The present work reports the pH-induced conformational changes of pepsin in solution at room temperature. The conformational change makes the protein surface active. The protein was found to be present in the partially denatured state at pH 8 as well as at pH 2. The fluorescence probe and circular dichroism (CD) spectra suggested that the most stable state of pepsin exists at pH 5. The binding affinities of pepsin in its native and denatured states for a D,L-carnitine-based cationic surfactant (3-hexadecylcarbamoyl-2-hydroxypropyl)trimethylammonium chloride (C16-CAR) were examined at very low concentrations of the surfactant. The thermodynamics of the binding processes were investigated by use of isothermal titration calorimetry. The results were compared with those of (3-hexadecylcarbamoylpropyl)trimethylammonium chloride (C16-PTAC), which is structurally similar to C16-CAR, but without the secondary -OH functionality near the headgroup. None of the surfactants were observed to undergo binding with pepsin at pH 2, in which it exists in the acid-denatured state. However, both of the surfactants were found to spontaneously bind to the most stable state at pH 5, the partially denatured state at pH 8, and the alkaline denatured state at pH 11. Despite the difference in the headgroup structure, both of the surfactants bind to the same warfarin binding site. Interestingly, the driving force for binding of C16-CAR was found to be different from that of C16-PTC at pH ≥ 5. The steric interaction of the headgroup in C16-CAR was observed to have a significant effect on the binding process.
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http://dx.doi.org/10.1021/acs.jpcb.5b07072 | DOI Listing |
Nat Commun
December 2024
College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, China.
Functional nanomaterials with enzyme-mimicking activities, termed as nanozymes, have found wide applications in various fields. However, the deviation between the working and optimal pHs of nanozymes has been limiting their practical applications. Here we develop a strategy to modulate the microenvironmental pHs of metal-organic framework (MOF) nanozymes by confining polyacids or polybases (serving as Brønsted acids or bases).
View Article and Find Full Text PDFChemistryOpen
December 2024
NUBAD LLC, Greer, 29650, USA.
Selective binding of small molecule ligands to nucleic acids with high affinity and limited toxicity remains an important goal in the development of compounds that can probe DNA or RNA in cells. Thiazole orange is a cell semi-permeant, fluorescent cyanine dye, with low background noise, that binds several forms of nucleic acids. However, thiazole orange can exhibit cytotoxicity when used at high concentration and/or with prolonged exposure.
View Article and Find Full Text PDFFront Plant Sci
December 2024
State key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
Introduction: Rye ( L.) played a very important role in wheat genetic improvement and forage production worldwide. However, since rye is a kind of cross-pollinated plant, high levels of genetic heterozygosity and heterogeneity existed in the genome.
View Article and Find Full Text PDFBiochem Biophys Res Commun
December 2024
Department of Biological Chemistry, School of Pharmacy and Biochemistry, University of Buenos Aires and Institute of Chemistry and Biological Physical Chemistry (IQUIFIB, UBA-CONICET), Junin 956, 1113, Buenos Aires, Argentina. Electronic address:
Here we explore the interplay between physical and chemical perturbants to unravel links among native folding, amorphous and ordered aggregation scenarios in IFABP (rat intestinal fatty acid binding protein). This small beta-barrel protein undergoes amyloid-like aggregation above 15 % v/v trifluoroethanol. Our aim was to address the influence of sub-aggregating TFE concentrations on the unfolding transitions of IFABP.
View Article and Find Full Text PDFAnal Chem
December 2024
Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
Nanoscale aggregates play a key role in the pathogenesis of neurodegenerative disorders such as Alzheimer's and Parkinson's disease. However, quantifying these aggregates in complex biological samples, such as biofluids and postmortem brain tissue, has been challenging due to their low concentration and small size, necessitating the development of methods with high sensitivity and specificity. Here, we have developed ultrasensitive assays utilizing the Quanterix Simoa platform to detect α-synuclein, β-amyloid and tau aggregates, including those with common posttranslational modifications such as truncation of α-synuclein and AT8 phosphorylation of tau aggregates.
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