M Yu Lobanov

Publications (10)10.66 Total impact

• Article: comparison of experimental and theoretical data on hydrogen-deuterium exchange for ten globular proteins.

  M Yu Suvorina, A K Surin, N V Dovidchenko, M Yu Lobanov, O V Galzitskaya
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  ABSTRACT: The number of protons available for hydrogen-deuterium exchange was predicted for ten globular proteins using a method described elsewhere by the authors. The average number of protons replaced by deuterium was also determined by mass spectrometry of the intact proteins in their native conformations. Based on these data, we find that two models proposed earlier agree with each other in estimation of the number of protons replaced by deuterium. Using a model with a probability scale for hydrogen bond formation, we estimated a number of protons replaced by deuterium that is close to the experimental data for long-term incubation in D(2)O (24 h). Using a model based on estimations with a scale of the expected number of contacts in globular proteins there is better agreement with the experimental data obtained for a short period of incubation in D(2)O (15 min). Therefore, the former model determines weakly fluctuating parts of a protein that are in contact with solvent only for a small fraction of the time. The latter model (based on the scale of expected number of contacts) predicts either flexible parts of a protein chain exposed to interactions with solvent or disordered parts of the protein.
  Biochemistry (Moscow) 06/2012; 77(6):616-23. · 1.06 Impact Factor
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  Article: Radius of gyration as an indicator of protein structure compactness

  M. Yu. Lobanov, N. S. Bogatyreva, O. V. Galzitskaya
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  ABSTRACT: Identification and study of the main principles underlying the kinetics and thermodynamics of protein folding generate a new insight into the factors that control this process. Statistical analysis of the radius of gyration for 3769 protein domains of four major classes (α, β, α/β, and α + β) showed that each class has a characteristic radius of gyration that determines the protein structure compactness. For instance, α proteins have the highest radius of gyration throughout the protein size range considered, suggesting a less tight packing as compared with β-and (α + β)-proteins. The lowest radius of gyration and, accordingly, the tightest packing are characteristic of α/β-proteins. The protein radius of gyration normalized by the radius of gyration of a ball with the same volume is independent of the protein size, in contrast to compactness and the number of contacts per residue.
  Molecular Biology 04/2012; 42(4):623-628. · 0.66 Impact Factor
• Article: Occurrence of disordered patterns and homorepeats in eukaryotic and bacterial proteomes.

  M Yu Lobanov, O V Galzitskaya
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  ABSTRACT: Combining the motif discovery and disorder protein segment identification in PDB allows us to create the first and largest library of disordered patterns. At present the library includes 109 disordered patterns. Here we offer a comprehensive analysis of the occurrence of selected disordered patterns and 20 homorepeats of 6 residues long in 123 proteomes. 27 disordered patterns occur sparsely in all considered proteomes, but the patterns of low-complexity-homorepeats-appear more often in eukaryotic than in bacterial proteomes. A comparative analysis of the number of proteins containing homorepeats of 6 residues long and the disordered selected patterns in these proteomes has been performed. The matrices of correlation coefficients between numbers of proteins where at least once a homorepeat of six residues long for each of 20 types of amino acid residues and 109 disordered patterns from the library appears in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside the considered kingdom than between them. The largest fraction of homorepeats of 6 residues belongs to Amoebozoa proteomes (D. discoideum), 46%. Moreover, the longest uninterrupted repeats belong to S306 from D. discoideum (Amoebozoa). Homorepeats of some amino acids occur more frequently than others and the type of homorepeats varies across different proteomes, . For example, E6 appears most frequent for all considered proteomes for Chordata, Q6 for Arthropoda, S6 for Nematoda. The averaged occurrence of multiple long runs of 6 amino acids in a decreasing order for 97 eukaryotic proteomes is as follows: Q6, S6, A6, G6, N6, E6, P6, T6, D6, K6, L6, H6, R6, F6, V6, I6, Y6, C6, M6, W6, and for 26 bacterial proteomes it is A6, G6, P6, and the others occur seldom. This suggests that such short similar motifs are responsible for common functions for nonhomologous, unrelated proteins from different organisms.
  Molecular BioSystems 01/2012; 8(1):327-37. · 3.53 Impact Factor
• Article: Statistical analysis of unstructured amino acid residues in protein structures.

