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N S Andreeva

Publications and source records attributed to N S Andreeva.

At least 37 records · Page 2Linked to original sources
PubMedDate not supplied

[How the features of three-dimensional structure of aspartate proteinases determine their properties].

There is given a brief account of the specific interactions of some amino acid residues in aspartic proteases of both higher organisms and retroviruses that determine their important properties: an anomalously low isoelectric point of pepsin and its stability at pH close to unity; the ability of one of the carboxyl groups in the active site of proteases of higher organisms to retain charged state at any pH value and protonated state of another carboxyl, which is necessary for their enzymatic activity. It is also explained how such states can be induced in retroviral proteases.

Aspartic Acid Endopeptidases↗
PubMedDate not supplied

[Molecular dynamics analysis of chymosin conformations in solution and in crystalline environment].

The method of molecular dynamics in explicit solvent was applied to test the hypothesis of the existence of a self-inhibited form of chymosin in solution. The paths and energies were calculated for chymosin in solution and in a crystalline environment. The modeling revealed that the intermolecular contacts of chymosin in crystal have negligible influence on the energy stabilization of its self-inhibited conformation. On the other hand, upon molecular dynamics simulation of the active and self-inhibited forms in solution their conformational energies proved to be quite close and the potential barrier between them relatively low. All this supports the possibility of chymosin to adopt spontaneously the self-inhibited conformation in solution, and indicates that it is one of the really existing enzyme forms rather than a crystal packing artifact. The results obtained open novel approaches to studying the specificity of chymosin as well as other aspartic proteinases.

Chymosin↗
PubMedDate not supplied

[Conserved interactions of the active carboxyls in pepsin-like enzymes and retroviral proteases].

In addition to previous studies, 30 crystal structures of retroviral proteases corresponding to the highest resolution were inspected to analyze the interactions of the active carboxyl with surroundings groups. The outer oxygen of the active carboxyl in retroviral enzymes form contacts only with the water molecule participating in catalysis. This is an important difference between retroviral proteases and pepsin-like enzymes, which form a net of hydrogen bonds of these outer oxygen with residues neighboring the catalytic site in 3D structures. At the same time, it was found that in all aspartic proteases the inner oxygen of the active carboxyl are also involved in the chain of interactions through peptide groups Thr-Gly adjacent to the active residues. Polarization of these peptide groups influences the donor-acceptor properties of the active carboxyl. The found chain of interactions is more extensive in retroviral than in pepsin-like proteases; however, its main part is conserved for the whole class of these enzymes. Some implications of the role of these interactions are discussed.

Aspartic Acid↗
PubMedDate not supplied

[Interdomain interactions in aspartic proteases of higher organisms and their analogs in retroviral enzymes].

A continuous chain of hydrogen bonded groups, which forms cross-hands interaction between domains in molecules of pepsin-like enzymes, has been revealed. The chain contains a pair of 6 symmetrically related hydrogen bonds between main chain atoms and the two conserved water molecules. The peptide groups forming hydrogen bond with the inner oxygens of the active carboxyls are important elements of the chain. The so-called "fireman grip" hydrogen bonding, consisting of a pair of the two symmetrically related bonds, is an integral part of this system of interactions. One of the water molecules in this system has a zero accessibility and forms a very short hydrogen bond with the active site interacting peptide group. This chain connects tightly the two regions of domains which have a high correlation in conformational mobility. The retroviral enzymes have an abortive chain of the interdomain interaction in this region which is reduced to the "fireman grip" net.

Animals↗
PubMedDate not supplied

[Various aspects of structural studies of aspartate proteinases].

The paper is a brief account of aspartic proteinases' structural studies developed in V.A. Engelhardt Institute of Molecular Biology during the last 3 years. The work on porcine pepsin has been finalized after the refinement of the monoclinic crystal form at 1.8 A resolution performed in collaboration with the group of protein structure and function studies of the University of Alberta in Canada. An important structural property of chymosin which explains the enzyme specificity has been found. Protein engineering work on chymosin is being developed. The structural template for aspartic proteinases has been elucidated and on the basis of this template the model of HIV-1 protease molecule has been built. Some approaches to the design of HIV-1 protease inhibitors were elucidated.

