scholarly journals Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

2021 ◽  
Author(s):  
Titouan Jaunet-Lahary ◽  
Tatsuro Shimamura ◽  
Masahiro Hayashi ◽  
Norimichi Nomura ◽  
Kouta Hirasawa ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Stone Formation ◽  
Underlying Mechanism ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
Bacterial Cells ◽  
Salt Bridges ◽  
Degrading Bacterium ◽  
Single Side ◽  
Metabolic Interactions

Oxalobacter formigenes is an oxalate-degrading bacterium in the gut microbiota that absorbs food-derived oxalate to use this as a carbon and energy source and thereby helps reduce the risk of kidney stone formation of the host animals. The bacterial oxalate transporter OxlT uptakes oxalate from the gut to bacterial cells and excrete formate as a degradation product, with a strict discrimination from other carboxylates that serve as nutrients. Nevertheless, the underlying mechanism remains unclear. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two different conformations, occluded and outward-facing states. The oxalate binding site contains two basic residues that form salt bridges with a dicarboxylate substrate while preventing the conformational switch to the occluded state without an acidic substrate, a disallowed state for an antiporter. The occluded ligand-binding pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the binding pocket are completely blocked by extensive interdomain hydrophobic and ionic interactions. Nevertheless, a molecular dynamics simulation showed that a flip of a single side chain neighbouring the substrate is sufficient to trigger the gate opening. The OxlT structure indicates the underlying metabolic interactions enabling favourable symbiosis at a molecular level.

scholarly journals Halo-Tolerant And Thermostable Mechanisms of An Endoglucanase From Marine Aspergillus Niger

2021 ◽  
Author(s):  
Li-Nian Cai ◽  
Sheng-Nan Xu ◽  
Tao Lu ◽  
Dong-Qiang Lin ◽  
Shan-Jing Yao
Keyword(s):  
Aspergillus Niger ◽  
High Salinity ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
Salt Bridges ◽  
Substrate Binding Pocket ◽  
Site Specific ◽  
Homologous Expression ◽  
The Stability ◽  
Mutagenesis Study

Abstract The cellulase cocktail of marine Aspergillus niger exhibited halo-tolerant and thermostable properties, which is of great potential in industrial application. In order to excavate the single tolerant cellulase components from complex cellulase cocktail, constitutive homologous expression was employed for direct obtainment of the endoglucanase (AnEGL). Enzymatic property study revealed that AnEGL exhibited a property of halo-tolerance and an outstanding thermostability in high salinity environment. Significantly, its activity increased by 29% and the half-life at 65 °C increased by 26.7-fold with the presence of 4.5 M NaCl. Molecular dynamics simulation revealed that Na+ and Cl－ could form salt bridges with charged residues, and then influenced the activity of loops and the stability of substrate binding pocket, which accounted for the halo-tolerance and thermostability. Further, site-specific mutagenesis study proved that the residues Asp95 and Asp99 in the pocket were of great concern for the tolerant properties. The halo-tolerant and thermostable AnEGL was of great value in lignocellulosic utilization and the conjectural mechanisms were of referential significance for other tolerant enzymes.

Molecular dynamics simulation of the dissociation mechanism of P-selectin from PSGL-1

2017 ◽  
Vol 16 (04) ◽  
pp. 1750035
Author(s):  
Hajar Hassani-Ardekani ◽  
Hanieh Niroomand-Oscuii ◽  
Ehsan Nikbin ◽  
Amir Shamloo
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Conformational Changes ◽  
Constant Velocity ◽  
Underlying Mechanism ◽  
Potential Of Mean Force ◽  
Dynamics Simulation ◽  
Salt Bridges ◽  
Tyrosine Residues ◽  
Dissociation Mechanism

Interactions between P-selectin, expressed on activated endothelium, and its counterpart P-selectin glycoprotein ligand-1 (PSGL-1), expressed on leukocytes, play a pivotal role in adhesive events that recruit circulating leukocytes toward inflamed or injured tissues. Atomistic understanding of the association and dissociation of these bonds under blood flow is necessary to define the underlying mechanism. In this study, steered molecular dynamics (SMD) simulations were applied to investigate the conformational changes of P-LE/SGP-3 construct (an effective binding unit of the P-selectin/PSGL-1 complex) under stretching with constant velocity. In the present simulations, a self-built force field parameterization was developed for sulfated tyrosine by using force field toolkit of Visual Molecular Dynamics (VMD) program. A dissociation mechanism was represented by analyzing the nonbonded energies between interface residues. The results indicate that the salt bridges between P-LE and SGP-3 and the hydrogen bonds between ion Ca[Formula: see text] and residue fucose of glycan group of PSGL-1 and also between sulfated tyrosine residues are the most effective bonds in binding. Finally, potential of mean force (PMF) was calculated by averaging the outcomes of eight independent runs and the results were discussed.

