Protein Structure Comparison Research Articles

Quantifying uncertainty of molecular mismatch introduced by mislabeled ancestry using haplotype-based HLA genotype imputation.

Modern histocompatibility algorithms depend on the comparison and analysis of high-resolution HLA protein sequences and structures, especially when considering epitope-based algorithms, which aim to model the interactions involved in antibody or T cell binding. HLA genotype imputation can be performed in the cases where only low/intermediate-resolution HLA genotype is available or if specific loci are missing, and by providing an individuals' race/ethnicity/ancestry information, imputation results can be more accurate. This study assesses the effect of imputing high-resolution genotypes on molecular mismatch scores under a variety of ancestry assumptions. We compared molecular matching scores from "ground-truth" high-resolution genotypes against scores from genotypes which are imputed from low-resolution genotypes. Analysis was focused on a simulated patient-donor dataset and confirmed using two real-world datasets, and deviations were aggregated based on various ancestry assumptions. We observed that using multiple imputation generally results in lower error in molecular matching scores compared to single imputation, and that using the correct ancestry assumptions can reduce error introduced during imputation. We conclude that for epitope analysis, imputation is a valuable and low-risk strategy, as long as care is taken regarding epitope analysis context, ancestry assumptions, and (multiple) imputation strategy.

Prediction of protein-ligand binding sites modulating activity of MAST protein kinases

Aim. Identification of the protein-ligand binding sites, that may be the target of compounds, affecting individual human protein kinases of the MAST family (MAST1, 2, 3, 4 and MASTL / GWL). Methods. Literature and database search. Comparison of protein and ligand structures. Protein structure modeling, structural superimposition, etc. Results. The structural alignment demonstrates significant similarity of catalytic domains in MAST1, 2, 3, 4 and MASTL (GWL). It justifies transferring of reference ligands from PDB structures to human MASTs, discovering potential sites of ligand binding. 13 sites of ligand-binding were specified based on refrence ligands, transferred from RCSB Protein Data Bank structures, and differences in sites amino acid composition of MAST family members were discovered. Сonclusions. Based on the differences in the amino acid composition of the studied pockets in MAST1, 2, 3, 4 and MASTL (GWL), the sites B, C, D, E, F, were selected for further study and virtual screening for new selective inhibitors of individual members of MAST protein kinase family.

Genomic transfers help to decipher the ancient evolution of filoviruses and interactions with vertebrate hosts.

Although several filoviruses are dangerous human pathogens, there is conflicting evidence regarding their origins and interactions with animal hosts. Here we attempt to improve this understanding using the paleoviral record over a geological time scale, protein structure predictions, tests for evolutionary maintenance, and phylogenetic methods that alleviate sources of bias and error. We found evidence for long branch attraction bias in the L gene tree for filoviruses, and that using codon-specific models and protein structural comparisons of paleoviruses ameliorated conflict and bias. We found evidence for four ancient filoviral groups, each with extant viruses and paleoviruses with open reading frames. Furthermore, we found evidence of repeated transfers of filovirus-like elements to mouse-like rodents. A filovirus-like nucleoprotein ortholog with an open reading frame was detected in three subfamilies of spalacid rodents (present since the Miocene). We provide evidence that purifying selection is acting to maintain amino acids, protein structure and open reading frames in these elements. Our finding of extant viruses nested within phylogenetic clades of paleoviruses informs virus discovery methods and reveals the existence of Lazarus taxa among RNA viruses. Our results resolve a deep conflict in the evolutionary framework for filoviruses and reveal that genomic transfers to vertebrate hosts with potentially functional co-options have been more widespread than previously appreciated.

Molecular insights into MpAGO1 and its regulatory miRNA, miR11707, in the high-temperature acclimation of Marchantia polymorpha.

