The myoglobin structure determined by John Kendrew and associates by X-ray crystallography is the first protein structure described in atomic detail. Plenty of myoglobin structures are available in the Protein Data Bank now. A visible feature of the structures is that confornnation of Lys79 and Lys98 of nonglycine residues has a positive value of the backbone dihedral angle 4). Here I suspect the conformation of both the residues to be wrong and persuade that angle 4) of the residues should be negative. Careful rebuilding of the structure model of EF and FG loops including Lys79 and Lys98 residues and anew refinement of the myoglobin structure by X-ray crystallography or other methods of structural biology is required. Verification of the suggestion is important for structural biology and bioinformatics. This would lead to further refinement of the existing many Mb structures and stimulate the studies on the improvement of other protein structures.

Backbone torsion angles  ,  of a vast majority of nonglycine residues in proteins lay within the peculiar insulated regions in the (  ,  ) space assigned to the conformations allowed for nonglycine residues that embrace the conformations with negative and positive values of  separately. Emphasizing this feature here, the abilities of nonglycine Trp-repressor

In many studies on the protein folding problem it is assumed that the internal rotational barriers about NCα and CαC backbone bonds in unfolded polypeptides are quite small, around 0.7 kcal/mol, of an order comparable to the energy of kT at normal temperature (where k is Boltzmann’s constant and T is the temperature in K) and hence that rotations about these bonds occur almost freely. Here it is highlighted that such consideration is an unfortunate mistake. Approximate values for the rotational barriers of NCα and CαC bonds are suggested from computations of U(\( \phi \), ψ) potential energy surface (PES) maps of a number of oligopeptides by a semiempirical method for conformational analysis. The proposed values are about 16 kcal/mol for NCα bonds and 6 kcal/mol for CαC bonds. The values of the same barriers estimated from some ab initio quantum-mechanical PES maps for several dipeptides available in literature are also highlighted.

Structural characteristics of numerous globular proteins in the denatured state have been reviewed using literature data. Recent more precise experiments show that in contrast to the conventional standpoint, proteins under strongly denaturing conditions do not unfold completely and adopt a random coil state, but contain significant residual ordered structure. These results cast doubt on the basis of the conventional approach representing the process of protein folding as a spontaneous transition of a polypeptide chain from the random coil state to the unique globular structure. The denaturation of proteins is explained in terms of the physical properties of proteins such as stability, conformational change, elasticity, irreversible denaturation, etc. The spontaneous renaturation of some denatured proteins most probably is merely the manifestation of the physical properties (e.g., the elasticity) of the proteins per se, caused by the residual structure present in the denatured state The pieces of the ordered structure might be the centers of the initiation of renaturation, where the restoration of the initial native conformation of denatured proteins begins. Studies on the denaturation of proteins hardly clarify how the proteins fold into the native conformation during the successive residue-by-residue elongation of the polypeptide chain on the ribosome.

The problem of protein folding, i.e. how does a polypeptide chain fold to native protein following its synthesis on the ribosome, is recognized as a major unsolved problem of biology at molecular level.To solve the problem experimental studies of denaturation and renaturation of native proteins and a variety of theoretical-computational simulations of full-length polypeptide chains have usually been used as relevant in vitro models.However, at present these conventional approaches evidently seem to be hypothetical and have been hardly found.Nevertheless, there are a lot of convincing evidences that proteins fold progressively during the residue-by-residue elongation on the ribosome from the N-to the C-terminus.On this basis, therefore, simulations of the folding and formation of the native spatial structure of the proteins will be expedient.These points are briefly highlighted in the current minireview.

To solve the problemof protein folding, denaturation-renaturation experiments on native proteins and a variety of theoretical-computational simulations of full-length polypeptide chains have usually been used as convenient in vitro models for the past several decades. However, there is a lot of irrefutable evidence that the information contained in the primary structure of a protein about its spatial structure is realized in the cells during the residue-by-residue elongation on the ribosome from the N- to the C-terminus. On this basis therefore, simulations of the folding and formation of the native spatial structure of proteinswill be of requirement.

The possibility to derive the analogs of native proteins by the chemical synthesis is considered to be a serious argument for the concept of posttranslational protein folding. The present paper analyzes for the first time chemically synthesized proteins to reveal whether they are relevant to the problem of protein folding. The results enable the following conclusions to be drawn. The acquisition of the peculiar conformations by the chemically synthesized proteins to exhibit the specific functions is conditioned by the highly marked features of the secondary and tertiary structures of the corresponding native proteins. These features will make themselves evident only if favorable conditions are carefully chosen during the experiments for each individual protein. Thus, in our opinion, the possibility to derive a synthetic protein is hardly evidence for the posttranslational folding of proteins.

