Nanosensors Based on Structural Memory Carbon Nanodots for Ag+ Fluorescence Determination

Ag+ pollution is of great harm to the human body and environmental biology. Therefore, there is an urgent need to develop inexpensive and accurate detection methods. Herein, lignin-derived structural memory carbon nanodots (CSM-dots) with outstanding fluorescence properties were fabricated via a green method. The mild preparation process allowed the CSM-dots to remain plentiful phenol, hydroxyl, and methoxy groups, which have a specific interaction with Ag+ through the reduction of silver ions. Further, the sulfur atoms doped on CSM-dots provided more active sites on their surface and the strong interaction with Ag nanoparticles. The CSM-dots can specifically bind Ag+, accompanied by a remarkable fluorescence quenching response. This “turn-off” fluorescence behavior was used for Ag+ determination in a linear range of 5–290 μM with the detection limit as low as 500 nM. Furthermore, findings showed that this sensing nano-platform was successfully used for Ag+ determination in real samples and intracellular imaging, showing great potential in biological and environmental monitoring applications.

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Nanosensors Based on Structural Memory Carbon Nanodots for Ag+ Fluorescence Determination

10.20944/preprints202108.0069.v1 ◽

2021 ◽

Author(s):

Xi Zhou ◽

Yufeng Cao ◽

Xinji Zhou ◽

Lina Xu ◽

Daihui Zhang ◽

...

Keyword(s):

Detection Methods ◽

Carbon Nanodots ◽

Structural Units ◽

Green Method ◽

Intracellular Imaging ◽

Real Samples ◽

Fluorescence Determination ◽

Monitoring Applications ◽

Precursor Molecules ◽

Structural Memory

Ag+ pollution is great of harm to the human body and the biology. Therefore, it is an urgent need to develop inexpensive and accurate detection methods. Herein, lignin-derived structural memory carbon nanodots (CSM-dots) with outstanding fluorescence property were fabricated via a green method, which reserve functional and structural units of the precursor molecules. The CSM-dots could specifically bind Ag+, accompanied with a remarkable fluorescence quenching response. This “turn-off” fluorescence behavior was used for Ag+ determination in a linear range of 5-290 μM with the detection limit as low as 500 nM. Furthermore, the finding showed that this sensing nano-platform was successfully used for Ag+ determination in real samples and intracellular imaging, showing great potential in biological and environmental monitoring applications.

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Rhamnolipids Nano-Micelles as a Potential Hand Sanitizer

Antibiotics ◽

10.3390/antibiotics10070751 ◽

2021 ◽

Vol 10 (7) ◽

pp. 751

Author(s):

Marwa Reda Bakkar ◽

Ahmed Hassan Ibrahim Faraag ◽

Elham R. S. Soliman ◽

Manar S. Fouda ◽

Amir Mahfouz Mokhtar Sarguos ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Antimicrobial Activity ◽

Active Sites ◽

Specific Interaction ◽

Virus Transmission ◽

Multidrug Resistant ◽

Future Perspective ◽

Resistant Bacteria ◽

In Silico Studies

COVID-19 is a pandemic disease caused by the SARS-CoV-2, which continues to cause global health and economic problems since emerging in China in late 2019. Until now, there are no standard antiviral treatments. Thus, several strategies were adopted to minimize virus transmission, such as social distancing, face covering protection and hand hygiene. Rhamnolipids are glycolipids produced formally by Pseudomonas aeruginosa and as biosurfactants, they were shown to have broad antimicrobial activity. In this study, we investigated the antimicrobial activity of rhamnolipids against selected multidrug resistant bacteria and SARS-CoV-2. Rhamnolipids were produced by growing Pseudomonas aeruginosa strain LeS3 in a new medium formulated from chicken carcass soup. The isolated rhamnolipids were characterized for their molecular composition, formulated into nano-micelles, and the antibacterial activity of the nano-micelles was demonstrated in vitro against both Gram-negative and Gram-positive drug resistant bacteria. In silico studies docking rhamnolipids to structural and non-structural proteins of SARS-CoV-2 was also performed. We demonstrated the efficient and specific interaction of rhamnolipids with the active sites of these proteins. Additionally, the computational studies suggested that rhamnolipids have membrane permeability activity. Thus, the obtained results indicate that SARS-CoV-2 could be another target of rhamnolipids and could find utility in the fight against COVID-19, a future perspective to be considered.