As a model plant for bryophytes, Marchantia polymorpha offers insights into the role of RNA silencing in aiding early land plants navigate the challenges posed by high-temperature environments. Genomic analysis revealed unique ARGONAUTE1 ortholog gene (MpAGO1) in M. polymorpha that is regulated by two species-specific microRNAs (miRNAs), miR11707.1 and miR11707.2. Comparative studies of small RNA profiles from M. polymorpha cellular and MpAGO1 immunoprecipitation (MpAGO1-IP) profiles at various temperatures, along with analyses of Arabidopsis AGO1 (AtAGO1), revealed that MpAGO1 has a low-selectivity for a diverse range of small RNA species than AtAGO1. Protein structural comparisons revealed no discernible differences in the MID domains of MpAGO1 and AtAGO1, suggesting the complexity of miRNA species specificity and necessitating further exploration. Small RNA profiling and size exclusion chromatography have pinpointed a subset of M. polymorpha miRNAs, notably miR11707, that remain in free form within the cell at 22°C but are loaded into MpAGO1 at 28°C to engage in RNA silencing. Investigations into the mir11707 gene editing (mir11707ge) mutants provided evidence of the regulation of miR11707 in MpAGO1. Notably, while MpAGO1 mRNA expression decreases at 28°C, the stability of the MpAGO1 protein and its associated miRNAs is essential for enhancing the RISC activity, revealing the importance of RNA silencing in enabling M. polymorpha to survive thermal stress. This study advances our understanding of RNA silencing in bryophytes and provides groundbreaking insights into the evolutionary resilience of land plants to climatic adversities.

Insights into structural vaccinology harnessed for universal coronavirus vaccine development.

Structural vaccinology is pivotal in expediting vaccine design through high-throughput screening of immunogenic antigens. Leveraging the structural and functional characteristics of antigens and immune cell receptors, this approach employs protein structural comparison to identify conserved patterns in key pathogenic components. Molecular modeling techniques, including homology modeling and molecular docking, analyze specific three-dimensional (3D) structures and protein interactions and offer valuable insights into the 3D interactions and binding affinity between vaccine candidates and target proteins. In this review, we delve into the utilization of various immunoinformatics and molecular modeling tools to streamline the development of broad-protective vaccines against coronavirus disease 2019 variants. Structural vaccinology significantly enhances our understanding of molecular interactions between hosts and pathogens. By accelerating the pace of developing effective and targeted vaccines, particularly against the rapidly mutating severe acute respiratory syndrome coronavirus 2 and other prevalent infectious diseases, this approach stands at the forefront of advancing immunization strategies. The combination of computational techniques and structural insights not only facilitates the identification of potential vaccine candidates but also contributes to the rational design of vaccines, fostering a more efficient and targeted approach to combatting infectious diseases.

Deciphering the Genetic Variation: A Comparative Analysis of Parental and Attenuated Strains of the QXL87 Vaccine for Infectious Bronchitis.

The QXL87 live attenuated vaccine strain for infectious bronchitis represents the first approved QX type (GI-19 lineage) vaccine in China. This strain was derived from the parental strain CK/CH/JS/2010/12 through continuous passage in SPF chicken embryos. To elucidate the molecular mechanism behind its attenuation, whole-genome sequencing was conducted on both the parental and attenuated strains. Analysis revealed 145 nucleotide mutations in the attenuated strain, leading to 48 amino acid mutations in various proteins, including Nsp2 (26), Nsp3 (14), Nsp4 (1), S (4), 3a (1), E (1), and N (1). Additionally, a frameshift mutation caused by a single base insertion in the ORFX resulted in a six-amino-acid extension. Subsequent comparison of post-translational modification sites, protein structure, and protein-protein binding sites between the parental and attenuated strains identified three potential virulence genes: Nsp2, Nsp3, and S. The amino acid mutations in these proteins not only altered their conformation but also affected the distribution of post-translational modification sites and protein-protein interaction sites. Furthermore, three potential functional mutation sites-P106S, A352T, and L472F, all located in the Nsp2 protein-were identified through PROVEAN, PolyPhen, and I-Mutant. Overall, our findings suggest that Nsp2, Nsp3, and S proteins may play a role in modulating IBV pathogenicity, with a particular focus on the significance of the Nsp2 protein. This study contributes to our understanding of the molecular mechanisms underlying IBV attenuation and holds promise for the development of safer live attenuated IBV vaccines using reverse genetic approaches.

