Title:	Structural modeling of ligand binding proteins.
DNr:	Berzelius-2025-150
Project Type:	LiU Berzelius
Principal Investigator:	Richard Neutze <richard.neutze@gu.se>
Affiliation:	Göteborgs universitet
Duration:	2025-04-15 – 2025-11-01
Classification:	10601
Keywords:

Abstract

Understanding how ligand-gated ion channels and metabolic enzymes respond to diverse ligands is key to unraveling complex biological signaling and drug interactions. Our work focuses on two systems: the polymodal receptor LGC-39 in C. elegans, and the human cytochrome P450 enzyme CYP3A4. LGC-39 was identified in our recent work to be uniquely activated by both acetylcholine and monoamines (doi: 10.1523/JNEUROSCI.1516-22.2022). Whether LGC-39 undergoes different conformational changes depending on the ligand remains unknown. Both neurotransmitter types appear to bind the same pocket, but structural studies are needed to confirm this. We will also attempt to address whether the ligand type affects the pore radius of the ion channel as this could influence the conductance through the pore in its open state. Using cryoEM, we aim to resolve its ligand-binding sites and structural responses. Such findings could provide the first structural insight into a polymodal receptor in any organism and suggest a novel mechanism for complex signaling in simple nervous systems. In parallel, we are studying CYP3A4, a major drug-metabolizing enzyme that belongs to the diverse family of cytochrome P450s enzymes that catalyze a range of different oxidation reactions. Inhibition of CYP3A4 may therefor lead to build-up and toxicity of common drugs, and a better understanding of ligand binding to the enzyme is of great importance for drug discovery. Structural studies of CYP3A4 are complicated due to its flexible binding pocket that challenges structural characterization, the pocket can exist in a collapsed state and various open states, depending on which ligand is bound We have successfully studied the structure of CYP3A4 using X-ray scattering in solution and X-ray crystallography at cryo- and room-temperature (doi: 10.1016/j.drudis.2014.03.012, doi: 10.1016/j.abb.2025.110419) Our aim is to solve the first cryo-EM structure of the enzyme. We believe that using this method, we will be able to characterize the structural landscape of the enzyme in detail. The long-term goal is to perform time-resolved cryo-EM studies to track the reaction of CYP3A4. For both of these projects, cryoEM data have already been collected at SciLifeLab and we aim to use the Berzelius cluster for accelerating our data processing while using publicly available software like cryoSPARC or RELION. Together, these projects aim to advance our understanding of ligand-specific structural mechanisms in both neural signaling and drug metabolism.