Publications by authors named "Mikhail Lobanov"

11 Publications

  • Page 1 of 1

Texturing and Phase Evolution in Ti-6Al-4V: Effect of Electron Beam Melting Process, Powder Re-Using, and HIP Treatment.

Materials (Basel) 2021 Aug 10;14(16). Epub 2021 Aug 10.

Heat Treatment & Physics of Metals Department, Ural Federal University, 620002 Ekaterinburg, Russia.

The research demonstrates microstructural changes and development of specific texture in Ti-6Al-4V specimens produced by electron beam melting (EBM) under different conditions. The effect of two factors, namely, raw material (powder) recycling and hot isostatic pressing (HIP), on the EBM produced samples structure and properties, has been explored. The as-printed and treated samples were investigated using electron backscattered diffraction (EBSD) analysis. Modification of mechanical properties after the EBM and HIP are explained by the EBSD data on microstructural phenomena and phase transformations. The work is devoted to assessing the possibility of reusing the residual titanium alloy powder for the manufacture of titanium components by the combination of EBM and HIP methods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ma14164473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8399233PMC
August 2021

Myosin Binding Protein-C Forms Amyloid-Like Aggregates In Vitro.

Int J Mol Sci 2021 Jan 13;22(2). Epub 2021 Jan 13.

Laboratory of the Structure and Functions of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia.

This work investigated in vitro aggregation and amyloid properties of skeletal myosin binding protein-C (sMyBP-C) interacting in vivo with proteins of thick and thin filaments in the sarcomeric A-disc. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) found a rapid (5-10 min) formation of large (>2 μm) aggregates. sMyBP-C oligomers formed both at the initial 5-10 min and after 16 h of aggregation. Small angle X-ray scattering (SAXS) and DLS revealed sMyBP-C oligomers to consist of 7-10 monomers. TEM and atomic force microscopy (AFM) showed sMyBP-C to form amorphous aggregates (and, to a lesser degree, fibrillar structures) exhibiting no toxicity on cell culture. X-ray diffraction of sMyBP-C aggregates registered reflections attributed to a cross-β quaternary structure. Circular dichroism (CD) showed the formation of the amyloid-like structure to occur without changes in the sMyBP-C secondary structure. The obtained results indicating a high in vitro aggregability of sMyBP-C are, apparently, a consequence of structural features of the domain organization of proteins of this family. Formation of pathological amyloid or amyloid-like sMyBP-C aggregates in vivo is little probable due to amino-acid sequence low identity (<26%), alternating ordered/disordered regions in the protein molecule, and S-S bonds providing for general stability.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms22020731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7828380PMC
January 2021

Disordered Residues and Patterns in the Protein Data Bank.

Molecules 2020 Mar 27;25(7). Epub 2020 Mar 27.

Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia.

We created a new library of disordered patterns and disordered residues in the Protein Data Bank (PDB). To obtain such datasets, we clustered the PDB and obtained the groups of chains with different identities and marked disordered residues. We elaborated a new procedure for finding disordered patterns and created a new version of the library. This library includes three sets of patterns: unique patterns, patterns consisting of two kinds of amino acids, and homo-repeats. Using this database, the user can: (1) find homologues in the entire Protein Data Bank; (2) perform a statistical analysis of disordered residues in protein structures; (3) search for disordered patterns and homo-repeats; (4) search for disordered regions in different chains of the same protein; (5) download clusters of protein chains with different identity from our database and library of disordered patterns; and (6) observe 3D structure interactively using MView. A new library of disordered patterns will help improve the accuracy of predictions for residues that will be structured or unstructured in a given region.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/molecules25071522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180803PMC
March 2020

Extracorporeal ureter handling during laparoscopic pyeloplasty: tips and tricks for beginners.

Cent European J Urol 2019 6;72(4):413-417. Epub 2019 Dec 6.

Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia.