The complete catalog of antimicrobial resistance secondary active transporters in Clostridioides difficile: evolution and drug resistance perspective

Secondary active transporters shuttle substrates across eukaryotic and prokaryotic membranes, utilizing different electrochemical gradients. They are recognized as one of the antimicrobial efflux pumps among pathogens. While primary active transporters within the genome of C. difficile 630 have been completely cataloged, the systematical study of secondary active transporters remains incomplete. Here, we not only identify secondary active transporters but also disclose their evolution and role in drug resistance in C. difficile 630. Our analysis reveals that C. difficile 630 carries 147 secondary active transporters belonging to 27 (super)families. Notably, 50 (34%) of them potentially contribute to antimicrobial resistance (AMR). AMR-secondary active transporters are structurally classified into five (super)families: the p-aminobenzoyl-glutamate transporter (AbgT), drug/metabolite transporter (DMT) superfamily, major facilitator (MFS) superfamily, multidrug and toxic compound extrusion (MATE) family, and resistance-nodulation-division (RND) family. Surprisingly, complete RND genes found in C. difficile 630 are likely an evolutionary leftover from the common ancestor with the diderm. Through protein structure comparisons, we have potentially identified six novel AMR-secondary active transporters from DMT, MATE, and MFS (super)families. Pangenome analysis revealed that half of the AMR-secondary transporters are accessory genes, which indicates an important role in adaptive AMR function rather than innate physiological homeostasis. Gene expression profile firmly supports their ability to respond to a wide spectrum of antibiotics. Our findings highlight the evolution of AMR-secondary active transporters and their integral role in antibiotic responses. This marks AMR-secondary active transporters as interesting therapeutic targets to synergize with other antibiotic activity.

Genome-wide analysis of gustatory receptor genes and identification of the fructose gustatory receptor in Arma chinensis

Gustatory receptors (GRs) allow insects to sense tastes in their external environment. Gustatory perception is crucial for distinguishing between beneficial and harmful or toxic compounds, affecting survival. This study is the first to identify and classify the GR genes and investigate their expression in the predatory Arma chinensis. Thirteen GR genes (ArmaGr1–ArmaGr13) were identified and classified into four families via phylogenetic analysis. In the predacious developmental stages, ArmaGr7 expression gradually increased from the 2nd to 5th instar stages and then to adults. However, ArmaGr7 was also highly expressed in the non-predation 1st instar nymph and egg stages. ArmaGr7 expression was localized in the antennae, scalpella, forelegs, wings, head, and midgut of male and female adults, with wings displaying the highest expression. Furthermore, ArmaGr7 expression was positively correlated with fructose solution intake; molecular docking results showed that fructose could effectively dock withArmaGr7. A protein structure comparison revealed that the ArmaGr7 structure was different from that of other GR43a-like proteins, which may be related to the gene splicing of the A. chinensis GR gene. These results elucidate the crucial role of ArmaGr7 in fructose recognition by A. chinensis and provide a foundation for further studies on gustatory perception.

LGP2 Facilitates Bacterial Escape through Binding Peptidoglycan via EEK Motif and Suppressing NOD2-RIP2 Axis in Cyprinidae and Xenocyprididae Families.

