scholarly journals The optimal pH of AID is skewed from that of its catalytic pocket by DNA-binding residues and surface charge

2021 ◽  
Author(s):  
Atefeh Ghorbani ◽  
Justin John King ◽  
Mani Larijani
Keyword(s):  
Catalytic Activity ◽  
Surface Charge ◽  
Cytidine Deaminase ◽  
Inverse Correlation ◽  
Acidic Ph ◽  
Structural Mechanism ◽  
Positive Surface Charge ◽  
Equivalent Residue ◽  
Binding Residues ◽  
Optimal Ph

Activation-induced cytidine deaminase (AID) is a member of the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family of cytidine deaminases. AID mutates immunoglobulin loci to initiate secondary antibody diversification. The APOBEC3 (A3) sub-branch mutates viral pathogens in the cytosol and acidic endosomal compartments. Accordingly, AID functions optimally near neutral pH, while most A3s are acid-adapted (optimal pH 5.5-6.5). To gain a structural understanding for this pH disparity, we constructed high-resolution maps of AID catalytic activity vs pH. We found AID’s optimal pH was 7.3 but it retained most (>70%) of the activity at pH 8. Probing of ssDNA-binding residues near the catalytic pocket, key for bending ssDNA into the pocket (e.g R25) yielded mutants with altered pH preference, corroborating previous findings that the equivalent residue in APOBEC3G (H216) underlies its acidic pH preference. AID from bony fish exhibited more basic optimal pH (pH 7.5-8.1) and several R25-equivalent mutants altered pH preference. Comparison of pH optima across the AID/APOBEC3 family revealed an inverse correlation between positive surface charge and overall catalysis.  The paralogue with the most robust catalytic activity (APOBEC3A) has the lowest surface charge, most acidic pH preference, while the paralogue with the most lethargic catalytic rate (AID) has the most positive surface charge and highest optimal pH. We suggest one possible mechanism is through surface charge dictating an overall optimal pH that is different from the optimal pH of the catalytic pocket microenvironment. These findings illuminate an additional structural mechanism that regulates AID/APOBEC3 mutagenesis.

scholarly journals Trimethylchitosan-Capped Silver Nanoparticles with Positive Surface Charge: Their Catalytic Activity and Antibacterial Spectrum Including Multidrug-Resistant Strains of Acinetobacter baumannii

2017 ◽  
Author(s):  
Tein-Yao Chang ◽  
Cheng-Cheung Chen ◽  
Kuang-Ming Cheng ◽  
Chia-Yin Chin ◽  
Yu-Hao Chen ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Catalytic Activity ◽  
Surface Charge ◽  
Acinetobacter Baumannii ◽  
Multidrug Resistant ◽  
Reducing Agent ◽  
Correlation Spectroscopy ◽  
X Ray ◽  
Positive Surface Charge ◽  
Broth Microdilution Method

We report a facile route for the green synthesis of trimethylchitosan nitrate-capped silver nanoparticles (TMCN-AgNPs) with positive surface charge. In this synthesis, silver nitrate, glucose, and trimethyl chitosan nitrate (TMCN) were used as silver precursor, reducing agent, and stabilizer, respectively. The reaction was carried out in a stirred basic aqueous medium at room temperature without the use of energy-consuming or expensive equipment. We investigated the effects of the concentrations of NaOH, glucose, and TMCN on the particle size, zeta potential, and formation yield. The AgNPs were characterized by UV-visible spectroscopy, photon correlation spectroscopy, laser Doppler anemometry, transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. The catalytic activity of the TMCN-AgNPs was studied by the reduction of 4-nitrophenol using NaBH4 as a reducing agent. We evaluated the antibacterial effects of the TMCN-AgNPs on Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus using the broth microdilution method. The results showed that both gram-positive and gram-negative bacteria were killed by the TMCN-AgNPs at very low concentration (< 6.13 μg/mL). Moreover, the TMCN-AgNPs also showed high antibacterial activity against clinically isolated multidrug-resistant A. baumannii strains, and the minimum inhibitory concentration (MIC) was ≤ 12.25 μg/mL.

pH-induced hysteretic properties of phosphofructokinase purified from rat myocardium

1986 ◽  
Vol 250 (3) ◽  
pp. R505-R511 ◽  
Author(s):  
S. C. Hand ◽  
J. F. Carpenter
Keyword(s):  
Catalytic Activity ◽  
Metabolic Regulation ◽  
Inverse Correlation ◽  
Rat Myocardium ◽  
Solution Ph ◽  
Reversible Inactivation ◽  
Ph Range ◽  
Hysteretic Loss ◽  
Fructose 1,6 Bisphosphate

