence.
Secondary structure of proteins
Secondary the structure is formed predominantly by hydrogen bonds that were formed between the hydrogen atoms of the NH group of one helix curl and the oxygen atoms of the CO group of the other and are directed along the spiral or between parallel folds of the protein molecule. The protein molecule is partially or entirely twisted into an α-helix or forms a β-sheet structure. For example, keratin proteins form an α-helix. They are part of hooves, horns, hair, feathers, nails, and claws. The proteins that make up silk have a β-sheet. Amino acid radicals (R-groups) remain outside the helix. Hydrogen bonds are much weaker than covalent bonds, but with a significant number of them they form a fairly strong structure.
Functioning in the form of a twisted spiral is characteristic of some fibrillar proteins - myosin, actin, fibrinogen, collagen, etc.
Protein tertiary structure
Tertiary protein structure. This structure is constant and unique for each protein. It is determined by the size, polarity of R-groups, shape and sequence of amino acid residues. The polypeptide helix is twisted and folded in a certain way. The formation of the tertiary structure of a protein leads to the formation of a special configuration of the protein - globules (from Latin globulus - ball). Its formation is determined by different types of non-covalent interactions: hydrophobic, hydrogen, ionic. Disulfide bridges appear between cysteine amino acid residues.
Hydrophobic bonds are weak bonds between non-polar side chains that result from the mutual repulsion of solvent molecules. In this case, the protein twists so that the hydrophobic side chains are immersed deep inside the molecule and protect it from interaction with water, while the hydrophilic side chains are located outside.
Most proteins have a tertiary structure - globulins, albumins, etc.
Quaternary protein structure
Quaternary protein structure. Formed as a result of the combination of individual polypeptide chains. Together they form a functional unit. There are different types of bonds: hydrophobic, hydrogen, electrostatic, ionic.
Electrostatic bonds occur between electronegative and electropositive radicals of amino acid residues.
Some proteins are characterized by a globular arrangement of subunits - this is globular proteins. Globular proteins easily dissolve in water or salt solutions. Over 1000 known enzymes belong to globular proteins. Globular proteins include some hormones, antibodies, and transport proteins. For example, the complex molecule of hemoglobin (red blood cell protein) is a globular protein and consists of four globin macromolecules: two α-chains and two β-chains, each of which is connected to heme, which contains iron.
Other proteins are characterized by association into helical structures - this is fibrillar (from Latin fibrilla - fiber) proteins. Several (3 to 7) α-helices are twisted together, like fibers in a cable. Fibrillar proteins are insoluble in water.
Proteins are divided into simple and complex.
Simple proteins (proteins)
Simple proteins (proteins) consist only of amino acid residues. Simple proteins include globulins, albumins, glutelins, prolamins, protamines, pistons. Albumins (for example, serum albumin) are soluble in water, globulins (for example, antibodies) are insoluble in water, but soluble in aqueous solutions of certain salts (sodium chloride, etc.).
Complex proteins (proteids)
Complex proteins (proteids) include, in addition to amino acid residues, compounds of a different nature, which are called prosthetic group. For example, metalloproteins are proteins containing non-heme iron or linked by metal atoms (most enzymes), nucleoproteins are proteins connected to nucleic acids (chromosomes, etc.), phosphoproteins are proteins that contain phosphoric acid residues (egg proteins yolk, etc.), glycoproteins - proteins combined with carbohydrates (some hormones, antibodies, etc.), chromoproteins - proteins containing pigments (myoglobin, etc.), lipoproteins - proteins containing lipids (included in the composition of membranes).
For every protein, in addition to the primary one, there is also a certain secondary structure. Usually a protein molecule resembles an extended spring.
This is the so-called a-helix, stabilized by many hydrogen bonds that arise between CO and NH groups located nearby. Hydrogen atom of NH group one amino acid forms such a bond with the oxygen atom of the CO group of another amino acid, separated from the first by four amino acid residues.