Introduction: Laparoscopic preparation of the ureter is a challenging part of upper urinary tract reconstruction, due to limited depth perception provided by the camera and lack of wristed motion of most laparoscopic instruments needed for adequate spatulation and scar tissue removal. One solution has been to perform the more difficult portions of the surgery in an extracorporeal manner. A hybrid intracorporeal-extracorporeal approach to upper tract ureteral reconstruction facilitates ureteral preparation at the stage of mastering the technique.

Material And Methods: This retrospective study included 100 patients with primary ureteropelvic junction obstruction, who underwent laparoscopic pyeloplasty from 2014 to 2017. The patients were stratified into 2 groups: those who underwent conventional laparoscopic surgery and those who were managed with the hybrid approach. For the hybrid approach, externalizing the ureter to skin level required additional mobilization of the upper urinary tract.

Results: A total of 47 patients underwent conventional laparoscopic pyeloplasty and 53 - hybrid surgery. The maximum body mass index was 32. The hybrid approach was 8.5 minutes shorter compared to the conventional approach (p <0.001). No complications higher than Clavien-Dindo IIIb (n = 2) were observed (in both groups). Complete success (the resolution of pain and/or hydronephrosis) was observed in 92.5% in the hybrid group and in 95.7% in the conventional treatment group.

Conclusions: Hybrid pyeloplasty may be considered safe and effective. It has the advantage of making the surgery less challenging and time-consuming while offering improved precision. The advantages of the technique are particularly apparent during training. This technique can be recommended in the learning process of the surgeon.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5173/ceju.2019.0022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979559PMC
December 2019

Repair of cystocele and apical genital prolapse using 6-strap mesh implant.

Urologia 2020 Aug 16;87(3):130-136. Epub 2019 Dec 16.

Institute for Urology and Reproductive Health, Sechenov University, Moscow, Russia.

Objective: To assess the outcomes of surgical repair of anterior apical prolapse using the 6-strap mesh implant.

Study Design: The prospective study included 100 patients with genitourinary prolapse. We used advanced 6-strap mesh implant. The results were assessed at 1 (n = 100) and 12 (n = 93) months after surgery. Maximum follow-up was over 4 years. The anatomical outcomes according to the Pelvic Organ Prolapse Quantification system and intraoperative and postoperative complications were assessed. Stage II and higher prolapse was considered to be a recurrence. The quality of life and sexual function were assessed using Pelvic Organ Prolapse Distress Inventory 20, Pelvic Floor Impact Questionnaire 7, and Pelvic Organ Prolapse/Incontinence Sexual Questionnaire 12.

Results: Median age was 57 years (34-78 years (95% confidence interval)). All patients had stage III cystocele. The anterior vaginal wall descent in all the patients was associated with uterine descent: 37 (37%), stage II; 60 (60%), stage III; in 3 (3%), stage IV. In eight cases, postoperative de novo stress urinary incontinence developed. The quality of life improved in 93 (93%) women as judged by the Pelvic Floor Distress Inventory 20 data and in 87 (87%) women, according to the Pelvic Floor Impact Questionnaire 7 data. The desirable anatomical result (⩽stage I according to the Pelvic Organ Prolapse Quantification system) was achieved in 97 (97%) patients. With the exception of mesh fragment excision due to erosion (grade 3a), all the complications were classified as grade I according to the Clavien-Dindo classification.

Conclusion: Genitourinary prolapse repair using 6-strap mesh is efficacious and relatively safe. The method demonstrates good anatomical results in relation to both anterior and apical prolapses with relatively short-term complications.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1177/0391560319890999DOI Listing
August 2020

Repeats in S1 Proteins: Flexibility and Tendency for Intrinsic Disorder.

Int J Mol Sci 2019 May 14;20(10). Epub 2019 May 14.

Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia.

