Alexei N. Nekrasov

Structural Features of the Interfaces in Enzyme-Inhibitor Complexes

Abstract Specific protein-protein interaction is essential for the function of life systems. A variety of computational methods are being extensively used now-a-days to investigate this interaction and to identify structural features of binding sites. In this paper, the informational structure analysis method was applied to the study of protein-protein interaction interfaces in enzyme-inhibitor complexes. The analysis of amino acid sequence by informational structure analysis method reveals three types of sites (ADD+, NORMAL and ADD-) which differ in the density of first rank elements in the informational structure. ADD+, NORMAL and ADD- sites also differ in their ability towards adaptive conformational reorganization which contributes to the formation of protein-protein interaction interfaces in enzyme-inhibitor complexes. The study of hydrolytic enzymes in complex with their protein inhibitors shows that at least one of the interaction interface sites is of ADD- type. ADD- sites possess an increased ability towards adaptive conformational changes thus enabling effective protein interaction.

Analysis of the Information Structure of Protein Sequences: A New Method for Analyzing the Domain Organization of Proteins

Abstract The amino acid sequences of γ-crystallin, Haloalkane Dehalogenase, Phthalate Dioxygenase, Porphobilinogen Deaminase and Myosin Regulatory Domain c-chain were analyzed for their information content. Sites of increased degree of information coordination between residues (IDIC-sites) were identified, and their organization was studied by means of analyzing the information structure of the protein sequences. Relationships between the structural units forming the spatial and informational structure of proteins were demonstrated. Associations of information-coordinated structural elements (IDIC-associa- tions) were mapped onto compact structural domains found in the spatial structures of globular proteins. The proposed method of analyzing the information structure of protein sequences may find applications in the biotechnology and structural chemistry of proteins.

Entropy of Protein Sequences: An Integral Approach

Abstract Several classifications of protein spatial structures and their structural elements are known. This makes revealing of the relation between these structural elements and sequence fragments rather topical. The most important move in this direction would be the determination of positional sensitivity levels and ranges between the residues in protein sequences. In this work the Shannon-Weaver informational entropy was used as a disorder criterion for solving this problem. This entropy was computed as function of the distance between the amino acid residues in different sets of unhomological protein sequences. Similarity of this function for different sets of protein sequences was shown. Analysis of informational entropy allows detecting a long-range positional correlation (≤30) between the amino acid residues and oscillations with periods of 3.6 and 2.9. These oscillation periods correspond to periodicity of α- and 310-helices.

Hydrolases: the correlation between informational structure and the catalytic sites organization.

Abstract The novel method allowing identification of protein structure elements responsible for catalytic activity manifestation is proposed. Structural organization of various hydrolases was studied using the ANIS (ANalysis of Informational Structure) method. ANIS allows to reveal a hierarchy of the ELements of Information Structure (ELIS) using protein amino acid sequence. The ELIS corresponds to the variable length sites with an increased density of structural information. The amino acid residues forming the enzyme catalytic site were shown to belong to the different top-ranking ELIS located in the contact area of the corresponding spatial structure clusters. In the protein spatial structure catalytic sites are located in the area of contact between fragments of polypeptide chain (structural blocs) allocation to the different top-ranking ELIS. According to our results we concluded that structural blocks corresponding to top-ranking ELIS are crucial for protein functioning. Such regions are structurally independent, and their determinate mobility relative to each other is vital for an efficient enzymatic reaction to occur.

The novel approach to the protein design: active truncated forms of human 1-CYS peroxiredoxin.

Abstract The object of the present study is the verification of a new approach to the design of the active truncated forms of enzymes. The method is based on a new way of investigating the protein sequences—the ANalysis of Informational Structure (ANIS). The analysis of informational structure allows to determine the hierarchically organized structures (IDIC-trees) formed by the sites with the Increased Degree of Informational Coordination between residues. The proposed approach involves the consequent removal of the fragments corresponding to the individual IDIC-trees from the wild-type enzyme sequences. The described procedure was applied to the design of the active truncated form of human 1-CYS peroxiredoxin (PrxVI). Two variants of the PrxVI truncated sequences were proposed according to ANIS method. These truncated forms of the enzyme were expressed in E. coli and purified. The respective antioxidant activities were measured. It was shown that one of the truncated recombinant proteins retains more than 90% of the wild-type PrxVI enzymatic activity. According to the results of our study we can assume that ANIS method can be an effective tool for the design of the active truncated forms of the enzymes or the chimeric proteins which combine the enzymatic activities of their wild-type prototypes.

Reversible “Wetting” of grain boundaries by the second solid phase in the Cu-In system

The reversible wetting of grain boundaries by the second solid phase in the copper-indium system has been observed. With an increase in the temperature, the contact angle θ between the (Cu)/(Cu) grain boundary in a Cu-based solid solution based and particles of the δ-phase (Cu70In30) decreases gradually. Above TW = 370°C, the first (Cu)/(Cu) grain boundaries completely “wetted” by the δ phase appear in Cu-In polycrystals. In other words, the δ phase forms continuous layers along grain boundaries and θ = 0. At 440°C, the fraction of completely wetted grain boundaries reaches a maximum (93%), whereas the average contact angle reaches a minimum (θ = 2°). With a further increase in the temperature, the fraction of completely wetted grain boundaries decreases and vanishes again at TDW = 520°C. This phenomenon can be explained by an anomalous shape of the solubility limit curve of indium in a solid solution (Cu).

Wetting of grain boundaries by the second solid phase in Al-based alloys

This work presents data on changes in the structure and properties of aluminum-based alloys subjected to severe plastic deformation by high-pressure torsion. Microstructure and the composition and change in temperature for phases are studied for double (Al-Zn, Al-Mg) and ternary (Al-Mg-Zn) alloys. Tie-lines of the liquid phase wetting of grain boundaries and grain boundary solvus lines are constructed on phase diagrams of our Al-Zn and Al-Mg systems. The shifting of the phase composition in the bulk of aluminum grains from the Al + τ region to the Al + η region of the Al-Mg-Zn phase diagram with an increase in the specific area of grain boundaries is described.

Grain Boundary Wetting in the Al-Mg System and Synthesis of Magnesium Diboride in Contact with Melt

The interaction between a Mg-containing melt and B under conditions of partial and complete wetting of Al/Al grain boundaries by Al-Mg melt has been investigated. The study was performed on Al polycrystals with Mg contents of 5, 10, 15, 18, and 25 wt %. Correspondingly, the Mg content in the melt was determined by the liquidus line and was in the range from 5 to 30 wt %. The obtained metal-matrix composites were investigated by light and scanning electron microscopy, electron-probe microanalysis, and X-ray diffraction. The possibility of synthesizing MgB2 in the contact with a melt having a relatively low Mg content (from 15 to 30 wt %) has been demonstrated.

Modeling of in vivo proteolytic degradation of hemoglobin.

Based on the amino acid sequences of endogenous peptides and X-ray spatial structure, mechanism of the in vivo proteolly degradation of bovine hemoglobin was analysed. The degradation was shown to be a multi-stage process. Its first stage is determined by the spatial organization of the native protein substrate, and the next stages-by the distribution of the electrostatic field potential of the protein fragments formed at the earlier stage.