The mechanism by which electron transfer is coupled to proton pumping in cytochrome c oxidase is a major unsolved problem in molecular bioenergetics. In this work it is shown that, at least under some conditions, proton release from the enzyme occurs before proton uptake upon electron transfer to the heme/Cu active site of the enzyme. This sequence is similar to that of proton release and uptake observed for the light-activated proton pump bacteriorhodopsin. In the case of cytochrome c oxidase, this observation means that both the ejected proton and the proton required for the chemistry at the enzyme active site must come from an internal proton pool.
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http://dx.doi.org/10.1073/pnas.0401521101 | DOI Listing |
Biochemistry
January 2025
School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, United Kingdom.
The enzyme 4-oxo-l-proline reductase (BDH2) has recently been identified in humans. BDH2, previously thought to be a cytosolic ()-3-hydroxybutyrate dehydrogenase, actually catalyzes the NADH-dependent reduction of 4-oxo-l-proline to -4-hydroxy-l-proline, a compound with known anticancer activity. Here we provide an initial mechanistic characterization of the BDH2-catalyzed reaction.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States.
Despite its importance in understanding biology and computer-aided drug discovery, the accurate prediction of protein ionization states remains a formidable challenge. Physics-based approaches struggle to capture the small, competing contributions in the complex protein environment, while machine learning (ML) is hampered by the scarcity of experimental data. Here, we report the development of p ML (KaML) models based on decision trees and graph attention networks (GAT), exploiting physicochemical understanding and a new experiment p database (PKAD-3) enriched with highly shifted p's.
View Article and Find Full Text PDFJ Hazard Mater
January 2025
Department of Plant and Environmental Health, Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei 230036, China; Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA. Electronic address:
Glyphosate is a non-selective herbicide widely used in agriculture, and its overexposure poses significant health and environmental risks. Herein, a novel Cu-coordinated fluorescent sensing system (HYBC-Cu system) based on acylhydrazone groups was designed, capable of glyphosate-specific recognition. The HYBC-Cu system was constructed with simple steps, with the advantages of short recognition time (< 1 min), good specificity, anti-interference, and excellent sensitivity (LOD = 95 nM).
View Article and Find Full Text PDFProc Natl Acad Sci U S A
February 2025
Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, People's Republic of China.
Carrier-free nanomedicines exhibited significant potential in elevating drug efficacy and safety for tumor management, yet their self assembly typically relied on chemical modifications of drugs or the incorporation of surfactants, thereby compromising the drug's inherent pharmacological activity. To address this challenge, we proposed a triethylamine (TEA)-mediated protonation-deprotonation strategy that enabled the adjustable-proportion self assembly of dual drugs without chemical modification, achieving nearly 100% drug loading capacity. Molecular dynamic simulations, supported by experiment evidence, elucidated the underlying self-assembly mechanism.
View Article and Find Full Text PDFMol Reprod Dev
January 2025
Liv Hospital, Centre for Regenerative Medicine and Stem Cell Manufacturing (LivMedCell), İstanbul, Turkey.
In vitro maturation (IVM) is a form of assisted reproductive technology (ART) applied to obtain mature oocytes in culture. Decline in IVM success rates by age has led consideration of novel approaches based on cellular dynamics. Our aim was to achieve proteostasis in old bovine oocytes from 13 to 16-year-old bovine with a lower potential for fertilization.
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