Thus amino acid 1 turns out to be connected to amino acid 5, amino acid 2 to amino acid 6, etc. X-ray structural analysis shows that there are 3.6 amino acid residues per turn of the helix.
Fully a-helical conformation and, therefore, keratin protein has a fibrillar structure. It's structural protein hair, wool, nails, beak, feathers and horns, which is also part of the skin of vertebrates.
Hardness and keratin stretchability vary depending on the number of disulfide bridges between adjacent polypeptide chains (the degree of cross-linking of the chains).
Theoretically, all CO and NH groups can participate in the formation hydrogen bonds, so the α-helix is a very stable and therefore very common conformation. Sections of the α-helix in the molecule resemble rigid rods. However, most proteins exist in a globular form, which also contains regions (3-layers (see below) and regions with an irregular structure.
This is explained by the fact that education hydrogen bonds a number of factors hinder this: the presence of certain amino acid residues in the polypeptide chain, the presence of disulfide bridges between different sections of the same chain, and, finally, the fact that the amino acid proline is generally incapable of forming hydrogen bonds.
Beta Layer, or folded layer is another type of secondary structure. The silk protein fibroin, secreted by the silk-secreting glands of silkworm caterpillars when curling cocoons, is represented entirely in this form. Fibroin consists of a number of polypeptide chains that are more elongated than chains with an alpha conformation. spirals.
These chains are laid in parallel, but neighboring chains are opposite in direction to each other (antiparallel). They are connected to each other using hydrogen bonds, arising between the C=0- and NH-groups of neighboring chains. In this case, all NH and C=0 groups also take part in the formation of hydrogen bonds, i.e. the structure is also very stable.
This conformation of polypeptide chains is called beta conformation, and the structure as a whole is a folded layer. It has high tensile strength and cannot be stretched, but this organization of polypeptide chains makes silk very flexible. In globular proteins, the polypeptide chain can fold on itself, and then at these points of the globule regions appear that have the structure of a folded layer.
Another method of organizing polypeptide chains we find in the fibrillar protein collagen. This is also a structural protein that, like keratin and fibroin, has high tensile strength. Collagen has three polypeptide chains twisted together, like strands in a rope, forming a triple helix. Each polypeptide chain of this complex helix, called tropocollagen, contains about 1000 amino acid residues. An individual polypeptide chain is free coiled spiral(but not a-helix;).
Three chains held together hydrogen bonds. Fibrils are formed from many triple helices arranged parallel to each other and held together by covalent bonds between adjacent chains. They in turn combine into fibers. The structure of collagen is thus formed in stages - at several levels - similar to the structure of cellulose. Collagen also cannot be stretched, and this property is essential for the function it performs, for example, in tendons, bones and other types of connective tissue.
Squirrels, existing only in a fully coiled form, like keratin and collagen, are an exception among other proteins.
L Due to the interaction of functional groups of amino acids, linear polypeptide chains of individual proteins acquire a certain spatial three-dimensional structure, called “conformation”. All molecules of individual proteins (i.e., those having the same primary structure) form the same conformation in solution. Consequently, all the information necessary for the formation of spatial structures is located in the primary structure of proteins.
In proteins, there are 2 main types of conformation of polypeptide chains: secondary and tertiary structures.
2. Secondary structure of proteins - spatial structure resulting from the interaction between functional groups of the peptide backbone.
In this case, peptide chains can acquire regular structures of two types: α-helices
β-structure By β-structure we mean a figure similar to a sheet folded like an accordion. The figure is formed due to the formation of many hydrogen bonds between the atoms of the peptide groups of the linear regions of one polypeptide chain making bends, or between different polypeptide groups.
Bonds are hydrogen, they stabilize individual fragments of macromolecules.
3. Tertiary structure of proteins - a three-dimensional spatial structure formed due to interactions between amino acid radicals, which can be located at a considerable distance from each other in the polypeptide chain.