RIG-I-like receptors and NOD-like receptors play pivotal roles in recognizing microbe-associated molecular patterns and initiating immune responses. The LGP2 and NOD2 proteins are important members of the RIG-I-like receptor and NOD-like receptor families, recognizing viral RNA and bacterial peptidoglycan (PGN), respectively. However, in some instances bacterial infections can induce LPG2 expression via a mechanism that remains largely unknown. In the current study, we found that LGP2 can compete with NOD2 for PGN binding and inhibit antibacterial immunity by suppressing the NOD2-RIP2 axis. Recombinant CiLGP2 (Ctenopharyngodon idella LGP2) produced using either prokaryotic or eukaryotic expression platform can bind PGN and bacteria in pull-down and ELISA assays. Comparative protein structure models and intermolecular interaction prediction calculations as well as pull-down and colocalization experiments indicated that CiLGP2 binds PGN via its EEK motif with species and structural specificity. EEK deletion abolished PGN binding of CiLGP2, but insertion of the CiLGP2 EEK motif into zebrafish and mouse LGP2 did not confer PGN binding activity. CiLGP2 also facilitates bacterial replication by interacting with CiNOD2 to suppress expression of NOD2-RIP2 pathway genes. Sequence analysis and experimental verification demonstrated that LGP2 having EEK motif that can negatively regulate antibacterial immune function is present in Cyprinidae and Xenocyprididae families. These results show that LGP2 containing EEK motif competes with NOD2 for PGN binding and suppresses antibacterial immunity by inhibiting the NOD2-RIP2 axis, indicating that LGP2 plays a crucial negative role in antibacterial response beyond its classical regulatory function in antiviral immunity.

Diversity, origin, and evolution of the ESCRT systems.

Endosomal sorting complexes required for transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold and using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The last archaeal common ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.IMPORTANCEAll eukaryotic cells possess complex intracellular membrane organization. Endosomal sorting complexes required for transport (ESCRT) play a central role in membrane remodeling which is essential for cellular functionality in eukaryotes. Recently, it has been shown that Asgard archaea, the archaeal phylum that includes the closest known relatives of eukaryotes, encode homologs of many components of the ESCRT systems. We employed protein sequence and structure comparisons to reconstruct the evolution of ESCRT systems in archaea and identified several previously unknown homologs of ESCRT subunits, some of which can be predicted to participate in cell division. The results of this reconstruction indicate that the last archaeal common ancestor already encoded a complex ESCRT system that was involved in protein sorting. In Asgard archaea, ESCRT systems evolved toward greater complexity, and in particular, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was established.

Diversity, Origin and Evolution of the ESCRT Systems.

All eukaryotic cells possess complex intracellular membrane organization. ESCRT (Endosomal Sorting Complexes Required for Transport) plays a central role in membrane remodeling which is essential for cellular functionality in eukaryotes. Recently, it has been shown that Asgard archaea, the archaeal phylum that includes the closest known relatives of eukaryotes, encode homologs of many components of the ESCRT systems. We employed protein sequence and structure comparisons to reconstruct the evolution of ESCRT systems in archaea and identified several previously unknown homologs of ESCRT subunits, some of which can be predicted to participate in cell division. The results of this reconstruction indicate that the Last Archaeal Common ancestor already encoded a complex ESCRT system that was involved in protein sorting. In Asgard archaea, ESCRT systems evolved towards greater complexity, and in particular, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was established.

Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison.

Protein structure comparison is pivotal for deriving homological relationships, elucidating protein functions, and understanding evolutionary developments. The burgeoning field of in-silico protein structure prediction now yields billions of models with near-experimental accuracy, necessitating sophisticated tools for discerning structural similarities among proteins, particularly when sequence similarity is limited. In this article, we have developed the align distance matrix with scale (ADAMS) pipeline, which synergizes the distance matrix alignment method with the scale-invariant feature transform algorithm, streamlining protein structure comparison on a proteomic scale. Utilizing a computer vision-centric strategy for contrasting disparate distance matrices, ADAMS adeptly alleviates challenges associated with proteins characterized by a high degree of structural flexibility. Our findings indicate that ADAMS achieves a level of performance and accuracy on par with Foldseek, while maintaining similar speed. Crucially, ADAMS overcomes certain limitations of Foldseek in handling structurally flexible proteins, establishing it as an efficacious tool for in-depth protein structure analysis with heightened accuracy. ADAMS can be download and used as a python package from Python Package Index (PyPI): adams · PyPI. Source code and other materials are available from young55775/ADAMS-developing (github.com). An online server is available: Bseek Search Server (cryonet.ai).