  M Yu Lobanov, S O Garbuzynskiy, O V Galzitskaya
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  ABSTRACT: We have performed a statistical analysis of unstructured amino acid residues in protein structures available in the databank of protein structures. Data on the occurrence of disordered regions at the ends and in the middle part of protein chains have been obtained: in the regions near the ends (at distance less than 30 residues from the N- or C-terminus), there are 66% of unstructured residues (38% are near the N-terminus and 28% are near the C-terminus), although these terminal regions include only 23% of the amino acid residues. The frequencies of occurrence of unstructured residues have been calculated for each of 20 types in different positions in the protein chain. It has been shown that relative frequencies of occurrence of unstructured residues of 20 types at the termini of protein chains differ from the ones in the middle part of the protein chain; amino acid residues of the same type have different probabilities to be unstructured in the terminal regions and in the middle part of the protein chain. The obtained frequencies of occurrence of unstructured residues in the middle part of the protein chain have been used as a scale for predicting disordered regions from amino acid sequence using the method (FoldUnfold) previously developed by us. This scale of frequencies of occurrence of unstructured residues correlates with the contact scale (previously developed by us and used for the same purpose) at a level of 95%. Testing the new scale on a database of 427 unstructured proteins and 559 completely structured proteins has shown that this scale can be successfully used for the prediction of disordered regions in protein chains.
  Biochemistry (Moscow) 02/2010; 75(2):192-200. · 1.06 Impact Factor
• Article: Prediction of amino acid residues protected from hydrogen-deuterium exchange in a protein chain.

  N V Dovidchenko, M Yu Lobanov, S O Garbuzynskiy, O V Galzitskaya
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  ABSTRACT: We have investigated the possibility to predict protection of amino acid residues from hydrogen-deuterium exchange. A database containing experimental hydrogen-deuterium exchange data for 14 proteins for which these data are known has been compiled. Different structural parameters related to flexibility of amino acid residues and their amide groups have been analyzed to answer the question whether these parameters can be used for predicting the protection of amino acid residues from hydrogen-deuterium exchange. A method for prediction of protection of amino acid residues, which uses only the amino acid sequence of a protein, has been elaborated.
  Biochemistry (Moscow) 08/2009; 74(8):888-97. · 1.06 Impact Factor
• Article: A search for structural factors responsible for the stability of proteins from thermophilic organisms

  A. V. Glyakina, M. Yu. Lobanov, O. V. Galzitskaya
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  ABSTRACT: A database was designed to include 392 pairs of homologous proteins from thermophilic and mesophilic organisms. Proteins from thermophilic organisms proved to contain more atom-atom contacts per residue as compared with their mesophilic homologs. Solvent-accessible exterior amino acid residues contribute to the increase in the number of contacts. The amino acid composition was analyzed for internal (solvent-inaccessible) and exterior amino acid residues of thermophilic and mesophilic proteins. The exterior residues of thermophils have higher contents of Lys, Arg, and Glu and lower contents of Ala, Asp, Asn, Gln, Ser, and Thr as compared with mesophilic proteins. Interior protein regions did not differ in amino acid composition.
  Molecular Biology 07/2007; 41(4):616-621. · 0.66 Impact Factor
• Article: A search for amyloidogenic regions in protein chains

  O. V. Galzitskaya, S. O. Garbuzynskiy, M. Yu. Lobanov
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  ABSTRACT: A new method was developed for identifying amyloidogenic regions in protein chains. The formation of amyloid fibrils was attributed to protein regions enriched in residues with a high expected packing density. Predictions consistent with experimental findings were obtained for 8 out of 11 amyloid-forming proteins examined.
  Molecular Biology 09/2006; 40(5):821-828. · 0.66 Impact Factor
• Article: Prediction of natively unfolded regions in protein chains