An important feature of ribosomal S1 proteins is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. For S1 proteins, little is known about the contribution of flexible regions to protein domain function. We exhaustively studied a tendency for intrinsic disorder and flexibility within and between structural domains for all available UniProt S1 sequences. Using charge-hydrophobicity plot cumulative distribution function (CH-CDF) analysis we classified 53% of S1 proteins as ordered proteins; the remaining proteins were related to molten globule state. S1 proteins are characterized by an equal ratio of regions connecting the secondary structure within and between structural domains, which indicates a similar organization of separate S1 domains and multi-domain S1 proteins. According to the FoldUnfold and IsUnstruct programs, in the multi-domain proteins, relatively short flexible or disordered regions are predominant. The lowest percentage of flexibility is in the central parts of multi-domain proteins. Our results suggest that the ratio of flexibility in the separate domains is related to their roles in the activity and functionality of S1: a more stable and compact central part in the multi-domain proteins is vital for RNA interaction, terminals domains are important for other functions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms20102377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6566611PMC
May 2019

Is there codon usage bias for poly-Q stretches in the human proteome?

J Bioinform Comput Biol 2019 02;17(1):1950010

* Institute of Protein Research, Russian Academy of Sciences, Institutskaya Str., 4, Pushchino, Moscow Region 142290, Russia.

We have analyzed codon usage for poly-Q stretches of different lengths for the human proteome. First, we have obtained that all long poly-Q stretches in Protein Data Bank (PDB) belong to the disordered regions. Second, we have found the bias for codon usage for glutamine homo-repeats in the human proteome. In the cases when the same codon is used for poly-Q stretches only CAG triplets are found. Similar results are obtained for human proteins with glutamine homo-repeats associated with diseases. Moreover, for proteins associated with diseases (from the HraDis database), the fraction of proteins for which the same codon is used for glutamine homo-repeats is less (22%) than for proteins from the human proteome (26%). We have demonstrated for poly-Q stretches in the human proteome that in some cases (28) the splicing sites correspond to the homo-repeats and in 11 cases, these sites appear at the -terminal part of the homo-repeats with statistical significance 10 .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1142/S0219720019500100DOI Listing
February 2019

Proteome Evolution of Deep-Sea Hydrothermal Vent Alvinellid Polychaetes Supports the Ancestry of Thermophily and Subsequent Adaptation to Cold in Some Lineages.

Genome Biol Evol 2017 02;9(2):279-296

Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29688 Roscoff, France.

Temperature, perhaps more than any other environmental factor, is likely to influence the evolution of all organisms. It is also a very interesting factor to understand how genomes are shaped by selection over evolutionary timescales, as it potentially affects the whole genome. Among thermophilic prokaryotes, temperature affects both codon usage and protein composition to increase the stability of the transcriptional/translational machinery, and the resulting proteins need to be functional at high temperatures. Among eukaryotes less is known about genome evolution, and the tube-dwelling worms of the family Alvinellidae represent an excellent opportunity to test hypotheses about the emergence of thermophily in ectothermic metazoans. The Alvinellidae are a group of worms that experience varying thermal regimes, presumably having evolved into these niches over evolutionary times. Here we analyzed 423 putative orthologous loci derived from 6 alvinellid species including the thermophilic Alvinella pompejana and Paralvinella sulfincola. This comparative approach allowed us to assess amino acid composition, codon usage, divergence, direction of residue changes and the strength of selection along the alvinellid phylogeny, and to design a new eukaryotic thermophilic criterion based on significant differences in the residue composition of proteins. Contrary to expectations, the alvinellid ancestor of all present-day species seems to have been thermophilic, a trait subsequently maintained by purifying selection in lineages that still inhabit higher temperature environments. In contrast, lineages currently living in colder habitats likely evolved under selective relaxation, with some degree of positive selection for low-temperature adaptation at the protein level.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/gbe/evw298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381640PMC
February 2017

How Common Is Disorder? Occurrence of Disordered Residues in Four Domains of Life.

Int J Mol Sci 2015 Aug 18;16(8):19490-507. Epub 2015 Aug 18.

Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia.