Comparative Structural Analysis of The Homeodomain Protein in the Bipolar Basidiomycete, Mycoleptodonoides aitchisonii (Bunaharitake)

Mycoleptodonoides aitchisonii is a bipolar mushroom with monokaryons can form clamp cells, regardless of the mating type. Previously, only HD2-18 was identifi ed and characterized at the A locus of Maspi18 (A1). In this study, unlike the A locus in strain Maspi18, HD1-7-like gene (Mahd1-7) and HD2-7 gene (Mahd2-7) were identifi ed at the A locus of the compatible strain Maspi7 (A2), but the nine fl anking genes were highly conserved, suggesting that recombination events may have occurred between HD1 and HD2 genes over evolutionary time. Following phylogenetic and HD protein structural comparisons with other basidiomycetes, homeodomains were identifi ed in HD2-7 and HD2-18, but the former lacked nuclear localization signals (NLS) whereas the latter, like the HD1-7-like protein, did not. These fi ndings indicated that one homeodomain and several NLS on the same or different HD proteins is the minimum suffi cient for driving clamp cell formation in M. aitchisonii. The fi ndings implied that over evolutionary time, unlike HD2, the homeodomain in HD1 does not play a major role in clamp cell formation, and that HD1-7 performs the function of carrying the NLS. Herein, we propose a new hypothesis for clamp cell formation in M. aitchisonii. The fi ndings of this study provide a foundation for understanding the role of heterokaryonization in basidiomycete mushrooms.

Associations between ALDOB polymorphisms and intrahepatic cholestasis of pregnancy susceptibility in the Chinese Han population.

To research the associations between fructose-bisphosphate aldolase B (ALDOB) gene polymorphisms and intrahepatic cholestasis of pregnancy (ICP) risk. Whole-genome sequencing (WGS) was performed to detect ALDOB polymorphisms. Five web-available tools were employed to predict the effect of the site variant on the protein. Protein structure comparisons between the reference and ALDOB-modified samples were performed by SWISS-MODEL and Chimera 1.14rc, respectively. We identified 28 genetic variants in the ALDOB gene. When the cut-off value of minor allele frequency (MAF) of loci was 0.001 in four databases, five missense variants, including rs747604233, rs759204107, rs758242037, rs371526091 and rs77718928, were reserved for subsequent analysis. These variants were absent from the 1029 control individuals. The influence of all five variants on protein function was predicted to be damaging by the abovementioned five prediction software programs. Bioinformatics analysis demonstrated that these five missense variants were highly conserved among vertebrates. Compared to the wild-type protein structure, all five mutated protein structures showed a slight change in the chemical bond lengths of the enzyme activity domains. The combined clinical data indicate that the variant group had a significantly older age (p = 0.038), a higher level of indirect bilirubin (IDBIL, p = 0.033), and lower counts of white blood cells (WBCs, p = 7.38E-05) and platelets (PLTs, p = 0.018) than the wild-type group. This is the first study to examine the associations between ALDOB polymorphisms and ICP disease in 249 Chinese patients with ICP. Our present study expands the understanding of the pathogenesis of ICP.