Phosphofructokinase (PFK) purified from the rat myocardium is reversibly inactivated under a pH regime approximating that reported for ischemic hearts. At pH 6.5 and 37 degrees C, the enzyme displays a hysteretic loss of activity during 60-min incubations, declining to 48% of control (pH 7.1, 37 degrees C) values. Citric acid increases the degree of inactivation (28% of control), whereas fructose 1,6-bisphosphate reduces the decline in activity. Simultaneous measurements of 90 decreases light scattering and catalytic activity suggest the inactivation is temporally linked to dissociation of active tetrameric enzyme into an inactive form of lower molecular weight. Fluorescence enhancement of the extrinsic probe sodium mansate, which binds preferentially to dimeric PFK, indicates that the equilibrium dimer concentration (cp1 infinity) increases as pH is lowered. This increase in cp1 infinity exhibits a strong inverse correlation (r = 0.984) with catalytic activity across the pH range of 8.0 to 6.5. Returning solution pH to 7.0 or above promotes a time-dependent reactivation and repolymerization of PFK. The rate of reactivation is increased at higher enzyme concentrations and in the presence of trimethylamine-N-oxide, a nitrogenous osmolyte noted for its ability to promote protein aggregation reactions. Thus these results demonstrate the capacity of rat heart PFK to undergo reversible inactivation and dissociation in vitro and represent the first phase of a two-part study testing the hypothesis that these pH-induced hysteretic processes are operative in the ischemic myocardium. The data are evaluated in terms of the potential roles of hysteretic enzymes in metabolic regulation.

scholarly journals Characterization of Liposomes for Cancer Cell Transfection

2007 ◽  
Vol 1 (1) ◽  
pp. 60-63
Author(s):  
Svetlana A Tatarkova ◽  
Satvinder Khaira
Keyword(s):  
Surface Charge ◽  
Cancer Cells ◽  
Cancer Cell ◽  
Surface Potential ◽  
Cell Transfection ◽  
Similar Extent ◽  
Positive Surface Charge ◽  
Negative Surface ◽  
Subsequent Addition

We have characterized a broad range of liposome formulations with varying DcChol:DOPE ratio. Subsequent addition of DcChol to liposomes increases its positive surface charge. However, loading the nuclear acids did not neutralize the overall negative surface potential to a similar extent. The liposomes were tested by transfection of DNA in living cancer cells.

Electrostatic-driven solid phase microextraction coupled with surface enhanced Raman spectroscopy for rapid analysis of pentachlorophenol

2017 ◽  
Vol 9 (3) ◽  
pp. 459-464 ◽  
Author(s):  
Weiwei Bian ◽  
Sha Zhu ◽  
Mingying Qi ◽  
Lanlan Xiao ◽  
Zhen Liu ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Surface Charge ◽  
Solid Phase Microextraction ◽  
Solid Phase ◽  
Surface Enhanced Raman Spectroscopy ◽  
Rapid Analysis ◽  
Positive Surface Charge ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Ag Substrate

Rapid analysis of pentachlorophenol by electrostatic-driven SPME–SERS on a nanoporous Ag substrate with positive surface charge.

Carbon dots with positive surface charge from tartaric acid and m-aminophenol for selective killing of Gram-positive bacteria

2021 ◽  
Vol 9 (1) ◽  
pp. 125-130
Author(s):  
Huibo Wang ◽  
Fang Lu ◽  
Chongqing Ma ◽  
Yurong Ma ◽  
Mengling Zhang ◽  
...  
Keyword(s):  
Surface Charge ◽  
Tartaric Acid ◽  
Carbon Dots ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Positive Surface Charge

Carbon dots with positive surface charge from tartaric acid and m-aminophenol for selective killing of Gram-positive bacteria.

scholarly journals Improved Catalytic Durability of Pt-Particle/ABS for H2O2 Decomposition in Contact Lens Cleaning

Nanomaterials ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 342 ◽  
Author(s):  
Yuji Ohkubo ◽  
Tomonori Aoki ◽  
Satoshi Seino ◽  
Osamu Mori ◽  
Issaku Ito ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Surface Charge ◽  
Contact Lens ◽  
Photoelectron Spectroscopy ◽  
Inductively Coupled Plasma ◽  
Pt Nanoparticles ◽  
Acrylonitrile Butadiene Styrene ◽  
Atomic Emission ◽  
Cross Sectional ◽  
H2o2 Decomposition

In a previous study, Pt nanoparticles were supported on a substrate of acrylonitrile–butadiene–styrene copolymer (ABS) to give the ABS surface catalytic activity for H2O2 decomposition during contact lens cleaning. Although the Pt-particle/ABS catalysts exhibited considerably high specific catalytic activity for H2O2 decomposition, the catalytic activity decreased with increasing numbers of repeated usage, which meant the durability of the catalytic activity was low. Therefore, to improve the catalytic durability in this study, we proposed two types of pretreatments, as well as a combination of these treatments before supporting Pt nanoparticles on the ABS substrate. In the first method, the ABS substrate was etched, and in the second method, the surface charge of the ABS substrate was controlled. A combination of etching and surface charge control was also applied as a third method. The effects of these pretreatments on the surface morphology, surface chemical composition, deposition behavior of Pt particles, and Pt loading weight were investigated by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), cross-sectional SEM, and inductively coupled plasma atomic emission spectroscopy (ICP-AES), respectively. Both etching and controlling the surface charge effectively improved the catalytic durability for H2O2 decomposition. In addition, the combination treatment was the most effective.

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