After the peptide chain leaves the ribosome, it must take its biologically active form, i.e. curl up in a certain way, tie up any groups, etc. The reactions of converting a polypeptide into an active protein are called processing or post-translational protein modification.
Post-translational modification of proteins
The main processing reactions include:
1. Deleting from the N-terminus of methionine or even several amino acids with specific aminopeptidases.
2. Education disulfide bridges between cysteine residues.
3. Partial proteolysis- removal of a part of the peptide chain, as is the case with insulin or proteolytic enzymes of the gastrointestinal tract.
4. Accession chemical group to the amino acid residues of the protein chain:
- phosphoric acids - for example, phosphorylation of the amino acids Serine, Threonine, Tyrosine is used to regulate the activity of enzymes or to bind calcium ions,
- carboxyl groups - for example, with the participation of vitamin K, γ-carboxylation of glutamate occurs in the composition of prothrombin, proconvertin, Stewart factor, Christmas, which makes it possible to bind calcium ions during the initiation of blood coagulation,
- methyl groups - for example, methylation of arginine and lysine in histones is used to regulate genome activity,
- hydroxyl groups - for example, the addition of the OH group to lysine and proline with the formation of hydroxyproline and hydroxylysine is necessary for the maturation of collagen molecules with the participation of vitamin C,
- iodine- for example, in thyroglobulin, the addition of iodine is necessary for the formation of thyroid hormone precursors iodothyronines,
5. Switching on prosthetic groups:
- carbohydrate residues - for example, glycation is required for the synthesis of glycoproteins.
- heme- for example, in the synthesis of hemoglobin, myoglobin, cytochromes, catalase,
- vitamin coenzymes - biotin, FAD, pyridoxal phosphate, etc.
6. Combining protomers into a single oligomeric protein, for example, hemoglobin, collagen, lactate dehydrogenase, creatine kinase.
Protein folding
Folding is the process of folding an elongated polypeptide chain into a regular three-dimensional spatial structure. A group of accessory proteins called chaperones ( chaperon, French - companion, nanny). They prevent the newly synthesized proteins from interacting with each other, isolate the hydrophobic regions of the proteins from the cytoplasm and "remove" them inside the molecule, and correctly arrange the protein domains.
folding, etc. "folding proteins- The process of folding a polypeptide chain into the correct spatial structure. Individual proteins, products of one gene, have an identical amino acid sequence and acquire the same conformation and function under the same conditions. for many proteins with a complex spatial structure, folding occurs with the participation of "chaperones"
Ribonuclease reactivation. the process of protein denaturation can be reversible. This discovery was made while studying ribonuclease denaturation, which cleaves bonds between nucleotides in RNA. Ribonuclease is a globular protein containing one polypeptide chain of 124 amino acid residues. Its conformation is stabilized by 4 disulfide bonds and many weak bonds.
The treatment of ribonuclease with mercaptoethanol leads to the rupture of disulfide bonds and the reduction of SH-groups of cysteine residues, which disrupts the compact structure of the protein. The addition of urea or chloridine guanidine leads to the formation of randomly folded ribonuclease-free polypeptide chains. enzyme denaturation. if, by dialysis, ribonuclease is purified from denaturing agents and mercaptoethanol, the enzymatic activity of the protein is gradually restored. This process is called renaturation.
The possibility of renewal has been proven for other proteins as well. a necessary condition for the restoration of its conformation is the integrity of the primary structure of the protein.
proteins capable of binding to proteins that are in an unstable, prone to aggregation state, capable of stabilizing their conformation, providing protein folding are called "chaperones".
Role of chaperones in protein folding
during the period of protein synthesis on the ribosome, protection of reactive radicals is carried out by III-70. The folding of many high-molecular proteins with a complex conformation is carried out in the space formed by III-60. III-60 function as an oligomeric complex consisting of 14 subunits. The chaperone complex has a high affinity for proteins, on the surface of which there are areas enriched with hydrophobic radicals). Once in the cavity of the chaperone complex, the protein binds to hydrophobic radicals in the apical regions of III-60.
The role of chaperones in the protection of cell proteins from denaturing stress effects
Chaperones involved in the protection of cellular proteins from denaturing influences are referred to as heat shock proteins. Under the action (high temperature, hypoxia, infection, UV, change in pH of the medium, change in the molarity of the medium, the effect of toxic chemicals, heavy metals) in cells, the synthesis of HSP is enhanced. ... they can prevent their complete denaturation and restore the native conformation of proteins.