We suppose that folding of proteins occurs cotranslationally by the following scheme. The polypeptide chains enter the folding sites from protein translocation complexes (ribosome, translocation machinery incorporated in membranes) directionally with the N-terminus and gradually. The chain starts to fold as soon as its N-terminal residue enters the folding site from the translocation complex. The folding process accompanies the translocation of the chain to its folding site and is completed after the C-terminal residue leaves the translocation complex. Proteins fold in sequential stages, by translocation of their polypeptide into folding compartments. At each stage a particular conformation of the N-terminal part of the chain that has emerged from the translocation complex is formed. The formation of both the particular conformations of the N-terminal chain segment at each folding stage and the final native protein conformation at the last stage occurs in a time that does not exceed the duration of the fastest elongation cycle on the ribosome.

Two concepts of protein folding are known. One of them, the cotranslational concept, states that a protein folds during the synthesis of the polypeptide chain on the ribosome. According to the other, the posttranslational concept, the protein starts to fold just after the synthesis of its polypeptide chain. This article attempts to show that the posttranslational concept is hardly suited to solve the problem of protein folding. In our opinion, polypeptide chains cannot be represented as random coils. They are stiff chain-like macromolecules rather than flexible ones: the single bond rotational barriers of a polypeptide substantially exceed the accepted standard values; even in strong denaturing conditions, a protein possesses a considerable amount of residual folded structures. We believe that the popular "hierarchical" models for the protein folding mechanism are not realistic because the formation of secondary and tertiary structures of proteins occurs simultaneously and cooperatively. The time for the elongation of a polypeptide chain by one amino acid residue during biosynthesis exceeds considerably the time of the formation of alpha-helices and beta-sheets in proteins as well as the time supposed for the spatial structure formation of a native protein during renaturation. Thus, we believe that the mechanism of protein folding in vivo cannot be clarified by denaturation-renaturation experiments. In our opinion, the phenomenon of protein renaturation is no more than the restoration of native protein conformation (which initially forms cotranslationally) disrupted during denaturation, and thus denaturation-renaturation experiments cannot serve as a model to clarify the mechanism of protein folding.

Polypeptide chain folds to native protein under physiological conditions. At least in vivo, in addition to physiological conditions, certain initial kinetic conditions are also required upon folding. These non-physiological conditions specify that amino acid residues of a polypeptide chain move to the folding place directionally beginning from the first N-terminal residue, sequentially one after another, and gradually one-by-one. Chaperonin complex provides in the cell for the initial kinetic requirements for co-translational folding of polypeptide chain to native protein in sites in the cytoplasm distant from the ribosome and in the plasma of organelles. A new model of the GroEL/GroES complex architecture is proposed using structural data on the GroEL and GroES chaperonins. The known models of the chaperonin complex structure suggest that it is formed by binding of a dome-like GroES oligomer to the end orifice of the GroEL cylinder via long mobile loops of its base. According to the new model, to form the complex two GroES oligomers one-by-one enter with their roofing, i.e., in an inverted way, into the GroEL cylinder end orifices and lock them. The proposed complex has the form of coaxial cylinders. It is sufficiently stable and cannot dissociate under physiological conditions. The complex becomes functionally active when it binds the incoming substrate polypeptide. An active GroEL/GroES complex resembles a hollow cylinder with end orifices. The diameter of the cavity and orifices is about 30 Angstrom.

The fact of enzymatic synthesis of a protein polypeptide chain have been mentioned. The potential energy surfaces of peptides have been analysed. Based on the obtained results and characteristic peculiarity of the enzymatic reactions have been concluded that the non-glycine residues in a three-dimensional (3-D) protein structure most likely should be in the negative conformations. The analysis of the amino acid residue conformations have been performed on the 185 3-D protein structures obtained by the X-ray crystallography at high resolution. It has been shown that the changes in the protein surrounding environment, in crystalline forms and functional state of protein, bindings of the ligands and inhibitors do not lead to the changes in the polarity of non-glycine residues conformational angles phi, and in the polarity of the conformational angles omega of all residues. Based on the results, 81 independent protein structures have been selected. The preliminary results of analysis of glycine and non-glycine residue conformations occurring in these structures have been presented.

Basing on the protein tertiary structure data analysis, the peculiarities of enzymatic catalysis, as well as on the results of ab initio conformational energy map calculations of dipeptides, the conclusion is drawn, that the synthesis of polypeptide chains on the ribosome occurs on the right hand conformation of amino acid residues. For the number of amino acid residues to transfer to left hand conformation, local and electoral conditions are necessary. Some possible errors in the X-ray crystal structure data of proteins are pointed out.

Different possibilities of H-bonds formation for formamide-water complexes and dimers of formamide were studied. Potential energy maps were calculated for di-, tri- and tetrapeptides. The maps provide necessary data to explain the relative stability of different oligopeptide conformers and Ramachandran maps for peptides.

Structure-activity correlationship of some potential-activity antiarrhythmic agents of lidocaine-like substances is found. Conformational properties of molecules of the substances are studied.