Structurally consists of elements of secondary structure, stabilized by various types of interactions, in which hydrophobic interactions play a critical role
stabilization of the tertiary structure of the protein takes 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 fold so that the nonpolar side groups of amino acids are isolated from the aqueous solution; polar hydrophilic side groups appear on the surface of the molecule.
4. Quaternary structure is the relative arrangement of several polypeptide chains within a single protein complex. Protein molecules that make up a protein with a quaternary structure are formed separately on ribosomes and only after completion of synthesis form a common supramolecular structure. A protein with a quaternary structure can contain both identical and different polypeptide chains. Participate in the stabilization of the quaternary structure the same types of interactions as in the stabilization of tertiary. Supramolecular protein complexes can consist of dozens of molecules.
Role.
The formation of peptides in the body occurs within a few minutes, while chemical synthesis in the laboratory is a rather lengthy process that can take several days, and the development of synthesis technology can take several years. However, despite this, there are quite strong arguments in favor of carrying out work on the synthesis of analogues of natural peptides. First, by chemical modification of peptides it is possible to confirm the primary structure hypothesis. The amino acid sequences of some hormones became known precisely through the synthesis of their analogues in the laboratory.
Secondly, synthetic peptides allow us to study in more detail the relationship between the structure of an amino acid sequence and its activity. To clarify the relationship between the specific structure of the peptide and its biological activity, a huge amount of work was carried out on the synthesis of more than one thousand analogues. As a result, it was possible to find out that replacing just one amino acid in the structure of a peptide can increase its biological activity several times or change its direction. And changing the length of the amino acid sequence helps determine the location of the active centers of the peptide and the site of receptor interaction.
Thirdly, thanks to the modification of the original amino acid sequence, it became possible to obtain pharmacological drugs. The creation of analogues of natural peptides makes it possible to identify more “effective” configurations of molecules that enhance the biological effect or make it last longer.
Fourthly, chemical synthesis of peptides is economically beneficial. Most therapeutic drugs would cost tens of times more if they were made from a natural product.
Often, active peptides are found in nature only in nanogram quantities. Plus, methods for purifying and isolating peptides from natural sources cannot completely separate the desired amino acid sequence from peptides of the opposite or different effect. And in the case of specific peptides synthesized by the human body, they can only be obtained through synthesis in laboratory conditions.
57. Classification of proteins: simple and complex, globular and fibrillar, monomeric and oligomeric. Functions of proteins in the body.
Classification by type of structure
Based on their general type of structure, proteins can be divided into three groups:
1. Fibrillar proteins - form polymers, their structure is usually highly regular and is maintained mainly by interactions between different chains. They form microfilaments, microtubules, fibrils, and support the structure of cells and tissues. Fibrillar proteins include keratin and collagen.
2. Globular proteins are water soluble, the general shape of the molecule is more or less spherical.
3. Membrane proteins - have domains that cross the cell membrane, but parts of them protrude from the membrane into the intercellular environment and the cytoplasm of the cell. Membrane proteins function as receptors, that is, they transmit signals and also provide transmembrane transport of various substances. Transporter proteins are specific; each of them allows only certain molecules or a certain type of signal to pass through the membrane.
Simple proteins , Complex proteins
In addition to peptide chains, many proteins also contain non-amino acid groups, and according to this criterion, proteins are divided into two large groups - simple and complex proteins(proteids). Simple proteins consist only of polypeptide chains; complex proteins also contain non-amino acid, or prosthetic, groups.
Simple.
