We provide a rigorous definition of free-energy transduction and its efficiency in arbitrary-linear or nonlinear-open chemical reaction networks (CRNs) operating at a steady state. Our method is based on the knowledge of the stoichiometric matrix and the chemostatted species (i.e., the species maintained at a constant concentration by the environment) to identify the fundamental currents and forces contributing to the entropy production. Transduction occurs when the current of a stoichiometrically balanced process is driven against its spontaneous direction (set by its force), thanks to other processes flowing along their spontaneous direction. In these regimes, open CRNs operate as thermodynamic machines. After exemplifying these general ideas using toy models, we analyze central energy metabolism. We relate the fundamental currents to metabolic pathways and discuss the efficiency with which they can transduce free energy.
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http://dx.doi.org/10.1063/5.0091035 | DOI Listing |
Molecules
December 2024
School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, Yuquan Road, Beijing 100049, China.
The src-homology 2 domain-containing phosphatase 2 (SHP2) is a human cytoplasmic protein tyrosine phosphatase that plays a crucial role in cellular signal transduction. Aberrant activation and mutations of SHP2 are associated with tumor growth and immune suppression, thus making it a potential target for cancer therapy. Initially, researchers sought to develop inhibitors targeting SHP2's catalytic site (protein tyrosine phosphatase domain, PTP).
View Article and Find Full Text PDFJ Mater Chem B
January 2025
Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
Biophys Chem
December 2024
Department of Chemistry and Center for Atomic, Molecular, Optical Sciences and Technologies (CAMOST), Indian Institute of Science, Education and Research (IISER) Tirupati, Yerpedu Mandal, Tirupati 517619, India. Electronic address:
Serotonin-receptor binding plays a key role in several neurological and biological processes, including mood, sleep, hunger, cognition, learning, and memory. In this article, we performed molecular dynamics simulation to examine the key residues that play an essential role in the binding of serotonin to the G-protein-coupled 5-HT receptor (5HTR) via electrostatic interactions. Key residues for electrostatic interactions were identified via bond distance analysis and frustration analysis methods.
View Article and Find Full Text PDFBiochem Biophys Res Commun
February 2025
Department of Applied Sciences, Indian Institute of Information of Technology Allahabad, Prayagraj, Uttar Pradesh, 211012, India. Electronic address:
Prostate cancer is a widespread health issue that affects men worldwide. It is one of the most common forms of cancer, and its development is influenced by a combination of hereditary, epigenetic, environmental, age, and lifestyle factors. Given that it is the second most common cause of cancer-related deaths in men, it is crucial to comprehend its complex facets.
View Article and Find Full Text PDFInt J Mol Sci
November 2024
Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China.
Obesity, characterized by abnormal or excessive fat accumulation, has become a chronic degenerative health condition that poses significant threats to overall well-being. Pharmacological intervention stands at the forefront of strategies to combat this issue. Recent studies, notably by Umut Ozcan's team, have uncovered the remarkable potential of Celastrol, a small-molecule compound derived from the traditional Chinese herb thunder god vine (Tripterygium wilfordii) as an anti-obesity agent.
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