[Mechanism of action of aspartic proteinases. V. Conformational characteristics of fragments of substrate-binding sites in rhizopuspepsin and HIV-1 proteinase]. / Mekhanizm deistviia aspartatnykh proteinaz. V. Konformatsionnye vozmozhnosti fragmentov substratsviazyvaiushchikh uchastkov rizopuspepsina i proteinazy HIV-1.

The conformational states of side chains of catalytic Asp residues in active sites of HIV-1 protease and rhizopuspepsin in the potential field of free enzymes were studied by using theoretical conformational analysis. Structural factors that stabilize the conformation of these residues in free enzymes were revealed. Methods of molecular mechanics were used to estimate the stabilization energy of the Met46-Phe53 labile fragments of HIV-1 protease in the potential field of their nearest surrounding amino acid residues for the conformations characteristic of the free protein and similar to that of the protein in enzyme-inhibitor complexes. In solution, the conformational state of the fragments of the free enzyme was concluded to be similar to that observed in the enzyme complex with the ligand and different from that determined by X-ray diffraction analysis. This difference was ascribed to the effect of crystal packing.

[Mechanism of action of aspartic proteases. III. Conformational characteristics of HIV-1 protease inhibitor JG-365]. / Mekhanizm deistviia aspartatnykh proteinaz. III. Konformatsionnye vozmozhnosti ingibitora JG-365 proteinazy HIV-1.

A set of conformations was shown to be characteristic of the free-state spatial structure of substrate-like inhibitor JG-365 for aspartic protease from HIV-1. Among them, the lowest-energy conformations have a folded form of the peptide backbone. The inhibitor has a noncleavable hydroxyethylamine group with an additional chiral center in its structure. Our calculations showed that only the S-isomer of the inhibitor displays conformational characteristics that practically coincide with those of the native substrate for HIV-1 protease. One of the calculated conformations with a completely extended main chain and a relative energy of 9.5 kcal/mol very closely mimics the experimentally observed structure of the inhibitor in the enzyme-inhibitor complex. The realization of this structure is unlikely for a free inhibitor, because it has only a small number of interresidual noncovalent interactions in the extended conformation; these are presumably compensated for by intermolecular interactions at the active site of the enzyme.

[Mechanism of action of aspartic proteases. IV.Conformational characteristics of a substrate and an inhibitor of rhizopuspepsin ]. / Mekhanizm deistviia aspartatnykh proteinaz. IV. Konformatsionnye vozmozhnosti molekul substrata i ingibitora pizopuspepsina.

On the basis of theoretical conformational analysis of separate peptide fragments, the conformational characteristics of two substrates and a substrate-like inhibitor of aspartic protease rhizopuspepsin were studied. It was shown that the spatial structure of these molecules is described by several families of conformations, the transition between which does not require the overcoming of high energy barriers. It was assumed that the stabilization of beta-structural conformations experimentally observed in inhibitor complexes is due to the greater predisposition of extended structures to the formation of effective intermolecular contacts with amino acid residues of the active site of the enzyme.

Protein folding as a nonlinear nonequilibrium thermodynamic process.

Biofurcational theory of protein folding is developed describing the process of formation of protein native structure as a sequence of non-equilibrium irreversible fluctuations, specific for a particular protein. The model gives explanation to all characteristic features of the folding process: stochastic mechanism, short time and precision of proteins self-assembling. A constructive role of entropy in the formation of a highly ordered structure out of disorder is discussed. A numerical method of a priori calculations of polypeptide structures basing on principles of bifractional folding model is presented.

[Mechanism of aspartyl proteinase action. VII. Noncovalent complexes of HIV-1 aspartyl proteinase with substrate and substrate-like inhibitors]. / Mekhanizm deistviia aspartil'nykh proteinaz. VII. Nevalentnye kompleksy aspartil'noi proteinazy HIV-1 s substratom i substratopodobnym ingibitorom.

A computer model of a noncovalent complex of HIV-1 aspartyl protease with substrate-like inhibitor JG-365 was a priori constructed by using the approaches of theoretical conformational analysis and molecular mechanics. The root mean square deviation of the calculated conformation of the inhibitor from the X-ray diffraction analysis data was 0.87 A. These results enabled the a priori calculation of the structure of noncovalent complex of HIV-1 protease with a hexapeptide fragment of its native specific substrate Ser-Gln-Asn-Tyr-Pro-Ile-Val. The only possible orientation of the cleavable peptide bond in this and the nucleophilic water molecule relative to the catalytically active Asp residues of the enzyme (Asp25 and Asp125) was found that provides for the chemical transformation of the substrate to a tetrahedral intermediate. An action mechanism of enzymes of this class was proposed on the basis of the analysis of calculated distances. We showed that neither steric distortion of the cleavable bond nor the formation of unfavorable contacts in molecules of the enzymes and their substrates accompany the optimum orientation of substrate molecules at the active sites of HIV-1 aspartyl proteases and rhizopuspepsin.