Diseases associated with impairment
folding proteins Alzheimer's disease- amyloidosis of the nervous system, which affects the elderly and is characterized by progressive memory impairment and complete personality degradation. Amyloid, a protein that forms insoluble fibrils that disrupt the structure and function of nerve cells, is deposited in the brain tissue.
Prion proteins a special class of proteins with infectious properties. Once in the human body, they are capable of causing severe, incurable diseases of the central nervous system, called prion diseases. The prion protein is encoded by the same gene as its normal analogue, i.e. they have an identical primary structure. However, the two proteins have different conformation: the prion protein is characterized by a high content of β-layers, while the normal protein has many helical regions. the prion protein is resistant to proteases.
An amazing game was developed by scientists from the University of Washington (USA). A program called Fold.it is a model for folding proteins into three-dimensional constructs. The gamer should try to do this in the best possible way. The program will be loaded with real data about real, just invented proteins, which are unclear how they fold. The results will be sent via the Internet to the processing center, where they will be checked on a supercomputer (this will be in the fall, but for now, the program contains already solved riddles, so now it acts as a simulator).
In fact, all gamers in our world spend billions of man-hours on games that are useless for humanity like WoW, Counter-Strike or Klondike Solitaire. At the same time, they could use their intelligence more effectively: for example, by folding proteins on their monitor screen. This is also interesting in its own way.
One of the game's developers, professor of biochemistry David Baker, truly believes that somewhere in the world there are talents who have the innate ability to calculate 3D protein models in their minds. Some 12-year-old boy from Indonesia will see the game and will be able to solve problems that even a supercomputer cannot do. Who knows, maybe there really are such people?
Each protein (there are more than 100,000 species in the human body) is a long molecule. To predict in what intricate shape this molecule will fold under certain conditions (and whether it is capable of folding into any stable shape at all) is a task of the highest degree of complexity. Computer simulation is a resource-intensive process, but at the same time critical in pharmaceuticals. After all, without knowing the form of a protein, it is impossible to simulate its properties. If these properties are useful, then proteins can be synthesized and based on them, new effective drugs can be made, for example, for the treatment of cancer or AIDS (the Nobel Prize is guaranteed in both cases).
Currently, hundreds of thousands of computers in a distributed computing network are working on calculating a model of each new protein molecule, but scientists from the University of Washington propose another way: not a dull enumeration of all options, but intellectual brainstorming through a computer game. The number of options is reduced by an order of magnitude, and the supercomputer will find the correct folding parameters much faster.
Everyone can play the three-dimensional "fun" Fold.it: even children and secretaries who have no idea about molecular biology. The developers tried to make such a game so that it would be interesting to everyone. And the result of the game may well become the basis for the Nobel Prize and save the lives of thousands of people.
The program is released in versions for Win and Mac. A distribution kit of 53 MB can be
Every cell in our body is a protein factory. Some of them are produced for internal use, to support the life of the cell, and the other part is “exported”. All properties of protein molecules (including the ability to amazingly accurately catalyze the transformation of other molecules in the cell) depend on the spatial structure of the protein, and the structure of each protein is unique.
The spatial structure is formed by a unique folding of the protein chain, consisting of different amino acid residues (beads of different colors - Fig. 1). The sequence of amino acids in the protein chain is determined by its genome and is synthesized by the ribosome, after which the spatial structure of the chain is formed "by itself" during the folding of the protein chain, which leaves the ribosome still practically disordered.
The formation of a unique protein globule from a disordered chain (as well as its unfolding) requires overcoming the “barrier” in the form of an unstable “semi-folded” globule (Fig. 1)
Alexey FinkelsteinThis chain of interaction of its amino acids is folded, and into the same structure - both in the body and in the test tube. The variety of possible layouts of the same chain is unimaginably great. But a given sequence of amino acids, as a rule, has only one stable ("correct") structure, which gives the protein its unique properties. It is stable because it is she who has the minimum energy.
The same principle works during the formation of crystals: the substance acquires the structure, the bond energy in which is minimal.
What protein and the universe have in common
Here the question arose before scientists: how can a protein chain spontaneously "find" its only stable structure if the search for a colossal number of all variants (about 10 100 for a chain of 100 amino acid residues) would take more time than the lifetime of the Universe. This "Levinthal's paradox", formulated half a century ago, has been resolved only now. To solve it, it was necessary to involve the methods of theoretical physics.