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Copper fumarate with high-bifunctional nanozyme activities at different pH for glucose and epinephrine colorimetric detection in human serum

The Analyst ◽

10.1039/d1an01817e ◽

2021 ◽

Author(s):

Meihui Ying ◽

Guizeng Yang ◽

Yuanjie Xu ◽

Hui-Ling Ye ◽

Xing Lin ◽

...

Keyword(s):

Human Serum ◽

Active Sites ◽

Colorimetric Detection ◽

Metal Organic Frameworks ◽

High Density ◽

Detection Methods ◽

Metal Organic

Metal-organic frameworks (MOFs) have attracted extensive attention in the construction of colorimetric detection methods due to their easy modification and high density of active sites. However, most of the reported...

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Immobilization and Characterization of Purified Aspergillus flavus Peroxidase Mediated Silver Nanoparticle Synthesis: Peroxidase Surface Reactive Residues are Implemented for Reduction of Silver Ions, More than Its Active Sites

Journal of Nanomedicine & Nanotechnology ◽

10.4172/2157-7439.1000420 ◽

2017 ◽

Vol 08 (01) ◽

Author(s):

Ashraf SA El Saye ◽

Rabie GH ◽

El Gazzar NS ◽

Gul Shad Ali

Keyword(s):

Aspergillus Flavus ◽

Silver Nanoparticle ◽

Active Sites ◽

Nanoparticle Synthesis ◽

Silver Ions ◽

Silver Nanoparticle Synthesis

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NMR Elucidation of Non-productive Binding Sites of 13C-Labeled Lignin Models with Carbohydrate Binding Module of Cellobiohydrolase I for Efficient Biomass Conversion

10.21203/rs.3.rs-36005/v1 ◽

2020 ◽

Author(s):

Yuki Tokunaga ◽

Takashi Nagata ◽

Keiko Kondo ◽

Masato Katahira ◽

Takashi Watanabe

Keyword(s):

Binding Sites ◽

Hydrophobic Interactions ◽

Biomass Conversion ◽

Specific Interaction ◽

Enzymatic Saccharification ◽

Cost Effective ◽

Carbohydrate Binding ◽

Carbohydrate Binding Module ◽

Cellobiohydrolase I ◽

Methoxy Groups

Abstract Background: Highly efficient enzymatic saccharification of pretreated lignocellulose is a primary key step in achieving lignocellulosic biorefinery. Cellobiohydrolase I (Cel7A) secreted by Trichoderma reesei is an industrially used cellulase possessing carbohydrate binding module 1 (TrCBM1) as the C-terminal domain. Non-productive binding of TrCBM1 to lignin significantly decreases enzymatic saccharification efficiency and enhance cost of biomass conversion due to required additional enzymes. Understanding of the interaction mechanism between lignin and TrCBM1 is essentially required to realize cost-effective biofuels production, but the binding sites in lignin have not been clearly elucidated. Results: Three types of 13C-labeled b-O-4 lignin oligomer models were synthesized and characterized. The 2D 1H-13C HSQC spectra of the 13C-labeled lignin models exhibited that 13C-labels were correctly incorporated in the (1) aromatic rings and b positions, (2) a positions, and (3) methoxy groups, respectively. The TrCBM1 binding sites in lignin were analyzed by observing NMR chemical shift perturbations (CSPs) using the synthetic 13C-labeled b-O-4 lignin oligomer models. Obvious CSPs were observed in signals from the aromatic regions in oligomers bound to TrCBM1, whereas perturbations in the signals from aliphatic regions and methoxy groups were insignificant. This indicated that hydrophobic interactions and p–p stacking were dominating factors in non-productive binding. The synthetic lignin models have two configurations whose terminal units were differently aligned and donated C(I) and C(II). The C(I) ring showed remarkable perturbation compared with C(II), which indicated that binding of TrCBM1 is evidently affected by configuration of lignin models. Long-chain lignins (DP 4.16–4.70) clearly bound to TrCBM1. Interactions with short-chain lignins (DP 2.64–3.12) were insignificant, indicating that a DP greater than 4 was necessary for TrCBM1 binding. Conclusion: The CSP analysis using 13C-labeled b-O-4 lignin oligomer models enabled us to identify TrCBM1 binding sites in lignin at the atomic level. This specific interaction analysis will lead to new molecular design of cellulase having controlled affinity to cellulose and lignin for cost-effective biorefinery process.

