| 1. |
- Uddin, Md Bashir, et al.
(författare)
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Molecular Detection of Colistin Resistance mcr-1 Gene in Multidrug-Resistant Escherichia coli Isolated from Chicken
- 2022
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Ingår i: Antibiotics. - : MDPI AG. - 0066-4774 .- 2079-6382. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Zoonotic and antimicrobial-resistant Escherichia coli (hereafter, E. coli) is a global public health threat which can lead to detrimental effects on human health. Here, we aim to investigate the antimicrobial resistance and the presence of mcr-1 gene in E. coli isolated from chicken feces. Ninety-four E. coli isolates were obtained from samples collected from different locations in Bangladesh, and the isolates were identified using conventional microbiological tests. Phenotypic disk diffusion tests using 20 antimicrobial agents were performed according to CLSI-EUCAST guidelines, and minimum inhibitory concentrations (MICs) were determined for a subset of samples. E. coli isolates showed high resistance to colistin (88.30%), ciprofloxacin (77.66%), trimethoprim/sulfamethoxazole (76.60%), tigecycline (75.53%), and enrofloxacin (71.28%). Additionally, the pathotype eaeA gene was confirmed in ten randomly selected E. coli isolates using primer-specific polymerase chain reaction (PCR). The presence of mcr-1 gene was confirmed using PCR and sequencing analysis in six out of ten E. coli isolates. Furthermore, sequencing and phylogenetic analyses revealed a similarity between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, indicating that the six tested isolates were colistin resistant. Finally, the findings of the present study showed that E. coli isolated from chicken harbored mcr-1 gene, and multidrug and colistin resistance. These findings accentuate the need to implement strict measures to limit the imprudent use of antibiotics, particularly colistin, in agriculture and poultry farms.
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| 2. |
- Hallin, Erik Ingmar, et al.
(författare)
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Molecular studies on structural changes and oligomerisation of violaxanthin de-epoxidase associated with the pH-dependent activation
- 2016
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Ingår i: Photosynthesis Research. - : Springer Science and Business Media LLC. - 0166-8595 .- 1573-5079. ; 129:1, s. 29-41
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Tidskriftsartikel (refereegranskat)abstract
- Violaxanthin de-epoxidase (VDE) is a conditionally soluble enzyme located in the thylakoid lumen and catalyses the conversion of violaxanthin to antheraxanthin and zeaxanthin, which are located in the thylakoid membrane. These reactions occur when the plant or algae are exposed to saturating light and the zeaxanthin formed is involved in the process of non-photochemical quenching that protects the photosynthetic machinery during stress. Oversaturation by light results in a reduction of the pH inside the thylakoids, which in turn activates VDE and the de-epoxidation of violaxanthin. To elucidate the structural events responsible for the pH-dependent activation of VDE, full length and truncated forms of VDE were studied at different pH using circular dichroism (CD) spectroscopy, crosslinking and small angle X-ray scattering (SAXS). CD spectroscopy showed the formation of α-helical coiled-coil structure, localised in the C-terminal domain. Chemical crosslinking of VDE showed that oligomers were formed at low pH, and suggested that the position of the N-terminal domain is located near the opening of lipocalin-like barrel, where violaxanthin has been predicted to bind. SAXS was used to generate models of monomeric VDE at high pH and also a presumably dimeric structure of VDE at low pH. For the dimer, the best fit suggests that the interaction is dominated by one of the domains, preferably the C-terminal domain due to the lost ability to oligomerise at low pH, shown in earlier studies, and the predicted formation of coiled-coil structure.
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| 3. |
- Hasan, Mahmudul, et al.