Disordered regions play important roles in protein adaptation to challenging environmental conditions. Flexible and disordered residues have the highest propensities to alter the protein packing. Therefore, identification of disordered/flexible regions is important for structural and functional analysis of proteins. We used the IsUnstruct program to predict the ordered or disordered status of residues in 122 proteomes, including 97 eukaryotic and 25 large bacterial proteomes larger than 2,500,000 residues. We found that bacterial and eukaryotic proteomes contain comparable fraction of disordered residues, which was 0.31 in the bacterial and 0.38 in the eukaryotic proteomes. Additional analysis of the total of 1540 bacterial proteomes of various sizes yielded a smaller fraction of disordered residues, which was only 0.26. Together, the results showed that the larger is the size of the proteome, the larger is the fraction of the disordered residues. A continuous dependence of the fraction of disordered residues on the size of the proteome is observed for four domains of life: Eukaryota, Bacteria, Archaea, and Viruses. Furthermore, our analysis of 122 proteomes showed that the fraction of disordered residues increased with increasing the length of homo-repeats for polar, charged, and small residues, and decreased for hydrophobic residues. The maximal fraction of disordered residues was obtained for proteins containing lysine and arginine homo-repeats. The minimal fraction was found in valine and leucine homo-repeats. For 15-residue long homo-repeats these values were 0.2 (for Val and Leu) and 0.7 (for Lys and Arg).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms160819490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581309PMC
August 2015

HRaP: database of occurrence of HomoRepeats and patterns in proteomes.

Nucleic Acids Res 2014 Jan 22;42(Database issue):D273-8. Epub 2013 Oct 22.

Group of Bioinformatics, Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.

We focus our attention on multiple repeats of one amino acid (homorepeats) and create a new database (named HRaP, at http://bioinfo.protres.ru/hrap/) of occurrence of homorepeats and disordered patterns in different proteomes. HRaP is aimed at understanding the amino acid tandem repeat function in different proteomes. Therefore, the database includes 122 proteomes, 97 eukaryotic and 25 bacterial ones that can be divided into 9 kingdoms and 5 phyla of bacteria. The database includes 1,449,561 protein sequences and 771,786 sequences of proteins with GO annotations. We have determined homorepeats and patterns that are associated with some function. Through our web server, the user can do the following: (i) search for proteins with the given homorepeat in 122 proteomes, including GO annotation for these proteins; (ii) search for proteins with the given disordered pattern from the library of disordered patterns constructed on the clustered Protein Data Bank in 122 proteomes, including GO annotations for these proteins; (iii) analyze lengths of homorepeats in different proteomes; (iv) investigate disordered regions in the chosen proteins in 122 proteomes; (v) study the coupling of different homorepeats in one protein; (vi) determine longest runs for each amino acid inside each proteome; and (vii) download the full list of proteins with the given length of a homorepeat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965023PMC
January 2014

A novel web server predicts amino acid residue protection against hydrogen-deuterium exchange.

Bioinformatics 2013 Jun 24;29(11):1375-81. Epub 2013 Apr 24.

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.

Motivation: To clarify the relationship between structural elements and polypeptide chain mobility, a set of statistical analyses of structures is necessary. Because at present proteins with determined spatial structures are much less numerous than those with amino acid sequence known, it is important to be able to predict the extent of proton protection from hydrogen-deuterium (HD) exchange basing solely on the protein primary structure.

Results: Here we present a novel web server aimed to predict the degree of amino acid residue protection against HD exchange solely from the primary structure of the protein chain under study. On the basis of the amino acid sequence, the presented server offers the following three possibilities (predictors) for user's choice. First, prediction of the number of contacts occurring in this protein, which is shown to be helpful in estimating the number of protons protected against HD exchange (sensitivity 0.71). Second, probability of H-bonding in this protein, which is useful for finding the number of unprotected protons (specificity 0.71). The last is the use of an artificial predictor. Also, we report on mass spectrometry analysis of HD exchange that has been first applied to free amino acids. Its results showed a good agreement with theoretical data (number of protons) for 10 globular proteins (correlation coefficient 0.73). We pioneered in compiling two datasets of experimental HD exchange data for 35 proteins.

Availability: The H-Protection server is available for users at http://bioinfo.protres.ru/ogp/

Supplementary Information: Supplementary data are available at Bioinformatics online.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt168DOI Listing
June 2013
-->