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Study of the adsorption of an organic pollutant onto a microporous metal organic framework

Water Science & Technology ◽

10.2166/wst.2020.566 ◽

2020 ◽

Author(s):

Mansouri Taki Eddine Mohammed ◽

Nibou Djamel ◽

Trari Mohamed ◽

Samira Amokrane

Keyword(s):

Methyl Orange ◽

Adsorption Capacity ◽

Active Sites ◽

Physical Adsorption ◽

Metal Organic Framework ◽

Specific Interaction ◽

Maximum Adsorption Capacity ◽

Film Diffusion ◽

Metal Organic ◽

Organic Framework

Abstract In this study, the microporous Metal Organic Framework-5 (MOF-5) has been synthesized to be used to remove methyl orange by adsorption. The adsorption experiments exhibit a good adsorption capacity at a catalyst dose of 0.1 g L−1 and for an initial concentration of 200 mg L−1, whereas the performance is stable over a wide pH range. The equilibrium adsorption data showed a sigmoidal course, which is well fitted by the Dubinin-Astakhov model applicable for physical adsorption processes (E = 0.055 kJ mol−1) onto heterogeneous surfaces and a more homogeneous pore structure (n = 9.9), with a maximum adsorption capacity of 1248.35 mg g−1. As can be observed from the evaluation of the kinetic data, the surface of the adsorbent is heterogeneous with different active sites for Methyl Orange (MO) adsorption. Moreover, based on the rate constant, it can be suggested that there is a specific interaction like electrostatic interaction between MO and the adsorbent for rapid and high uptake of the dye, whereas the adsorption phenomenon is reversible. According to the adsorption mechanisms, intra-particle and film diffusion models simultaneously controlled the rate sorption, which was confirmed by the calculated intra-particle diffusion and the film diffusion coefficients. The evaluation of the thermodynamic parameters revealed that the MO adsorption is spontaneous, endothermic and the randomness increases with the adsorption of MO.

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NMR elucidation of nonproductive binding sites of lignin models with carbohydrate-binding module of cellobiohydrolase I

Biotechnology for Biofuels ◽

10.1186/s13068-020-01805-w ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Yuki Tokunaga ◽

Takashi Nagata ◽

Keiko Kondo ◽

Masato Katahira ◽

Takashi Watanabe

Keyword(s):