Amino Acid Sequence↗
PubMedDate not supplied

[The role of peripheral interactions in chymosin specificity].

Kinetic parameters for the splitting of model peptide substrates and chi-casein with chymosin have been interpreted on the basis of the three-dimensional structure of chymosin. Model peptide substrates contain a fragment of the chi-casein sequence in the region of the bond Phe-105--Met-106 splitted with the enzyme. It was shown that the possible reason of the enormous milk-clotting efficiency of chymosin may be partly associated with the electrostatic interaction of the positive charged segment 98-102 (His-Pro-His-Pro-His) of the substrate and outer loop of the enzyme which contains Glu-245, Asp-247, Asp-249, Asp-251.

Amino Acids↗
PubMedDate not supplied

[Theoretical studies of the electrostatic interactions in aspartic proteinases, intramolecular interactions in pepsin and penicillopepsin].

A semi-empirical approach has been used to estimate the intramolecular electrostatic interactions in pepsin and penicillopepsin. The pH-dependence of the free energy electrostatic term was calculated, and the pH-dependence of the domain interactions has been estimated. As it was shown, the contribution of electrostatic interactions is rather small for the stabilization of the native structure. At the same time the electrostatic repulsion between domains increases with the increase of pH. The later can be the cause of the alkaline denaturation of pepsin and domain mobility.

Aspartic Acid Endopeptidases↗
PubMedDate not supplied

[X-ray structural analysis of pepsin. V. Conformation of the main chain of the enzyme].

A detailed description of structural investigations of pepsin from 3.5 to 2.7 A resolution are given. The main attention is drawn to the conformation of the polypeptide backbone of the enzyme. The numbers of amino acid residues involved in the formation of various structural elements are listed. The structure of pepsin is similar to that of acid proteases isolated from lower organisms. The two domain structure of all acid proteases has a periodicity in the sequence of beta-segments and helices and a very specific symmetrical structure of each domain. This makes it possible to describe the structure of acid proteases in simple terms.

Pepsin A↗
PubMedDate not supplied

[The structure of pepsin. I. Molecular self-symmetry of the enzyme and implications for the evolution of aspartate proteinases].

This is the first paper in the series of publications on the detailed description of different aspects of pepsin structure. It concerns the domain structure of the enzyme and the topology of the arrangement of beta-strands in pepsin and related aspartic proteases, this topology being quite different from that of all other beta-proteins. The topology, molecular symmetry and the close proximity of the N- and C-termini of domains suggest that at the first stages of evolution polypeptide chains of some preproteins could be closed in rings, which become open at the subsequent stages. Their genes duplicated twice, and the fusion process resulted in a gene consisting of similar parts.

Amino Acid Sequence↗
PubMedDate not supplied

[The structure of pepsin. II. Structure of the enzyme active site (at 2 angstroms resolution)].

Detailed structure of the pepsin active site in the region of the active aspartic acid residues and substrate binding S1 and S1' sites is considered. At the active site of the enzyme crystals studied several molecules of ethanol were detected, which interact with active groups. The catalytic properties of aspartyl proteinases towards dipeptide substrates were explained on the base of the specific structure of S1 and S1' binding sites.

Aspartic Acid Endopeptidases↗
PubMedDate not supplied

[X-ray study of chymosin. I. Molecular replacement at a 3 angstroms resolution].

The determination of the three dimensional structure of chymosin at 3 A resolution by molecular replacement method is described. The rotation functions for various aspartic proteases were calculated and combined results were used for the refinement of orientational parameters of chymosin molecules in the unit cell. The interpretation of Crowther-Blow translation function map with packing consideration enable to place correctly the molecules in the chymosin unit cell. Several difference Fourier syntheses for chymosin were calculated and differences between pepsin and chymosin structures were detected.

Amino Acid Sequence↗