Crystals of various proteins grown on the Mir space station and during NASA shuttle flights
NASA Marshall Space Flight CenterScientists from the Institute of Protein of the Russian Academy of Sciences (IB) have created a theory of the rates of formation of spatial structures of protein molecules. The results of the work were recently published in journals Atlas of Science , Chem Phys Chem and "Biophysics"... Work supported by by a grant from the Russian Science Foundation (RSF).
“The ability of proteins to spontaneously form their spatial structures in a matter of seconds or minutes is a long-standing mystery in molecular biology.
In our work, a physical theory is presented that makes it possible to estimate the rate of this process depending on the size of proteins and the complexity of their structure, "- a corresponding member of the Russian Academy of Sciences, Doctor of Physical and Mathematical Sciences, Chief Researcher of the Institute of Protein of the Russian Academy of Sciences, head of the Russian Science Foundation grant begins. Alexey Finkelstein.
“It has long been known that a protein chain acquires its unique structure under certain environmental conditions, while under other conditions (for example, when a solution is acidified or heated), this structure unfolds. At the junction of these conditions, the unique structure of the protein is in dynamic equilibrium with the unfolded shape of its chain, he continues. - The processes of folding and unfolding coexist there, their physics is the most transparent. Therefore, we focused precisely on such equilibrium and quasi-equilibrium conditions - in contrast to other researchers who seemed to reasonably (but erroneously, as it turned out) believed that the way to the secret of protein folding should be sought where it proceeds most rapidly. "
Unrolling squirrels is a good start, but not an option.
“The first approach to the Levinthal problem was developed by us a long time ago,” says Aleksey Finkelstein, “and consisted in the following: since it is very difficult to theoretically trace the path of protein folding, it is necessary to study the process of its unfolding. It sounds paradoxical, but in physics there is a principle of "detailed balance", which says: any process in an equilibrium system proceeds along the same path and at the same speed as the opposite one. And since the rates of folding and unfolding are the same in dynamic equilibrium, we considered a simpler process of protein unfolding (after all, breaking it down is easier than doing it) and characterized the “barrier” (see Figure 1), the instability of which determines the rate of the process ”.
Following the principle of detailed balance, scientists from the Institute of Protein of the Russian Academy of Sciences have estimated both "from above" and "from below" the folding rate of proteins, both large and small, with both simple and complex chain folding. Small and simply arranged proteins fold faster (“top” estimate), while large and / or complex proteins fold more slowly (“bottom” estimate). The values of all other possible folding rates are enclosed between them.
However, not all biologists were satisfied with the solution, since, firstly, they were interested in the way of folding (not unfolding) the protein, and secondly, the physical "principle of detailed balance" was, apparently, poorly understood by them.
And the work continued: this time, scientists from the Institute of Biology, Russian Academy of Sciences, calculated the complexity of protein folding. It has long been known that interactions in proteins are mainly associated with the so-called secondary structures. Secondary structures are standard, rather large local “building blocks” of a protein structure, determined mainly by local amino acid sequences in them. The number of possible options for folding such blocks into the structure of a folded protein can be calculated, which was done by scientists from the Institute of Biology, Russian Academy of Sciences. The number of such variants is enormous - about 10 10 (but far from 10 100!) For a chain of about 100 amino acids, and the protein chain can, according to theoretical estimates, "scan" them in minutes or, for longer chains, in hours. This is how the highest estimate of the protein folding time was obtained.
Regular secondary structure - alpha helix
WillowWThe results obtained in two ways (i.e., when analyzing both the unfolding and folding of the protein) converge and confirm each other.
“Our work is of fundamental importance for the design of new proteins in the future for the needs of pharmacology, bioengineering, nanotechnology,” concludes Alexey Finkelstein.
"The questions of protein folding rate are relevant when it comes to predicting the structure of a protein by its amino acid sequence, and especially about the design of new, not naturally occurring proteins."
“What has changed after receiving the RSF grant? There was an opportunity to purchase new modern equipment and reagents for work (after all, our laboratory is mainly experimental, although I only talked about our theoretical work here). But the main thing: the grant from the Russian Science Foundation allowed specialists to engage in science, and not look for a side job on the side or in distant lands, ”says Alexey Finkelstein.
