Exploring Sodium Channels and Acetylcholine Receptors Through X-ray Crystallography, AlphaFold 3, Cryo-EM, and Ligand Interactions: Advancing Neurobiology Education
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2025
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| author | Papadopoulou, Paraskevi |
| author_facet | Papadopoulou, Paraskevi |
| contents | <p><span>Sodium channels </span><span>and </span><span>acetylcholine receptors</span><span>, including nicotinic (</span><span>nAChRs</span><span>) and muscarinic receptors (</span><span>mAChRs</span><span>), are critical for neuronal signaling. This study presents a comparative meta-analysis of these structures using </span><span>X-ray crystallography</span><span>, </span><span>AlphaFold</span><span> 3</span><span>, </span><span>cryo-electron microscopy (cryo-EM), </span><span>and </span><span>ligand</span><span> interaction studies. </span><span>Case 1 </span><span>examines sodium channels, essential for rapid neuronal depolarization during action potentials. </span><span>AlphaFold</span><span> 3 models the </span><span>α-</span><span>subunit structure</span><span>, revealing insights into voltage-sensing and pore regions critical for ion conduction and gating. Cryo-EM and X-ray crystallography validate these predictions by capturing conformational changes during channel activation. </span><span>Case 2</span><span> investigates </span><span>nAChRs</span><span> and </span><span>mAChRs</span><span>, vital for synaptic transmission. </span><span>nAChRs</span><span> are pentameric, activated by acetylcholine, while </span><span>mAChRs</span><span> are G-protein-coupled receptors involved in cellular signaling. </span><span>AlphaFold</span><span> 3 models nAChR subunit structures, while cryo-EM and X-ray crystallography provide high-resolution images of receptor conformational changes. Ligand binding studies elucidate how acetylcholine and other agonists and antagonists influence receptor activity.</span></p> <p><span>For </span><span>students</span><span>, this </span><span>meta-analysis</span><span> presents </span><span>hands-on tasks</span><span>: using </span><span>AlphaFold</span><span> 3 to predict protein structures and analyze functional implications; exploring X-ray crystallography and cryo-EM data to visualize conformational changes; and conducting ligand interaction studies to understand how different molecules modulate channel and receptor activity. These activities provide valuable experience in </span><span>computational modeling</span><span>, </span><span>experimental validation</span><span>, and integrating advanced tools, helping to bridge </span><span>theoretical knowledge</span><span> with </span><span>practical applications in neurobiology education</span><span>.</span></p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15587068 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Exploring Sodium Channels and Acetylcholine Receptors Through X-ray Crystallography, AlphaFold 3, Cryo-EM, and Ligand Interactions: Advancing Neurobiology Education Papadopoulou, Paraskevi <p><span>Sodium channels </span><span>and </span><span>acetylcholine receptors</span><span>, including nicotinic (</span><span>nAChRs</span><span>) and muscarinic receptors (</span><span>mAChRs</span><span>), are critical for neuronal signaling. This study presents a comparative meta-analysis of these structures using </span><span>X-ray crystallography</span><span>, </span><span>AlphaFold</span><span> 3</span><span>, </span><span>cryo-electron microscopy (cryo-EM), </span><span>and </span><span>ligand</span><span> interaction studies. </span><span>Case 1 </span><span>examines sodium channels, essential for rapid neuronal depolarization during action potentials. </span><span>AlphaFold</span><span> 3 models the </span><span>α-</span><span>subunit structure</span><span>, revealing insights into voltage-sensing and pore regions critical for ion conduction and gating. Cryo-EM and X-ray crystallography validate these predictions by capturing conformational changes during channel activation. </span><span>Case 2</span><span> investigates </span><span>nAChRs</span><span> and </span><span>mAChRs</span><span>, vital for synaptic transmission. </span><span>nAChRs</span><span> are pentameric, activated by acetylcholine, while </span><span>mAChRs</span><span> are G-protein-coupled receptors involved in cellular signaling. </span><span>AlphaFold</span><span> 3 models nAChR subunit structures, while cryo-EM and X-ray crystallography provide high-resolution images of receptor conformational changes. Ligand binding studies elucidate how acetylcholine and other agonists and antagonists influence receptor activity.</span></p> <p><span>For </span><span>students</span><span>, this </span><span>meta-analysis</span><span> presents </span><span>hands-on tasks</span><span>: using </span><span>AlphaFold</span><span> 3 to predict protein structures and analyze functional implications; exploring X-ray crystallography and cryo-EM data to visualize conformational changes; and conducting ligand interaction studies to understand how different molecules modulate channel and receptor activity. These activities provide valuable experience in </span><span>computational modeling</span><span>, </span><span>experimental validation</span><span>, and integrating advanced tools, helping to bridge </span><span>theoretical knowledge</span><span> with </span><span>practical applications in neurobiology education</span><span>.</span></p> |
| title | Exploring Sodium Channels and Acetylcholine Receptors Through X-ray Crystallography, AlphaFold 3, Cryo-EM, and Ligand Interactions: Advancing Neurobiology Education |
| url | https://doi.org/10.5281/zenodo.15587068 |