Homo- and heterodimerization is becoming an assessed concept in G-protein coupled receptor (GPCR) pharmacology, and the notion that GPCRs may dimerize or oligomerize is allowing for a reinterpretation of some inconsistencies or anomalies and is providing medicinal chemists with potentially relevant novel molecular targets for a variety of therapeutic conditions. Recently, it has been reported that two unrelated GPCRs, namely class C metabotropic glutamate receptor type-2 (mGluR2) and class A 5HT(2A) serotoninergic receptor, can heterodimerize at the transmembrane domain level. We performed a 40 ns molecular dynamics simulation of the mGluR2/5HT(2A) heterocomplex constructed around a TM4/TM5 interface and embedded in an explicit phospholipidic bilayer surrounded by water molecules. In a separate experiment, the monomeric 5HT(2A) receptor was simulated for additional 40 ns under the same conditions. The analysis and the comparison of the two simulations allowed us to clearly identify a cross-talk between the two protomers and to put forward an effect of the heterodimerization on the shape of the binding pocket of 5HT(2A). This result provides the first molecular explanation for the reported allosteric effect of mGluR2 on 5HT(2A)-mediated response and suggests that the heterocomplex can be a more suitable target for in silico screening than the monomeric protomers.
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http://dx.doi.org/10.1021/ci900067g | DOI Listing |
J Chem Inf Model
January 2025
Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States.
Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In recent years, it has been extensively applied to diverse types of biomedical data sets. Concurrently, our ability to perform long-time scale molecular dynamics (MD) simulations on proteins and other materials has increased exponentially.
View Article and Find Full Text PDFJ Cereb Blood Flow Metab
January 2025
A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
Zero echo time (zero-TE) pulse sequences provide a quiet and artifact-free alternative to conventional functional magnetic resonance imaging (fMRI) pulse sequences. The fast readouts (<1 ms) utilized in zero-TE fMRI produce an image contrast with negligible contributions from blood oxygenation level-dependent (BOLD) mechanisms, yet the zero-TE contrast is highly sensitive to brain function. However, the precise relationship between the zero-TE contrast and neuronal activity has not been determined.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China.
Herein, the interfacial effects on calcium carbonate clustering within two-dimensional (2D) graphene nanochannels were systematically investigated using molecular dynamics simulations. The distribution characteristics of the ions at the interface can be attributed to the ordered water layers within the 2D nanochannels. The orientation of CO is approximately perpendicular to the interface, which can be attributed to hydrogen bonding and its association with Ca at the interface region.
View Article and Find Full Text PDFBioinform Adv
December 2024
Structural and Computational Biology Group, Nutritional and Industrial Biochemistry Research Unit, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria.
Motivation: Investigating novel drug-target interactions is crucial for expanding the chemical space of emerging therapeutic targets in human diseases. Herein, we explored the interactions of dipeptidyl peptidase-4 and protein tyrosine phosphatase 1B with selected terpenoids from African antidiabetic plants.
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Front Vet Sci
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Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China.
Introduction: The H9N2 avian influenza virus is widely disseminated in poultry and poses a zoonotic threat, despite vaccination efforts. Mutations at residue 198 of hemagglutinin (HA) are critical for antigenic variation and receptor-binding specificity, but the underlying molecular mechanisms remain unclear. This study explores the molecular mechanisms by which mutations at the HA 198 site affect the antigenicity, receptor specificity, and binding affinity of the H9N2 virus.
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