Effect of fat concentration on protein digestibility of Chinese sausage

Chinese sausage is a popular traditional Chinese meat product, but its high-fat content makes consumers hesitant. The purpose of this study is to compare the nutritional differences of Chinese sausages with different fermentation times (0, 10, 20, 30 d) and fat content (the initial content was 11.59% and 20.14%) during digestion. The comparison of digestion degree, protein structure, and peptide composition between different sausages were studied through in vitro simulated digestion. Chinese sausages with high-fat content had higher α-helix, β-turn, and random coil, making them easier to digest. The fermentation process made this phenomenon more pronounced. The high-fat sausage fermented for 10 d showed the highest release of primary amino acids (about 9.5%), which was about 3.5% higher than the low-fat sausage under the same conditions. The results of peptidomics confirmed the relevant conclusions. After gastric digestion, the types of peptides in the digestive fluid of high-fat sausages were generally more than those in low-fat sausages, while after intestinal digestion, the opposite results were observed. The type of peptide reached its peak after fermentation for 20 d. These findings are of obvious significance for selecting the appropriate fermentation time and fat content of Chinese sausages.

Transcriptome-based network analysis of cell cycle-related genes in response to blue and red light in maize

Abstract In maize, blue and red light are key environmental factors regulating cell-cycle progression. We used transcriptomics to investigate and compare differential gene expression under the four light conditions: red light, blue light, red converted to blue and blue converted to red. A total of 23 differentially expressed genes were identified. The gene–gene interaction analysis indicated a significant interaction between four unidentified genes, 100191551, pco143873, 100284747 and pco060490, and cell-cycle-related genes. Using multiple sequence alignment analysis and protein structure comparisons, we show here that these four unidentified genes were characterized as ALP1-like, ALP1, cyclin P1-1 and AEBP2, respectively. By constructing a protein–protein interaction network, we inferred that 100191551 and pco143873 are potentially regulated to avoid DNA damage by abiotic stress response factors in the cell cycle. The gene 100284747 regulates the cell cycle in response to phosphate starvation signalling. The gene pco060490 potentially negatively regulates the cell cycle through the mediation of Histone H3 and CYCD6 in response to red light. In conclusion, the cell-cycle-related genes are sensitive to blue and red light, and four novel functional genes may be involved in the cell cycle.

Biodegradation of poly(ethylene terephthalate) through PETase surface-display: From function to structure

Polyethylene terephthalate (PET) is one of the most used plastics which has caused some environmental pollution and social problems. Although many newly discovered or modified PET hydrolases have been reported at present, there is still a lack of comparison between their hydrolytic capacities, as well as the need for new biotechnology to apply them for the PET treatment. Here, we systematically studied the surface-display technology for PET hydrolysis using several PET hydrolases. It is found that anchoring protein types had little influence on the surface-display result under T7 promoter, while the PET hydrolase types were more important. By contrast, the newly reported FAST-PETase showed the strongest hydrolysis effect, achieving 71.3% PET hydrolysis in 24 h by pGSA-FAST-PETase. Via model calculation, FAST-PETase indeed exhibited higher temperature tolerance and catalytic capacity. Besides, smaller particle size and lower crystallinity favored the hydrolysis of PET pellets. Through protein structure comparison, we summarized the common characteristics of efficient PET-hydrolyzing enzymes and proposed three main crystal structures of PET enzymes via crystal structural analysis, with ISPETase being the representative and main structure. Surface co-display of FAST-PETase and MHETase can promote the hydrolysis of PET, and the C-terminal of the fusion protein is crucial for PET hydrolysis. The results of our research can be helpful for PET contamination removal as well as other areas involving the application of enzymes. SynopsisThis research can promote the development of better PET hydrolase and its applications in PET pollution treatment via bacteria surface-display.