Binding Sites ◽

Specific Interaction ◽

Enzymatic Saccharification ◽

Cost Effective ◽

Biofuel Production ◽

Carbohydrate Binding ◽

Carbohydrate Binding Module ◽

Cellobiohydrolase I ◽

Methoxy Groups ◽

Nonproductive Binding

Abstract Background Highly efficient enzymatic saccharification of pretreated lignocellulose is a key step in achieving lignocellulosic biorefinery. Cellobiohydrolase I (Cel7A) secreted by Trichoderma reesei is an industrially used cellulase that possesses carbohydrate-binding module 1 (TrCBM1) at the C-terminal domain. The nonproductive binding of TrCBM1 to lignin significantly decreases the enzymatic saccharification efficiency and increases the cost of biomass conversion because of the additionally required enzymes. Understanding the interaction mechanism between lignin and TrCBM1 is essential for realizing a cost-effective biofuel production; however, the binding sites in lignin have not been clearly elucidated. Results Three types of 13C-labeled β-O-4 lignin oligomer models were synthesized and characterized. The 2D 1H–13C heteronuclear single-quantum correlation (HSQC) spectra of the 13C-labeled lignin models confirmed that the three types of the 13C labels were correctly incorporated in the (1) aromatic rings and β positions, (2) α positions, and (3) methoxy groups, respectively. The TrCBM1-binding sites in lignin were analyzed by observing NMR chemical shift perturbations (CSPs) using the synthetic 13C-labeled β-O-4 lignin oligomer models. Obvious CSPs were observed in signals from the aromatic regions in oligomers bound to TrCBM1, whereas perturbations in the signals from aliphatic regions and methoxy groups were insignificant. These findings indicated that hydrophobic interactions and π–π stacking were dominating factors in nonproductive binding. The synthetic lignin models have two configurations whose terminal units were differently aligned and donated C(I) and C(II). The C(I) ring showed remarkable perturbation compared with the C(II), which indicated that the binding of TrCBM1 was markedly affected by the configuration of the lignin models. The long-chain lignin models (degree of polymerization (DP) 4.16–4.70) clearly bound to TrCBM1. The interactions of TrCBM1 with the short-chain lignin models (DP 2.64–3.12) were insignificant, indicating that a DP greater than 4 was necessary for TrCBM1 binding. Conclusion The CSP analysis using 13C-labeled β-O-4 lignin oligomer models enabled the identification of the TrCBM1 binding sites in lignins at the atomic level. This specific interaction analysis will provide insights for new molecular designs of cellulase having a controlled affinity to cellulose and lignin for a cost-effective biorefinery process.

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Role of Guanidinium-Carboxylate Interaction in Enzyme Inhibition with Implication for Drug Design

10.26434/chemrxiv.8425400.v1 ◽

2019 ◽

Author(s):

Aswathy Muttathukattil ◽

Sriraksha Srinivasan ◽

Antarip Halder ◽

Govardhan Reddy

Keyword(s):

Amino Acids ◽

Active Sites ◽

Density Functional ◽

Specific Interaction ◽

Density Functional Theory Calculations ◽

Enzyme Active Site ◽

Acidic Amino Acids ◽

Low Concentrations ◽

Activity Measurements ◽

Acidic Residues

Guanidinium cation (Gdm+) interacts strongly with amino acids of different polarities modulating protein structure and function. Using density functional theory calculations and molecular dynamics simulations we studied the interaction of Gdm+ with carboxylate ions mimicking its interaction with acidic amino acids and explored its effect in enzymatic folding and activity. We show that in low concentrations, Gdm+ stabilizes carboxylate ion dimers by acting as a bridge between them thereby reducing the electrostatic repulsion. We further show that this carboxylate-Gdm+-carboxylate interaction can have an effect on the structure-activity relationship in enzymes with active sites containing two acidic residues. Using five enzymes (hen egg white lysozyme, T4 lysozyme, HIV-1 protease, pepsin and creatine kinase), which have two acidic amino acids in their active sites, we show that in low concentrations (< 0.5 M), Gdm+ strongly binds to the enzyme active site, thereby potentially inhibiting its activity without unfolding it. This can lead to misleading conclusions in experiments, which infer the extent of enzyme unfolding from activity measurements. However, the carboxylate-Gdm+-carboxylate specific interaction can be exploited in drug discovery as drugs based on guanidinium derivatives are already being used to treat various maladies related to muscle weakness, cancer, diabetes etc. Guanidinium derivatives can be designed as potential drug molecules to inhibit activity or functioning of enzymes, which have binding pockets with two acidic residues in close vicinity.

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Rapid detection of silver ions based on luminescent carbon nanodots for multicolor patterning, smartphone sensors, and bioimaging applications

Analytical Methods ◽

10.1039/d1ay01746b ◽

2021 ◽

Author(s):

Sonaimuthu Mohandoss ◽

Palanisamy Subramanian ◽

SangGuan You ◽

Jae-Jin Shim ◽

Yong Rok Lee

Keyword(s):

Rapid Detection ◽

Silver Ions ◽

Hydrothermal Carbonization ◽

Single Step ◽

Carbon Nanodots ◽

Smartphone Sensors ◽

Co Doped

Photoluminescent nitrogen and sulfur co-doped carbon nanodots (N,S-CNDs) are prepared via single-step hydrothermal carbonization using 2,4-diaminobenzenesulfonic acid (2,4-DABSA) as a sole precursor. The synthesized N,S-CNDs are easily dispersed in aqueous...

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