Among the globular proteins we can distinguish:
1. albumins - soluble in water over a wide pH range (from 4 to 8.5), precipitated with a 70-100% solution of ammonium sulfate;
2. polyfunctional globulins with a higher molecular weight, less soluble in water, soluble in saline solutions, often contain a carbohydrate part;
3. histones are low molecular weight proteins with a high content of arginine and lysine residues in the molecule, which determines their basic properties;
4. protamines are distinguished by an even higher arginine content (up to 85%), like histones, they form stable associates with nucleic acids, acting as regulatory and repressor proteins - an integral part of nucleoproteins;
5. prolamines are characterized by a high content of glutamic acid (30-45%) and proline (up to 15%), insoluble in water, soluble in 50-90% ethanol;
6. Glutelins contain about 45% glutamic acid, like prolamins, and are often found in cereal proteins.
Fibrillar proteins are characterized by a fibrous structure and are practically insoluble in water and saline solutions. Polypeptide chains in molecules are located parallel to one another. Participate in the formation of structural elements of connective tissue (collagens, keratins, elastins).
Complex proteins
(proteids, holoproteins) are two-component proteins that, in addition to peptide chains (simple protein), contain a non-amino acid component - a prosthetic group. When complex proteins are hydrolyzed, in addition to amino acids, the non-protein part or its breakdown products are released.
Various organic (lipids, carbohydrates) and inorganic (metals) substances can act as a prosthetic group.
Depending on the chemical nature of the prosthetic groups, the following classes are distinguished among complex proteins:
· Glycoproteins containing covalently bound carbohydrate residues as a prosthetic group and their subclass - proteoglycans, with mucopolysaccharide prosthetic groups. Hydroxyl groups of serine or threonine usually participate in the formation of bonds with carbohydrate residues. Most extracellular proteins, in particular immunoglobulins, are glycoproteins. The carbohydrate part of proteoglycans is ~95%; they are the main component of the intercellular matrix.
· Lipoproteins containing non-covalently bound lipids as a prosthetic part. Lipoproteins are formed by apolipoprotein proteins that bind lipids 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 bound DNA or RNA, in particular, chromatin, which makes up chromosomes, is a nucleoprotein.
· Phosphoproteins containing covalently bound phosphoric acid residues as a prosthetic group. Hydroxyl groups of serine or threonine participate in the formation of an ester bond with phosphate; milk casein, in particular, is a phosphoprotein:
· Chromoproteins are the collective name for complex proteins with colored prosthetic groups of various chemical natures. These include many proteins with a metal-containing porphyrin prosthetic group that perform various functions - hemoproteins (proteins containing heme as a prosthetic group - hemoglobin, cytochromes, etc.), chlorophylls; flavoproteins with a flavin group, etc.
1. Structural function
2. Protective function
3. Regulatory function
4. Alarm function
5. Transport function
6. Spare (backup) function
7. Receptor function
8. Motor (motor) function
A protein molecule of any type in its native state has a characteristic spatial structure, often called conformation. Different terms are used to refer to different levels of protein structure. The term secondary structure refers to the elongated or coiled-coil conformation of polypeptide chains. The term tertiary structure refers to the way a polypeptide chain is folded into a compact, tightly packed structure. The more general term conformation is used to simultaneously characterize the secondary and tertiary structure of a chain, i.e. its spatial configuration. The term quaternary structure refers to the method of unification (arrangement in space) of individual polypeptide chains in a protein molecule consisting of several similar chains.
As a rule, polypeptide chains of proteins contain from 100 to 300 amino acid residues. Some proteins have longer chains; these include serum albumin (about 550 residues), myosin (about 1800 residues), etc. However, if the molecular weight of a protein exceeds 50,000, there is every reason to assume that the molecule of such a protein contains at least two polypeptide chains.
Proteins are high-molecular compounds with a strictly defined chemical structure. A protein molecule consists of one or more polypeptide chains formed as a result of polycondensation of amino acids. When amino acids are combined into a protein chain, peptide bonds (-NH-CO-) are formed, with an NH+3 group at one end and a COO- group at the other.
Let's look at the structure of a peptide bond.
A special feature of the bond is that 4 atoms N,H,C,O are located in the same plane (circled area in the figure). It is known that rotation in a molecule around a single bond leads to the appearance of rotary isomers.
