Determining the stability constant of the complex formed by an organic ligand with a protein is the first stage in the screening of new drugs. Nuclear spin long-lived states, in particular the singlet state, can be used to study the reversible binding of ligands to proteins. In a complex with a protein, the spins of the ligand interact with the spins of the protein, the system of protein and ligand nuclei can relax by a dipole-dipole mechanism, and the lifetime of the singlet state is strongly reduced. In this theoretical study, a system of encounter theory equations with the condition of fast relaxation in free protein was solved to determine the lifetime of the LLS in the presence of protein. It was shown that in the limit of fast chemical exchange, the relaxation of the LLS of the ligand nuclei due to dipole interaction with the protein nuclei is reduced to relaxation by the mechanism of dipole interaction with one proton of the protein, which is located at some effective distance from the ligand nuclei. Numerical calculations were made to test the applicability of the approximations used to process the experimental lifetime dependencies on the ligand concentration and external field, and it was shown that these approximations coincide with the limit of fast exchange in strong and weak magnetic fields, but not in the medium field. An analytical expression for the lifetime of the singlet state of ligand nuclei in an arbitrary magnetic field in the absence of protein was obtained.
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http://dx.doi.org/10.1063/5.0240659 | DOI Listing |
BMC Genomics
December 2024
Departments of Biology and Biomedical Engineering, and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
Background: STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues.
Results: We describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed.
Front Immunol
December 2024
The Federal Medical Biological Agency (FMBA of Russia), Moscow, Russia.
COVID-19 is characterized by systemic pro-inflammatory shifts with the development of serious alterations in the functioning of the immune system. Investigations of the gene expression changes accompanying the infection state provide insight into the molecular and cellular processes depending on the sickness severity and virus variants. Severe Delta COVID-19 has been characterized by the appearance of a monocyte subset enriched for proinflammatory gene expression signatures and a shift in ligand-receptor interactions.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Novosibirsk State University, Novosibirsk 630090, Russia.
Determining the stability constant of the complex formed by an organic ligand with a protein is the first stage in the screening of new drugs. Nuclear spin long-lived states, in particular the singlet state, can be used to study the reversible binding of ligands to proteins. In a complex with a protein, the spins of the ligand interact with the spins of the protein, the system of protein and ligand nuclei can relax by a dipole-dipole mechanism, and the lifetime of the singlet state is strongly reduced.
View Article and Find Full Text PDFCommun Chem
December 2024
Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Am Botanischen Garten 14, 24118, Kiel, Germany.
The signal amplification by reversible exchange process (SABRE) enhances NMR signals by unlocking hidden polarization in parahydrogen through interactions with to-be-hyperpolarized substrate molecules when both are transiently bound to an Ir-based organometallic catalyst. Recent efforts focus on optimizing polarization transfer from parahydrogen-derived hydride ligands to the substrate in SABRE. However, this requires quantitative information on ligand exchange rates, which common NMR techniques struggle to provide.
View Article and Find Full Text PDFCommun Biol
December 2024
School of Chemistry and Chemical Engineering, University of South China, Hengyang, China.
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