Same Target, Different Therapeutic Outcomes: The Case of CAY10471 and Fevipiprant on CRTh2 Receptor in Treatment of Allergic Rhinitis and Asthma

2019 ◽  
Vol 22 (8) ◽  
pp. 521-533 ◽  
Author(s):  
Abdul R. Issahaku ◽  
Clement Agoni ◽  
Opeyemi S. Soremekun ◽  
Patrick A. Kubi ◽  
Ransford O. Kumi ◽  
...  
Keyword(s):  
Active Site ◽  
Inflammatory Cells ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
Th2 Cells ◽  
Salt Bridges ◽  
Strategic Design ◽  
Therapeutic Outcomes ◽  
Comparative Binding ◽  
The Common

Objective: Prostaglandin 2 (PGD2) mediated signalling of Chemoattractant Receptorhomologous molecule expressed on Th2 cells (CRTh2) receptor has been implicated in the recruitment of inflammatory cells. This explains the design of highly selective compounds with innate abilities to antagonize PGD2-CRTh2 interactions and prevent pro-inflammatory allergies such as rhinitis and uncontrolled asthma. The development of PGD2-competitive CRTh2 binders; CAY10471 and Fevipiprant represent remarkable therapeutic progress even though they elicit disparate pharmacological propensities despite utilizing the same binding pocket. Methods & Results: In this study, we seek to pinpoint the underlying phenomenon associated with differential CRTh2 therapeutic inhibition by CAY10471 and Fevipiprant using membraneembedded molecular dynamics simulation. Findings revealed that the common carboxylate group of both compounds elicited strong attractive charges with active site Arg170 and Lys210. Interestingly, a distinctive feature was the steady occurrence of high-affinity salt-bridges and an Arg170-mediated pi-cation interaction with the tetrahydrocarbozole ring of CAY10471. Further investigations into the active site motions of both ligands revealed that CAY10471 was relatively more stable. Comparative binding analyses also revealed that CAY10471 exhibited higher ΔG, indicating the cruciality of the ring stabilization role mediated by Arg170. Moreover, conformational analyses revealed that the inhibitory activity of CAY10471 was more prominent on CRTh2 compared to Fevipiprant. Conclusion: These findings could further advance the strategic design of novel CRTh2 binders in the treatment of diseases related to pro-inflammatory allergies.

Modulation of Gut Microbiota through Dietary Phytochemicals as a Novel Anti-infective Strategy

2020 ◽  
Vol 17 (4) ◽  
pp. 498-506 ◽  
Author(s):  
Pavan K. Mujawdiya ◽  
Suman Kapur
Keyword(s):  
Microbial Community ◽  
Quorum Sensing ◽  
Population Density ◽  
Gut Microbiota ◽  
Biofilm Formation ◽  
Chemical Interaction ◽  
Bacterial Species ◽  
Critical Role ◽  
Bacterial Cells ◽  
Gut Microbes