In proteins, rotation around the peptide C-N bond is difficult (activation energy 40 - 80 kJ/mol), because this bond has the character of a double bond and, in addition, in the peptide group there is a hydrogen bond between the C=O group and the hydrogen atom of the N-H group (with an activation energy of 20-30 kJ/mol).
Therefore, a protein can be considered as a chain of planar peptide units connected to each other. Rotation of these units is possible only around single bonds - carbon and amino acids (see figure).
The angle of rotation around the C-C bond is indicated, around the C-N bond is indicated.
Finding the most stable conformation of a protein chain requires minimizing its total energy, including the energy of intramolecular hydrogen bonds. Pauling and Curie established 2 main variants of the structure of the protein chain, which are called -helix and -form.
|
-spiral |
-form |
|
|
Rice. Orientation of hydrogen bonds in protein structure.
The spiral can be right-handed (=132o, =123o) and left-handed (=228o, =237o). -forms can be parallel (=61o, =239o) and antiparallel (=380o, =325o).
In addition, there are regions in proteins that do not form any regular structure. For example, in hemoglobin, 75% of the amino acids form right-handed α-helices, and the remaining parts of the chain are not ordered at all. Ordered regions are often called crystalline part protein molecule, and disordered areas - amorphous form squirrel.
Amorphous areas- a depot of building material, which, if necessary, is used to build ordered areas.
Polypeptide chains synthesized in the cell, formed as a result of the sequential connection of amino acid residues, are, as it were, fully unfolded protein molecules. In order for a protein to acquire its inherent functional properties, the chain must fold in space in a certain way, forming a functionally active (“native”) structure. Despite the enormous number of spatial structures theoretically possible for an individual amino acid sequence, the folding of each protein leads to the formation of a single native conformation. Thus, there must be a code that specifies the relationship between the amino acid sequence of a polypeptide chain and the type of spatial structure it forms.
It turned out that the process of protein folding in vivo can be considered neither spontaneous nor energy independent. Thanks to the highly coordinated regulatory system existing inside the cell, from the very moment of its “birth”, leaving the ribosome, it comes under the control of factors that, without changing the specific folding path (determined by the genetic code), provide optimal conditions for the implementation of rapid and efficient formation native spatial structure.
The ability of a particular section of a polypeptide chain to form a secondary structure element (for example, to fold into an a-helix) depends on the nature of the amino acid sequence of a given section of the chain. Thus, the number and location of a-helices, b-strands and loops along the polypeptide chain varies among different proteins and is determined by the genetic code. This explains the potential ability of any polypeptide chain to spontaneously fold into a unique tertiary structure.
Rice. Diagram of the spatial structure of a small protein (pancreatic trypsin inhibitor). The course of the main chain is depicted against the background of the general contour of the molecule; -helices, -strands, sharp chain rotation (t) and cysteine bridges (- - -) are highlighted. Since the protein folds itself, all this can be predicted from the primary structure of the protein alone. The side groups are not shown here, but - in principle - their location in space can also be predicted.
According to modern concepts, the process of folding has a hierarchical nature: first, elements of the secondary structure are formed very quickly (in milliseconds), serving as “seeds” for the formation of more complex architectural motifs (stage 1). The second stage (also occurring very quickly) is the specific association of some elements of the secondary structure with the formation of a supersecondary structure (this can be combinations of several a-helices, several b-chains, or mixed associates of these elements).
The formation of the native structure of proteins consisting of two or more domains is complicated by an additional stage - the establishment of specific contacts between domains. The situation becomes even more complicated when the oligomeric form of the protein is functionally active (that is, consisting of several polypeptide chains, each of which, after folding, forms a so-called subunit). In these cases, another stage is added - the establishment of contacts between subunits.