Genome-wide identification and evolutionary analysis of the FGF gene family in buffalo

Fibroblast growth factors (FGFs) are important polypeptide growth factors that play a critical role in many developmental processes, including differentiation, cell proliferation, and migration in mammals. This study employs in silico analyses to characterize the FGF gene family in buffalo, investigating their genome-wide identification, physicochemical properties, and evolutionary patterns. For this purpose, genomic and proteomic sequences of buffalo, cattle, goat, and sheep were retrieved from NCBI database. We identified a total of 22 FGF genes in buffalo. Physicochemical properties observed through ProtParam tool showed notable features of these proteins including in-vitro instability, thermostability, hydrophilicity, and basic nature. Phylogenetic analysis grouped 22 identified genes into nine sub-families based on evolutionary relationships. Additionally, analysis of gene structure, motif patterns, and conserved domains using TBtools revealed the remarkable conservation of this gene family across selected species throughout the course of evolution. Comparative amino acid analysis performed through ClustalW demonstrated significant conservation between buffalo and cattle FGF proteins. Mutational analysis showed three non-synonymous mutations at positions R103 > G, P7 > L, and E98 > Q in FGF4, FGF6, and FGF19, respectively in buffalo. Duplication events revealed only one segmental duplication (FGF10/FGF22) in buffalo and two in cattle (FGF10/FGF22 and FGF13/FGF13-like) with Ka/Ks values <1 indicating purifying selection pressure for these duplications. Comparison of protein structures of buffalo, goat, and sheep exhibited more similarities in respective structures. In conclusion, our study highlights the conservation of the FGF gene family in buffalo during evolution. Furthermore, the identified non-synonymous mutations may have implications for the selection of animals with better performance. Communicated by Ramaswamy H. Sarma

Differences in amino acid composition of carrot α-tubulin potentially confer the resistance to dinitroaniline herbicides

Aim. To reveal the features of amino acid composition of carrot α-tubulin isotypes that potentially determine natural tolerance to dinitroaniline herbicides. Methods. Literature and database search. Comparison of protein sequences and structures: multiple sequence alignment, phylogenetic profiling, protein and ligand structure modeling, etc. Results. Genomic and proteomic analysis of Daucus carota has revealed at least eight unique isotypes of α-tubulin that differ in amino acid sequences and gene loci. Remarkable differences in amino acid composition of the dinitroanilinebinding-like (DBL) region of analyzed α-tubulin have been revealed, which may be the reason of its natural resistance to these compounds. Сonclusions. Differences in amino acids at positions of canonical mutations – Cys4 (TBA1, 2, 3, 6, 7 and 8), Thr53 (TBA6), Ile202 (TBA1 and 7) and Met202 (TBA5), as well as previously undescribed non-canonical substitutions – Ile4 (TBA4 and 5), Cys52 (TBA6), Ser201 (TBA1, 2, 3 and 8) and Val194 (TBA4 and 5), were noted as potentially associated with natural tolerance of the carrot to dinitroaniline herbicides.

Structural profile of ligand-based inhibition of bacterial FtsZ

Aim. The idea of the study was to compare and generalize RCSB Protein Data Bank and ChEMBL data in order to establish the structural and biological relationship of experimentaly proved effectors of FtsZ with binding sites. Methods. Literature and database search. Comparison of protein and ligand structures. Protein structure modeling, MD, structural superimposition, etc. Results. The experimental protein-ligand complexes structures of bacterial FtsZ were revised. The structural superimposition of experinental PDB and full-atomic AlphaFold2 models of bacterial FtsZs confirmed their significant structural similarity. Three protein-ligand binding sites were identified by structural alignment. The rating based on database (RCSB Protein Data Bank, ChEMBL, DrugBank, BindingDB, PubChem), patente and literature information on FtsZ-ligand interactions identify perspective sites and main reference compounds. Сonclusions. It was identifyd 3 main protein-ligand binding regions in FtsZ: I. Nucleotide Binding Domain (Ia. Site of GTP/GDP and Ib. MB3 site); II. Site of inter-domain cleft (IDC) and III. Site of coumarin bindig (4HC = 4-hydroxycoumarin). It was indicated that benzamide-binding site, located in the region of inter-domain cleft of FtsZ, demonstrate highest site- and target-specificity.