: Quorum Sensing (QS) is a phenomenon in which bacterial cells communicate with each other with the help of several low molecular weight compounds. QS is largely dependent on population density, and it triggers when the concentration of quorum sensing molecules accumulate in the environment and crosses a particular threshold. Once a certain population density is achieved and the concentration of molecules crosses a threshold, the bacterial cells show a collective behavior in response to various chemical stimuli referred to as “auto-inducers”. The QS signaling is crucial for several phenotypic characteristics responsible for bacterial survival such as motility, virulence, and biofilm formation. Biofilm formation is also responsible for making bacterial cells resistant to antibiotics. : The human gut is home to trillions of bacterial cells collectively called “gut microbiota” or “gut microbes”. Gut microbes are a consortium of more than 15,000 bacterial species and play a very crucial role in several body functions such as metabolism, development and maturation of the immune system, and the synthesis of several essential vitamins. Due to its critical role in shaping human survival and its modulating impact on body metabolisms, the gut microbial community has been referred to as “the forgotten organ” by O`Hara et al. (2006) [1]. Several studies have demonstrated that chemical interaction between the members of bacterial cells in the gut is responsible for shaping the overall microbial community. : Recent advances in phytochemical research have generated a lot of interest in finding new, effective, and safer alternatives to modern chemical-based medicines. In the context of antimicrobial research various plant extracts have been identified with Quorum Sensing Inhibitory (QSI) activities among bacterial cells. This review focuses on the mechanism of quorum sensing and quorum sensing inhibitors isolated from natural sources.

Modulation of gut microbiota and intestinal barrier function during alleviation of antibiotic-associated diarrhea with Rhizoma Zingiber officinale (Ginger) extract

2020 ◽  
Vol 11 (12) ◽  
pp. 10839-10851
Author(s):  
Zhi-jie Ma ◽  
Huan-jun Wang ◽  
Xiao-jing Ma ◽  
Yue Li ◽  
Hong-jun Yang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Barrier Function ◽  
Intestinal Barrier ◽  
Zingiber Officinale ◽  
Underlying Mechanism ◽  
Intestinal Barrier Function ◽  
Ginger Extract ◽  
Beneficial Effects ◽  
Antibiotic Associated Diarrhea

Ginger extract showed beneficial effects on rats with antibiotic-associated diarrhea, and the underlying mechanism might be associated with the recovery of gut microbiota and intestinal barrier function.

scholarly journals Pharmacophore Modelling-Based Drug Repurposing Approaches for SARS-CoV-2 Therapeutics

2021 ◽  
Vol 9 ◽  
Author(s):  
Shailima Rampogu ◽  
Keun Woo Lee
Keyword(s):  
Effective Treatment ◽  
Pharmacophore Model ◽  
Drug Repurposing ◽  
Binding Pocket ◽  
Binding Mode ◽  
Computational Method ◽  
Dynamics Simulation ◽  
Potential Candidate ◽  
Pharmacophore Modelling ◽  
Discovery Studio

The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating effect globally with no effective treatment. The swift strategy to find effective treatment against coronavirus disease 2019 (COVID-19) is to repurpose the approved drugs. In this pursuit, an exhaustive computational method has been used on the DrugBank compounds targeting nsp16/nsp10 complex (PDB code: 6W4H). A structure-based pharmacophore model was generated, and the selected model was escalated to screen DrugBank database, resulting in three compounds. These compounds were subjected to molecular docking studies at the protein-binding pocket employing the CDOCKER module available with the Discovery Studio v18. In order to discover potential candidate compounds, the co-crystallized compound S-adenosyl methionine (SAM) was used as the reference compound. Additionally, the compounds remdesivir and hydroxycholoroquine were employed for comparative docking. The results have shown that the three compounds have demonstrated a higher dock score than the reference compounds and were upgraded to molecular dynamics simulation (MDS) studies. The MDS results demonstrated that the three compounds, framycetin, kanamycin, and tobramycin, are promising candidate compounds. They have represented a stable binding mode at the targets binding pocket with an average protein backbone root mean square deviation below 0.3 nm. Additionally, they have prompted the hydrogen bonds during the entire simulations, inferring that the compounds have occupied the active site firmly. Taken together, our findings propose framycetin, kanamycin, and tobramycin as potent putative inhibitors for COVID-19 therapeutics.

scholarly journals Altered Fecal Metabolites and Colonic Glycerophospholipids Were Associated With Abnormal Composition of Gut Microbiota in a Depression Model of Mice

2021 ◽  
Vol 15 ◽  
Author(s):  
Xue Gong ◽  
Cheng Huang ◽  
Xun Yang ◽  
Jianjun Chen ◽  
Juncai Pu ◽  
...  
Keyword(s):  
Correlation Analysis ◽  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Underlying Mechanism ◽  
Rrna Gene ◽  
Mice Model ◽  
Microbial Composition ◽  
Gas And Liquid Chromatography ◽  
Correlation Analysis Method ◽  
Rrna Gene Sequencing