(författare)
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Solution Structure of the dATP-Inactivated Class I Ribonucleotide Reductase From Leeuwenhoekiella blandensis by SAXS and Cryo-Electron Microscopy
- 2021
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Ingår i: Frontiers in Molecular Biosciences. - : Frontiers Media SA. - 2296-889X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The essential enzyme ribonucleotide reductase (RNR) is highly regulated both at the level of overall activity and substrate specificity. Studies of class I, aerobic RNRs have shown that overall activity is downregulated by the binding of dATP to a small domain known as the ATP-cone often found at the N-terminus of RNR subunits, causing oligomerization that prevents formation of a necessary alpha(2)beta(2) complex between the catalytic (alpha(2)) and radical generating (beta(2)) subunits. In some relatively rare organisms with RNRs of the subclass NrdAi, the ATP-cone is found at the N-terminus of the beta subunit rather than more commonly the alpha subunit. Binding of dATP to the ATP-cone in beta results in formation of an unusual beta(4) tetramer. However, the structural basis for how the formation of the active complex is hindered by such oligomerization has not been studied. Here we analyse the low-resolution three-dimensional structures of the separate subunits of an RNR from subclass NrdAi, as well as the alpha(4)beta(4) octamer that forms in the presence of dATP. The results reveal a type of oligomer not previously seen for any class of RNR and suggest a mechanism for how binding of dATP to the ATP-cone switches off catalysis by sterically preventing formation of the asymmetrical alpha(2)beta(2) complex.
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| 4. |
- Hasan, Mahmudul
(författare)
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Structural characterization of proteins to investigate their roles in diseases: Focus on MID & LTA4H
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Protein molecules are responsible for many biological functions in cells. In order to fulfill their various biological roles, these chain-like molecules must fold into precise three-dimensional shapes. The knowledge of accurate molecular structures is a prerequisite for rational drug design and for structure based functional studies. Getting structural information of proteins can be a very difficult task, especially when it comes to high resolution. Moraxella catarrhalis is widely recognized human-restricted gram-negative bacterium for which it has become clear that it is a true pathogen of both the upper and lower respiratory tract. After Haemophilus influenzae and Streptococcus pneumonia, it is the third most common cause of otitis media in children. The bacterium can directly stimulate B-cells without any recognition of T-cells and it can therefore be classified as a T-cell independent antigen. The mitogenic activity of Moraxella catarhallis is performed by a 2139 residue long outer membrane protein MID. An IgD binding domain (MID962-1200) has been described and the colonization to human respiratory tract cells is mediated by a 150-residue adhesin domain (MID764-913). SAXS studies on the IgD binding domain showed that this domain has an elongated 3-fold organization and that there is the presence of unordered/flexible structures. CD data and prediction of secondary structure for both of the domains indicated the presence of large amounts of (∼33%) ß-sheet and ∼10% α-helix content. Native datasets for MID962-1200 to 2.3 Å resolution and for MID764-913 to 2.7 Å resolution are collected and processed. Vertebrate leukotriene A4 hydrolases are zinc metalloenzymes with an epoxide hydrolase and aminopeptidase activity belonging to the M1 family of aminopeptidases. The human enzyme produces LTB4, a powerful mediator of inflammation and is implicated in a wide variety of rheumatoid diseases. The yeast homolog scLTA4H contains only a rudimentary epoxide hydrolase activity and was shown to undergo a large conformational change upon binding of the inhibitor bestatin. In SAXS studies XlLTA4H shows a more compact form upon bestatin binding, but humLTA4H did not. It was confirmed that the LTA4H from Xenopus is a dimer and that it seems to contract in size upon bestatin binding. In contrast the human enzyme does not show any major difference in SAX scattering patterns upon inhibitor binding and it seems therefore that this enzyme does not display larger conformational changes.
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| 5. |
- Hasan, Mahmudul, et al.
(författare)
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The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms
- 2021
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 12:5, s. 1869-1885
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Tidskriftsartikel (refereegranskat)abstract
- Dermatan sulfate epimerase 1 (DS-epi1, EC 5.1.3.19) catalyzes the conversion of d-glucuronic acid to l-iduronic acid on the polymer level, a key step in the biosynthesis of the glycosaminoglycan dermatan sulfate. Here, we present the first crystal structure of the catalytic domains of DS-epi1, solved at 2.4 Å resolution, as well as a model of the full-length luminal protein obtained by a combination of macromolecular crystallography and targeted cross-linking mass spectrometry. Based on docking studies and molecular dynamics simulations of the protein structure and a chondroitin substrate, we suggest a novel mechanism of DS-epi1, involving a His/double-Tyr motif. Our work uncovers detailed information about the domain architecture, active site, metal-coordinating center and pattern of N-glycosylation of the protein. Additionally, the structure of DS-epi1 reveals a high structural similarity to proteins from several families of bacterial polysaccharide lyases. DS-epi1 is of great importance in a range of diseases, and the structure provides a necessary starting point for design of active site inhibitors.