[Mechanism of action of aspartyl proteinases. VI. Nonvalent enzyme-inhibitory and enzyme-substrate complexes of the aspartyl proteinase rhizopus pepsin]. / Mekhanizm deistviia aspartil'nykh proteinaz. VI. Nevalentnye ferment- ingibitornyi i ferment-substratnyi kompleksy aspartil'noi proteinazy rizopuspepsina.

The structure of a complex of rhizopuspepsin, a fungal aspartyl protease, with Pro1-Phe2-His3-Phe4-psi[CH2-NH]-Phe5-Val6, its substrate-like inhibitor, was calculated by theoretical conformational analysis. The search for energetically favorable conformational variants of the ligand structure was based on the fragmental approach using the dynamic library of peptide fragments, which were successively extended in the potential field of the protein. The root-mean-square deviation of atom positions in the calculated and experimental inhibitor conformations was 0.56 A. A similar approach was used to model a noncovalent complex of rhizopuspepsin with Pro1-Phe2-His3-Lys4-Phe5-Val6, its specific substrate. As a result, two isoenergetic structures of the complex with different arrangements of the cleavable peptide group and a nucleophilic water molecule were calculated. The possibility of the achieving each of these conformations during the catalytic act is considered. It is shown that there are no structural prerequisites for the distortion of the cleavable bond in the active site of the enzyme. On the basis of the resulting structural data, the assumption was made that Asp35 may be protonated at a late stage of formation of the tetrahedral intermediate rather than at the basic state of the complex.

[Mechanism of action of aspartic proteinases. 2. Conformational possibilities of an HIV-1 proteinase substrate]. / Mekhanizm deistviia aspartatnykh proteinaz. 2. Konformatsionnye vozmozhnosti molekuly substrata proteinazy HIV-1.

Theoretical conformational analysis of a hexapeptide fragment p17-p24 of the native substrate of the HIV-1 protease was reported. The geometrical and energy parameters of all possible optimal conformations were determined. The data which are necessary for the calculation of the mechanism of the catalytic act of HIV-1 protease were obtained.

[Mechanism of aspartic proteinase action. I. Theory and method]. / Mekhanizm deistviia aspartatnykh proteinaz. !. Teoriia i metod.

Starting from experimental results and contemporary theories of biocatalysis, stereochemistry of aspartic protease functioning was discussed. A general theory of biocatalysis was suggested, which is based on the structural and functional organization of enzyme and substrate molecules and allow a quantitative description of a catalytic act as a continuous, spontaneous, and self-controlled process.

[Structure-functional organization of the angiotensin II molecule. III. Polyfunctional nature]. / Strukturno-funktsional'naia organizatsiia molekuly angiotenzina II. III. Priroda polifunktsional'nosti.

Conformational properties of the molecules of angiotensin II and some of its analogs are analysed with regard to the quantitative characteristics of their biological activities. Connections between low-energy conformations of angiotensin II and its biological functions are established. The hormone's spatial structures plausible in terms of interactions with the specific receptors located in smooth muscles and adrenal cortex tissues have been identified.

[Structure-function organization of the angiotensin II molecule. II. Reverse structural problem]. / Strukturno-funktsional'naia organizatsiia molekuly angiotenzina II. II. Obratnaia strukturnaia zadacha.

A number of modifications of the amido acids sequence of the peptide hormone angiotensin II leading to the hormone's analogues with restricted conformational properties are considered. The relative conformational energies for all the analogues were evaluated in conformations similar to the low-energy conformations of the native hormone. Presented is the comparative analysis of the spatial structures of the native hormone and its analogues.

[Approach to the study of natural peptides from structure to functions. III. Structural organization of an adrenorphin molecule and its synthetic analogs]. / Podkhod k izucheniiu prirodnykh peptidov ot struktury k funktsii. III. Strukturnaia organizatsiia molekuly adrenorfina i ego iskusstvennykh analogov.

Spatial structure of the peptide hormone adrenorphin was investigated by the theoretical conformational method. A solution of the "reverse conformational problem" for adrenorphin made it possible to predict a series of the modified synthetic analogues, which may assume one of the low-energy conformations of the native hormone.