The microbiota–gut–brain axis has been considered to play an important role in the development of depression, but the underlying mechanism remains unclear. The gastrointestinal tract is home to trillions of microbiota and the colon is considered an important site for the interaction between microbiota and host, but few studies have been conducted to evaluate the alterations in the colon. Accordingly, in this study, we established a chronic social defeated stress (CSDS) mice model of depression. We applied 16S rRNA gene sequencing to assess the gut microbial composition and gas and liquid chromatography–mass spectroscopy to identify fecal metabolites and colonic lipids, respectively. Meanwhile, we used Spearman’s correlation analysis method to evaluate the associations between the gut microbiota, fecal metabolites, colonic lipids, and behavioral index. In total, there were 20 bacterial taxa and 18 bacterial taxa significantly increased and decreased, respectively, in the CSDS mice. Further, microbial functional prediction demonstrated a disturbance of lipid, carbohydrate, and amino acid metabolism in the CSDS mice. We also found 20 differential fecal metabolites and 36 differential colonic lipids (in the category of glycerolipids, glycerophospholipids, and sphingolipids) in the CSDS mice. Moreover, correlation analysis showed that fecal metabolomic signature was associated with the alterations in the gut microbiota composition and colonic lipidomic profile. Of note, three lipids [PC(16:0/20:4), PG(22:6/22:6), and PI(18:0/20:3), all in the category of glycerophospholipids] were significantly associated with anxiety- and depression-like phenotypes in mice. Taken together, our results indicated that the gut microbiota might be involved in the pathogenesis of depression via influencing fecal metabolites and colonic glycerophospholipid metabolism.

scholarly journals In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite and Struvite Urolithiasis

Kidney360 ◽  
2020 ◽  
pp. 10.34067/KID.0006942020
Author(s):  
Jessica J. Saw ◽  
Mayandi Sivaguru ◽  
Elena M. Wilson ◽  
Yiran Dong ◽  
Robert A. Sanford ◽  
...  
Keyword(s):  
Calcium Oxalate ◽  
Stone Formation ◽  
Human Kidney ◽  
Rrna Gene ◽  
Bacterial Cells ◽  
Stone Formers ◽  
Bacteria And Fungi ◽  
Struvite Stones

Background: Human kidney stones form via repeated events of mineral precipitation, partial dissolution and reprecipitation, which are directly analogous to similar processes in other natural and man-made environments where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Methods: Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, while one patient each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from 7 of these 20 patients (5 CaOx, 1 brushite and 1 struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, superresolution autofluorescence (SRAF) and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Results: Bulk entombed DNA was sequenced from stone fragments in 11 of the 18 CaOx patients, as well as the brushite and struvite patients. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells ~1  µm in diameter were also optically observed to be entombed and well-preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. Conclusions: These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.

scholarly journals The Gut Microbiota and Human Health with an Emphasis on the Use of Microencapsulated Bacterial Cells

2011 ◽  
Vol 2011 ◽  
pp. 1-12 ◽  
Author(s):  
Satya Prakash ◽  
Catherine Tomaro-Duchesneau ◽  
Shyamali Saha ◽  
Arielle Cantor
Keyword(s):  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Cell Viability ◽  
Crucial Role ◽  
Bacterial Population ◽  
Significant Loss ◽  
Bacterial Cells ◽  
Lower Gastrointestinal Tract ◽  
Viable Cells ◽  
Harsh Conditions

The gut microbiota plays a crucial role in maintaining health. Alterations of the gut bacterial population have been associated with a number of diseases. Past and recent studies suggest that one can positively modify the contents of the gut microbiota by introducing prebiotics, probiotics, synbiotics, and other therapeutics. This paper focuses on probiotic modulation of the gut microbiota by their delivery to the lower gastrointestinal tract (GIT). There are numerous obstacles to overcome before microorganisms can be utilized as therapeutics. One important limitation is the delivery of viable cells to the lower GIT without a significant loss of cell viability and metabolic features through the harsh conditions of the upper GIT. Microencapsulation has been shown to overcome this, with various types of microcapsules available for resolving this limitation. This paper discusses the gut microbiota and its role in disease, with a focus on microencapsulated probiotics and their potentials and limitations.

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