scholarly journals Marine Morbilliviruses: Diversity and Interaction with Signaling Lymphocyte Activation Molecules

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 606 ◽  
Author(s):  
Kazue Ohishi ◽  
Tadashi Maruyama ◽  
Fumio Seki ◽  
Makoto Takeda
Keyword(s):  
Three Dimensional ◽  
Lymphocyte Activation ◽  
In Silico Analysis ◽  
Cetacean Species ◽  
Baleen Whales ◽  
Phocine Distemper Virus ◽  
H Protein ◽  
Dimensional Crystal ◽  
Silico Analysis ◽  
Insight Into

Epidemiological reports of phocine distemper virus (PDV) and cetacean morbillivirus (CeMV) have accumulated since their discovery nearly 30 years ago. In this review, we focus on the interaction between these marine morbilliviruses and their major cellular receptor, the signaling lymphocyte activation molecule (SLAM). The three-dimensional crystal structure and homology models of SLAMs have demonstrated that 35 residues are important for binding to the morbillivirus hemagglutinin (H) protein and contribute to viral tropism. These 35 residues are essentially conserved among pinnipeds and highly conserved among the Caniformia, suggesting that PDV can infect these animals, but are less conserved among cetaceans. Because CeMV can infect various cetacean species, including toothed and baleen whales, the CeMV-H protein is postulated to have broader specificity to accommodate more divergent SLAM interfaces and may enable the virus to infect seals. In silico analysis of viral H protein and SLAM indicates that each residue of the H protein interacts with multiple residues of SLAM and vice versa. The integration of epidemiological, virological, structural, and computational studies should provide deeper insight into host specificity and switching of marine morbilliviruses.

scholarly journals A new insight into role of phosphoketolase pathway in Synechocystis sp. PCC 6803

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Anushree Bachhar ◽  
Jiri Jablonsky
Keyword(s):  
In Silico Analysis ◽  
Bioinformatic Analysis ◽  
Phosphoglycerate Mutase ◽  
Phosphoketolase Pathway ◽  
Multi Level ◽  
Silico Analysis ◽  
Insight Into ◽  
Synechocystis Sp ◽  
Pcc 6803

AbstractPhosphoketolase (PKET) pathway is predominant in cyanobacteria (around 98%) but current opinion is that it is virtually inactive under autotrophic ambient CO2 condition (AC-auto). This creates an evolutionary paradox due to the existence of PKET pathway in obligatory photoautotrophs. We aim to answer the paradox with the aid of bioinformatic analysis along with metabolic, transcriptomic, fluxomic and mutant data integrated into a multi-level kinetic model. We discussed the problems linked to neglected isozyme, pket2 (sll0529) and inconsistencies towards the explanation of residual flux via PKET pathway in the case of silenced pket1 (slr0453) in Synechocystis sp. PCC 6803. Our in silico analysis showed: (1) 17% flux reduction via RuBisCO for Δpket1 under AC-auto, (2) 11.2–14.3% growth decrease for Δpket2 in turbulent AC-auto, and (3) flux via PKET pathway reaching up to 252% of the flux via phosphoglycerate mutase under AC-auto. All results imply that PKET pathway plays a crucial role under AC-auto by mitigating the decarboxylation occurring in OPP pathway and conversion of pyruvate to acetyl CoA linked to EMP glycolysis under the carbon scarce environment. Finally, our model predicted that PKETs have low affinity to S7P as a substrate.

scholarly journals Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective

2020 ◽  
Vol 8 (5) ◽  
pp. 723
Author(s):  
Guillermo Blanco ◽  
Lorena Ruiz ◽  
Hector Tamés ◽  
Patricia Ruas-Madiedo ◽  
Florentino Fdez-Riverola ◽  
...  
Keyword(s):  
In Silico ◽  
Genetic Background ◽  
Bifidobacterium Longum ◽  
In Silico Analysis ◽  
Glycoside Hydrolases ◽  
Computational Tools ◽  
Beneficial Effects ◽  
Silico Analysis ◽  
Insight Into

Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest.

scholarly journals Trophoblast glycoprotein is a new candidate gene for Parkinson’s disease

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sanghyun Park ◽  
Jeong-Eun Yoo ◽  
Gyu-Bum Yeon ◽  
Jin Hee Kim ◽  
Jae Souk Lee ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Candidate Gene ◽  
In Silico Analysis ◽  
Substantia Nigra Pars Compacta ◽  
Behavioral Deficits ◽  
Genetic Ablation ◽  
Progressive Degeneration ◽  
Silico Analysis ◽  
Insight Into

AbstractParkinson’s disease (PD) is a movement disorder caused by progressive degeneration of the midbrain dopaminergic (mDA) neurons in the substantia nigra pars compacta (SNc). Despite intense research efforts over the past decades, the etiology of PD remains largely unknown. Here, we discovered the involvement of trophoblast glycoprotein (Tpbg) in the development of PD-like phenotypes in mice. Tpbg expression was detected in the ventral midbrain during embryonic development and in mDA neurons in adulthood. Genetic ablation of Tpbg resulted in mild degeneration of mDA neurons in aged mice (12–14 months) with behavioral deficits reminiscent of PD symptoms. Through in silico analysis, we predicted potential TPBG-interacting partners whose functions were relevant to PD pathogenesis; this result was substantiated by transcriptomic analysis of the SNc of aged Tpbg knockout mice. These findings suggest that Tpbg is a new candidate gene associated with PD and provide a new insight into PD pathogenesis.

scholarly journals A new insight into identification of in silico analysis of natural compounds targeting GPR120