  O. V. Galzitskaya, S. O. Garbuzynskiy, M. Yu. Lobanov
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  ABSTRACT: Analysis showed that the globular or natively unfolded state of a protein can be inferred not only from a lower hydrophobicity or a higher charge, but also from the average environment density (average number of close residues located within a certain distance of a given one) of its residues. A database of 6626 protein structures was used to construct a statistical scale of the average number of close residues in globular structures for the 20 amino acids. The portion of false predictions in distinguishing between 80 globular and 90 natively unfolded proteins was 11% with the new scale and 17% with a hydrophobicity scale. The new scale proved suitable for predicting the folded or unfolded state for native proteins or the natively unfolded regions for protein chains. In comparisons with the available algorithms, the new method yielded the highest portion of true predictions (87 and 77% with averaging over residues and over proteins, respectively).
  Molecular Biology 02/2006; 40(2):298-304. · 0.66 Impact Factor
• Article: Prediction of protein domain boundaries from statistics of appearance of amino acid residues

  O. V. Galzitskaya, N. V. Dovidchenko, M. Yu. Lobanov, S. O. Garbuzynskiy
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  ABSTRACT: A database of 452 two-domain proteins with less than 25% homology was constructed. One half of the database was used to obtain statistics on the appearance of amino acid residues at domain boundaries. Small and hydrophilic residues (proline, glycine, asparagine, glutamic acid, arginine, etc.) occurred more often at domain boundaries than in total proteins. Hydrophobic residues (tryptophan, methionine, phenylalanine, etc.) were rarer at domain boundaries than in total proteins. Probability scales of amino acid appearance in boundary-flanking regions were constructed with these statistics and used to predict the domain boundaries in proteins of the other half of the database. The probability scale obtained by averaging the appearance of amino acids over an 8-residue region (±4 residues from the real domain boundaries) yielded the best results: domain boundaries were predicted within 40 residues of the real boundary in 57% of proteins and within 20 residues of the real boundary in 41% of proteins. The probability scale was used to predict the domain boundaries in proteins with unknown structures (CASP6).
  Molecular Biology 12/2005; 40(1):96-106. · 0.66 Impact Factor
• Article: The difference between protein structures obtained by x-ray analysis and nuclear magnetic resonance

  B. S. Melnik, S. O. Garbuzynskiy, M. Yu. Lobanov, O. V. Galzitskaya
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  ABSTRACT: We have analyzed the pairs of protein structures obtained by X-ray diffraction analysis and nuclear magnetic resonance (X-ray and NMR structures) that display no major differences when superimposed on one another (61 pairs). Analyzing atom-to-atom contacts (contact distances 2–8 ), it has been found that the NMR structures (compared to the X-ray structures) have more contacts at distances below 3.5 and above 5.5 . In the case of residue-to-residue contacts, the NMR structures have more contacts at distances below 3 and between 4.5 and 6.5 . At other distances analyzed, the X-ray structures have more contacts. The difference in the numbers of atom-to-atom and residue-to-residue contacts is greater for buried residues inaccessible to water than for surface residues. Another important difference is related to the number of hydrogen bonds in the main chain: this number is greater in the X-ray structures. The coefficient of correlation between the numbers of hydrogen bonds identified in the structures obtained by both methods is only 32%. If a complete set of NMR models of protein structure is considered, the total number of hydrogen bonds proves to be 1.2 times greater than in the X-ray structures, whereas the correlation coefficient increases to only 65%. We have also demon-strated that -helices in the NMR structures are more distorted (compared to the ideal -helix) than those in the X-ray structures.
  Molecular Biology 12/2004; 39(1):113-122. · 0.66 Impact Factor