The stage of transformation of the “molten globule” into native protein is the slowest, limiting the rate of the entire process. This is due to the fact that the establishment of an “optimal set” of specific interactions that stabilize the native conformation is associated with the need for structural rearrangements that occur relatively slowly. These include cis-trans isomerization of the peptide bond preceding the proline residue. Since the trans conformation is more stable, it predominates in the newly synthesized polypeptide chain. However, for the formation of the native protein structure, it is necessary that about 7% of the bonds formed by proline residues isomerize into the cis conformation. This reaction, which results in a chain rotation of 1800 around the C-N bond, is extremely slow. In vivo, it is accelerated due to the action of a special enzyme - peptidyl-prolyl-cis/trans-isomerase.
The second enzyme, which accelerates the folding process, catalyzes the formation and isomerization of disulfide bonds. It is localized in the lumen of the endoplasmic reticulum and promotes the folding of proteins secreted by cells containing disulfide bridges (for example, insulin, ribonuclease, immunoglobulins). Rice. 3 explains the role of this enzyme in the formation of disulfide bonds that stabilize the native protein structure and in the cleavage of “wrong” S-S bridges.
Secondary structure of protein. First of all, we will talk about regular secondary structures - a-helices and b-structure.
The arrangement of a and b structures into a globule determines the tertiary structure of the protein. These secondary structures are distinguished by certain, periodic conformations of the main chain - with a variety of conformations of side groups.
Fig.. Secondary structure of the polypeptide chain (a-helix and b-sheet strand) and tertiary structure of the protein globule.
Let's start with the spirals. They can be left or right, they can have different periods and steps. Right (R) spirals come to us by curling counterclockwise (which corresponds to a positive angle in trigonometry); left (L) - come rotating in the direction of the arrow.
The most important helices in the polypeptide chain are held together by hydrogen bonds, where the C=O groups of the polypeptide backbone are linked to the H-N groups lying away from them towards the C-terminus of the chain. In principle, the following H-bonded helices are possible: 27, 310, 413 (usually called a) and 516 (also called p). Here in the name "27" - "2" means the bond with the 2nd residue in the chain, and "7" is the number of atoms in the ring (O......H-N-C"-Ca-N-C") closed by this bond. The numbers in the names of other spirals have the same meaning.
Rice. Hydrogen bonds (they are shown by arrows), characteristic of different helices.
Which of these helical structures predominate in proteins? a-helices. Why? The answer to this question is provided by the Ramachandran map for a typical amino acid residue, alanine, which shows the conformations whose periodic repetition leads to the formation of the hydrogen bonds shown in the figure.
Rice. Conformations of various secondary structures against the background of a map of allowed and prohibited conformations of amino acid residues. 27R, 27L: right and left spiral 27; 310R, 310L: right and left spiral 310; R, L - right and left -helix; R, L - right and left -helix. - -structure (for details see Fig. 7-8b). P - Poly(Pro)II helix. - conformations allowed for alanine (Ala); - areas allowed only for glycine, but not for alanine and other residues; - areas prohibited for all residues. and are the angles of internal rotation in the protein chain.
It can be seen that only the R (-right) helix lies deep enough inside the region allowed for alanine (and for all other residues). Other helices lie either at the edge of this region (for example, left-handed helix L or right-handed helix 310), where conformational stress is already increasing, or in a region accessible only to glycine. Therefore, one can expect that it is the right -helix that should, as a rule, be more stable, and therefore predominate in proteins - which is what is observed. In the right α-helix, all atoms are packed optimally: tightly, but without tension; Therefore, it is not surprising that there are many such helices in proteins, and in fibrillar proteins they reach a gigantic length and include hundreds of amino acid residues.
In the mid-1980s, a new era began in the study of mechanisms regulating protein folding in vivo. It was discovered that in the cell there is a special category of proteins, the main function of which is to ensure the correct folding of polypeptide chains into the native structure. These proteins, by binding to the unfolded or partially unfolded conformation of the polypeptide chain, prevent it from “getting confused” and forming incorrect structures. They retain the partially unfolded protein, facilitate its transfer to different subcellular formations, and also create conditions for its effective folding. These proteins are called “molecular chaperones,” figuratively reflecting their function (the English word chaperone is close in meaning to the word “governess”).