Evidence is presented for a role of disulfide bridging in forming the ligand binding site of the beta 2-adrenergic receptor (beta AR). The presence of disulfide bonds at the ligand binding site is indicated by "competitive" inhibition by dithiothreitol (DTT) in radioligand binding assays, by specific protection by beta-adrenergic ligands of these effects, and by the requirement of disulfide reduction for limit proteolysis of affinity ligand labeled receptor. The kinetics of binding inhibition by DTT suggest at least two pairs of disulfide-bonded cysteines essential for normal binding. Through site-directed mutagenesis, we indeed were able to identify four cysteines which are critical for normal ligand binding affinities and for the proper expression of functional beta AR at the cell surface. Unexpectedly, the four cysteines required for normal ligand binding are not those located within the hydrophobic transmembrane domains of the receptor (where ligand binding is presumed to occur) but lie in the extracellular hydrophilic loops connecting these transmembrane segments. These findings indicate that, in addition to the well-documented involvement of the membrane-spanning domains of the receptor in ligand binding, there is an important and previously unsuspected role of the hydrophilic extracellular domains in forming the ligand binding site.
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http://dx.doi.org/10.1021/bi00461a018 | DOI Listing |
J Phys Chem B
January 2025
School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia.
A systematic series of QM cluster models has been developed to predict the trend in the carbonic anhydrase binding affinity of a structurally diverse dataset of ligands. Reference DLPNO-CCSD(T)/CBS binding energies were generated for a cluster model and used to evaluate the performance of contemporary density functional theory methods, including Grimme's "3c" DFT composite methods (rSCAN-3c and ωB97X-3c). It is demonstrated that when validated QM methods are used, the predictive power of the cluster models improves systematically with the size of the cluster models.
View Article and Find Full Text PDFDrugs
January 2025
Palliative Medicine, Geisinger Medical Center, Danville, PA, USA.
Buprenorphine is an agonist at the mu opioid receptor (MOR) and antagonist at the kappa (KOR) and delta (DOR) receptors and a nociceptin receptor (NOR) ligand. Buprenorphine has a relatively low intrinsic efficacy for G-proteins and a long brain and MOR dwell time. Buprenorphine ceiling on respiratory depression has theoretically been related multiple factors such as low intrinsic efficacy at MOR, binding to six-transmembrane MOR and interactions in MOR/NOR heterodimers.
View Article and Find Full Text PDFJ Virol
January 2025
Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA.
Unlabelled: Human norovirus (HuNoV) is a leading cause of gastroenteritis worldwide and is associated with significant morbidity, mortality, and economic impact. There are currently no licensed antiviral drugs for the treatment of HuNoV-associated gastroenteritis. The HuNoV protease plays a critical role in the initiation of virus replication by cleaving the polyprotein.
View Article and Find Full Text PDFIET Syst Biol
January 2025
School of Computer Science and Technology, Baotou Medical College, Baotou, China.
Metal ions are significant ligands that bind to proteins and play crucial roles in cell metabolism, material transport, and signal transduction. Predicting the protein-metal ion ligand binding residues (PMILBRs) accurately is a challenging task in theoretical calculations. In this study, the authors employed fused amino acids and their derived information as feature parameters to predict PMILBRs using three classical machine learning algorithms, yielding favourable prediction results.
View Article and Find Full Text PDFJ Biomol Struct Dyn
January 2025
Department of Chemistry, National Institute of Technology Silchar, Silchar, Assam, India.
A series of 2,6-di(pyrazine-2-yl)pyridine (dppy) ligands - of varying substituents of different electronic nature (-NMe, -OMe,-Me, and -Cl) in the 4-position of the pyridine moiety has been designed and synthesized to study the binding behavior of the dppy ligands towards Bovine Serum Albumin (BSA), a low-cost serum albumin protein. The interaction between ligands and BSA has been studied using UV-Visible and fluorescence spectroscopy and molecular docking studies. The fluorescence of BSA was found to be quenched in the presence of all the ligands , in which ligand , having the most electron donating group NMe exhibits the maximum binding affinity towards BSA.
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