2018 ◽  
Vol 7 (1) ◽  
Author(s):  
Nagaraju Chinthakunta ◽  
Srinivasulu Cheemanapalli ◽  
Surekha Chinthakunta ◽  
C. M. Anuradha ◽  
Suresh Kumar Chitta
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Natural Compounds ◽  
Silico Analysis ◽  
Insight Into

scholarly journals Effect of human secretory calcium-binding phosphoprotein proline-glutamine rich 1 protein on Porphyromonas gingivalis and identification of its active portions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Charline Mary ◽  
Aurélien Fouillen ◽  
Pierre Moffatt ◽  
Dainelys Guadarrama Bello ◽  
Rima M. Wazen ◽  
...  
Keyword(s):  
Oral Health ◽  
Calcium Binding ◽  
In Silico Analysis ◽  
The Body ◽  
Bacterial Number ◽  
Gingival Epithelium ◽  
Silico Analysis ◽  
Insight Into ◽  
Antibacterial Capacity ◽  
Antibacterial Potential

AbstractThe mouth environment comprises the second most significant microbiome in the body, and its equilibrium is critical in oral health. Secretory calcium-binding phosphoprotein proline-glutamine rich 1 (SCPPPQ1), a protein normally produced by the gingival epithelium to mediate its attachment to teeth, was suggested to be bactericidal. Our aim was to further explore the antibacterial potential of human SCPPPQ1 by characterizing its mode of action and identifying its active portions. In silico analysis showed that it has molecular parallels with antimicrobial peptides. Incubation of Porphyromonasgingivalis, a major periodontopathogen, with the full-length protein resulted in decrease in bacterial number, formation of aggregates and membrane disruptions. Analysis of SCPPPQ1-derived peptides indicated that these effects are sustained by specific regions of the molecule. Altogether, these data suggest that human SCPPPQ1 exhibits antibacterial capacity and provide new insight into its mechanism of action.

In silico analysis of Nattokinase from Bacillus subtilis sp natto

2017 ◽  
Vol 9 (04) ◽  
Author(s):  
Cambyz Irajie ◽  
Milad Mohkam ◽  
Navid Nezafat ◽  
Fatemeh Mohammadi ◽  
Younes Ghasemi
Keyword(s):  
Bacillus Subtilis ◽  
Serine Protease ◽  
In Silico ◽  
Three Dimensional ◽  
In Silico Analysis ◽  
Dimensional Structure ◽  
Cardiovascular Therapy ◽  
And Function ◽  
Outlier Region ◽  
Silico Analysis

Nattokinase or subtilisin NAT (EC 3.4.21.62) is one of the most remarkable enzymes produced by Bacillus subtilis sp. Natto, which posses direct fibrinolytic activity. The aim of this study is in silico analysis of Nattokinase structure and function. The three-dimensional structure of serine protease Nattokinase from Bacillus subtilis sp. natto was determined using homology modeling performed by Geno3D2 Web Server and refined by ModRefiner. The obtained models were validated via programs such as RAMPAGE, ERRAT, 3D Match and verify 3D for consistency; moreover, functional analysis performed by PFP from Kihara Bioinformatics laboratory. RAMPAGE analysis showed that 96.7% of the residues are located in the favored region, 3.0% in allowed region and 0.4% in outlier region of the Ramachandran plot. The verify 3D value of 0.73 indicates that the environmental sketch of the model is fine. SOPMA and PSIPRED were exploited for computation of the secondary structural properties of serine protease Nattokinase. Active site determination via AADS suggested that this enzyme can be applied as a potent enzyme for cardiovascular therapy. However, these results should be more confirmed by wet lab researches for designing the more active enzyme for better functions on its fibrinolysis activity.

scholarly journals Selectively Receptor-Blind Measles Viruses: Identification of Residues Necessary for SLAM- or CD46-Induced Fusion and Their Localization on a New Hemagglutinin Structural Model

2004 ◽  
Vol 78 (1) ◽  
pp. 302-313 ◽  
Author(s):  
Sompong Vongpunsawad ◽  
Numan Oezgun ◽  
Werner Braun ◽  
Roberto Cattaneo
Keyword(s):  
Amino Acids ◽  
Conformational Changes ◽  
Measles Virus ◽  
Structural Model ◽  
Three Dimensional ◽  
Lymphocyte Activation ◽  
Cell Receptor ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
H Protein

ABSTRACT Measles virus (MV) enters cells either through the signaling lymphocyte activation molecule SLAM (CD150) expressed only in immune cells or through the ubiquitously expressed regulator of complement activation, CD46. To identify residues on the attachment protein hemagglutinin (H) essential for fusion support through either receptor, we devised a strategy based on analysis of morbillivirus H-protein sequences, iterative cycles of mutant protein production followed by receptor-based functional assays, and a novel MV H three-dimensional model. This model uses the Newcastle disease virus hemagglutinin-neuraminidase protein structure as a template. We identified seven amino acids important for SLAM- and nine for CD46 (Vero cell receptor)-induced fusion. The MV H three-dimensional model suggests (i) that SLAM- and CD46-relevant residues are located in contiguous areas in propeller β-sheets 5 and 4, respectively; (ii) that two clusters of SLAM-relevant residues exist and that they are accessible for receptor contact; and (iii) that several CD46-relevant amino acids may be shielded from direct receptor contacts. It appears likely that certain residues support receptor-specific H-protein conformational changes. To verify the importance of the H residues identified with the cell-cell fusion assays for virus entry into cells, we transferred the relevant mutations into genomic MV cDNAs. Indeed, we were able to recover recombinant viruses, and we showed that these replicate selectively in cells expressing SLAM or CD46. Selectively receptor-blind viruses will be used to study MV pathogenesis and may have applications for the production of novel vaccines and therapeutics.

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