[Structure-activity organization of angiotensin II molecules. I. The structural problem]. / Strukturno-funktsional'naia organizatsiia molekuly angiotenzina II. I.Strukturnaia zadacha.

Conformational energy calculations were carried out for angiotensin II. Its spatial structure can be described by two groups of low-energy conformations. The values of all dihedral angles of the backbone and side chains as well as intra- and inter-residual interaction energies were calculated for all potential physiologically active conformations.

[Approach to studying the structure-activity relationship of native peptides. I. Structural organization of the opioid peptide Tyr-Glu-Gly-Phe-Met-Arg-Gly-Leu and its artificial analogs]. / Podkhod k izucheniiu prirodnykh peptidov ot struktury k funktsii. I. Strukturnaia organizatsiia opioidnogo peptida Tyr-Gly-Gly-Phe-Met-Arg-Gly-Leu i ego iskusstvennykh analogov.

Theoretical conformational analysis was carried out for the octapeptide Tyr1-Gly2-Gly3-Phe4-Met5-Arg6-Gly7-Leu8. Possible structure of the opioid peptide under physiological conditions may be described by a set of low-energy conformations belonging to 14 different forms of the backbone. The solution of the "reverse conformational problem" for the opioid peptide enables one to predict the modified amino acid sequences (Ala2, D-Ala2, Ala3, D-Ala3, Ala7, D-Ala7, MeMet5, MeArg6-analogues) which may assume one of the low-energy states of the native hormone. The influence of the solute was not taken into account in our calculations.

[Approach to studying the structure-activity relationship of native peptides. II. Structural organization of alpha- and beta-neoendorphins]. / Podkhod k izucheniiu prirodnykh peptidov ot struktury k funktsii. II. Strukturnaia organizatsiia molekul alpha- i beta-neoéndorfinov.

By means of a semi-empirical method, an a priori conformational analysis of alpha- and beta-neo-endorphins was carried out. Calculations yielded the values of all dihedral angles of the backbone and side chains of the peptide's various forms as well as intra- and inter-residue interaction energies.

[Approach to studying natural oligopeptides in the area of structure relationship to function]. / Podkhod k issledovaniiu prirodnykh oligopeptidov v napravlenii ot struktury k funktsii.

Structure and structure-function relations of naturally occurring oligopeptides and peptide receptors are discussed. An approach to inferring function of low-molecular peptides in the direction from their structure is postulated. Diverse biological activities of oligopeptides supposedly arise from a limited number of preferable spatial structures which may exist under physiological conditions. Each particular function of an oligopeptide is connected with a definite spatial structure, belonging to the set of the low-energy conformations. A method is suggested for constructing a synthetic analogue with a predetermined physiologically active conformation, prior to all chemical and biological tests.

[Structural organization of [met]enkephalin and endorphin molecules. III. Theoretical conformation analysis of beta-endorphin]. / Strukturnaia organizatsiia molekul [met]énkefalina i éndorfinov. III. Teoreticheskii konformatsionnyi analiz beta-éndorfina.

Conformational energy calculations were carried out for beta-endorphin. Its spatial structure can be described by nine low-energy conformations. The calculations yielded the values of all dihedral angles of the backbone and side chains of these forms as well as intra- and inter-residue interaction energies.

[Structural organization of [met]enkephalin and endorphin molecules. II. Theoretical conformation analysis of alpha-, gamma- and delta-endorphins]. / Strukturnaia organizatsiia molekul [met]énkefalina i éndorfinov. II. Teoreticheskii konformatsionnyi analiz alpha-, gamma- i delta-endfinov.

Conformational energy calculations were carried out for neuropeptides alpha-, gamma- and delta-endorphins, which are 1-16, 1-17 and 1-19 fragments respectively, of beta-endorphin. The proposed computational scheme yielded all possible low-energy conformational sets for these hormones. Specific features of spatial organization of each compound and similarities of their structures are discussed.

[Structural organization of [Met]enkephalin and endorphin molecules. I. Theoretical conformation analysis of [Met]enkephalin]. / Strukturnaia organizatsiia molekul [Met]énkefalina i éndorfinov. I. Teoreticheskii konformatsionnyi analiz [Met]énkefalina.

Using a semi-empirical method, an a priori conformational analysis of the [Met]-enkephalin molecule was carried out. Calculations yielded the values of all dihedral angles of the backbone and side chains of the peptide's forms as well as intra- and inter-residue interaction energies.