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| 6. |
- Helgstrand, Charlotte, et al.
(författare)
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A Leukotriene A(4) Hydrolase-Related Aminopeptidase from Yeast Undergoes Induced Fit upon Inhibitor Binding.
- 2011
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 1089-8638 .- 0022-2836. ; 406, s. 120-134
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Tidskriftsartikel (refereegranskat)abstract
- Vertebrate leukotriene A(4) hydrolases are bifunctional zinc metalloenzymes with an epoxide hydrolase and an aminopeptidase activity. In contrast, highly homologous enzymes from lower organisms only have the aminopeptidase activity. From sequence comparisons, it is not clear why this difference occurs. In order to obtain more information on the evolutionary relationship between these enzymes and their activities, the structure of a closely related leucine aminopeptidase from Saccharomyces cerevisiae that only shows a very low epoxide hydrolase activity was determined. To investigate the molecular architecture of the active site, the structures of both the native protein and the protein in complex with the aminopeptidase inhibitor bestatin were solved. These structures show a more spacious active site, and the protected cavity in which the labile substrate leukotriene A(4) is bound in the human enzyme is partially obstructed and in other parts is more solvent accessible. Furthermore, the enzyme undergoes induced fit upon binding of the inhibitor bestatin, leading to a movement of the C-terminal domain. The main triggers for the domain movement are a conformational change of Tyr312 and a subtle change in backbone conformation of the PYGAMEN fingerprint region for peptide substrate recognition. This leads to a change in the hydrogen-bonding network pulling the C-terminal domain into a different position. Inasmuch as bestatin is a structural analogue of a leucyl dipeptide and may be regarded as a transition state mimic, our results imply that the enzyme undergoes induced fit during substrate binding and turnover.
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| 7. |
- Joardder, Mohammad U. H., et al.
(författare)
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Significance of Glass Transition Temperature of Food Material in Selecting Drying Condition: An In-Depth Analysis
- 2023
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Ingår i: Food reviews international (Print). - : TAYLOR & FRANCIS INC. - 8755-9129 .- 1525-6103.
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Forskningsöversikt (refereegranskat)abstract
- Drying is a complicated phenomenon involving a combination of transport, deformation, and chemical kinetics. It is an energy intensive lengthy process and results in deterioration of food quality. The glass transition temperature (GTT) significantly affects the internal mass transfer mechanism and hence significantly affects the drying kinetics. Moreover, the rheological and transport characteristics of food materials are remarkably impacted by GTT, which has an influence on the energy consumption and quality of food products during drying. Similarly, molecular weight and drying conditions also affect the GTT. This comprehensive review uncovers the fundamental understanding of GTT and demonstrates its crucial relationship with physio-structural and transport properties of food items. It has been demonstrated that a clear understanding of the glass transition temperature may help in determining appropriate drying conditions while ensuring great food quality.
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| 8. |
- Mittal, Monica, et al.
(författare)
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Investigation of calcium-dependent activity and conformational dynamics of zebra fish 12-lipoxygenase
- 2017
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : Elsevier BV. - 0304-4165. ; 1861:8, s. 2099-2111
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Tidskriftsartikel (refereegranskat)abstract
- Background A 12-lipoxygenase in zebra fish (zf12-LOX) was found to be required for normal embryonic development and LOXs are of great interest for targeted drug designing. In this study, we investigate the structural-functional aspects of zf12-LOX in response to calcium. Methods A soluble version of zf12-LOX was created by mutagenesis. Based on multiple sequence alignment, we mutated the putative calcium-responsive amino acids in N-PLAT domain of soluble zf12-LOX. Using a series of biophysical methods, we ascertained the oligomeric state, stability, structural integrity and conformational changes of zf12-LOX in response to calcium. We also compared the biophysical properties of soluble zf12-LOX with the mutant in the absence and presence of calcium. Results Here we provide a detailed characterization of soluble zf12-LOX and the mutant. Both proteins exist as compact monomers in solution, however the enzyme activity of soluble zf12-LOX is significantly increased in presence of calcium. We find that the stimulatory effect of calcium on zf12-LOX is related to a change in protein structure as observed by SAXS, adopting an open-state. In contrast, enzyme with a mutated calcium regulatory site has reduced activity-response to calcium and restricted large re-modeling, suggesting that it retains a closed-state in response to calcium. Taken together, our study suggests that Ca2 +-dependent regulation is associated with different domain conformation(s) that might change the accessibility to substrate-binding site in response to calcium. General significance The study can be broadly implicated in better understanding the mode(s) of action of LOXs, and the enzymes regulated by calcium in general.
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| 9. |
- Paul, S. I., et al.
(författare)
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Bioprospecting potential of marine microbial natural bioactive compounds
- 2021
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Ingår i: Journal of Applied Biotechnology Reports. - 2322-1186. ; 8:2, s. 96-108
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Tidskriftsartikel (refereegranskat)abstract
- The ocean is considered to be an immense reservoir of biological and microbial diversity on the planet. In marine biospheres, microbial communities are ecologically significant as intermediaries of energy. By decomposing the dead as well as decaying organic matter with the assistance of microbial communities, it plays an indispensable role in nutrient regeneration cycles of marine ecosystems. Marine environments associated with microorganisms such as bacteria, fungi and bacterial virus have renowned potential to produce novel bioactive natural products and chemically diverse secondary metabolites like antibiotics, antifungal, antiviral, antitumor, anticancer and also different hydrolyzing enzymes, namely, protease, lipase, amylase, chitinase, etc. Hence, the bioprospecting for these compounds is of greater importance. Numerous effective and efficient application of marine microbial metabolites contribute to the fields of pharmaceuticals, biotechnological, agricultural, cosmetics industries, and so on. This review attempts to summarize the present status of bioprospecting marine microorganisms and their role in natural product discovery. © 2021 The Author(s).
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| 10. |
- Paul, S. I., et al.
(författare)
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Fish Biodiversity, Threat Status and Conservation Significance of the Jamuna River, Bangladesh
- 2021
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Ingår i: Ribarstvo, Croatian Journal of Fisheries. - : Walter de Gruyter GmbH. - 1330-061X .- 1848-0586. ; 79:4, s. 173-186
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Tidskriftsartikel (refereegranskat)abstract
- The present survey aimed to explore the fish fauna diversity, abundance and conservation status in the Jamuna River, a tributary of the River Brahmaputra, Bangladesh. During the study period from November 2018 to October 2019, a total of 55 species of fish were recorded, belonging to 6 orders, 20 families and 41 genera from the five selected stations near the river. Orders Cypriniformes and Siluriformes were recorded as the dominant group in the fish fauna community that comprises 34.55% and 30.91% of total species, respectively. Various types of Small Indigenous Species (SIS) and a total of 26 International Union for Conservation of Nature (IUCN) red-listed species were recorded. Population indices, viz. Shannon-Weaver index (H), Simpson's dominance index (D), Simpson's index of diversity (1-D), Margalef's index (d) and Evenness (E), were applied to demonstrate the species diversity, richness and evenness of fish, and their overall values were 1.28-1.48, 0.26-0.33, 0.67-0.74, 1.22-1.46 and 0.77-0.86, respectively. To sustain the prospect of fisheries biodiversity in the Jamuna River of Bangladesh, different fish management and conservation plan of action specifically establishing and maintaining fish sanctuaries, banning indiscriminate fishing and the use of destructive fishing gears for the protection of the breeding and nursery grounds of fish should be taken into consideration with utmost priority. © 2021 Sulav Indra Paul et al., published by Sciendo.
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