Exploring the Conformational Impact of Glycine Receptor TM1-2 Mutations Through Coarse-Grained Analysis and Atomistic Simulations

Abstract

Pentameric ligand-gated ion channels (PLGICs) are a family of proteins that convert chemical signals into ion fluxes through cellular membranes. Their structures are highly conserved across all kingdoms from bacteria to eukaryotes. Beyond their classical roles in neurotransmission and neurological disorders, PLGICs have been recently related to cell proliferation and cancer. Here, we focus on the best characterized eukaryotic channel, the glycine receptor (GlyR), to investigate its mutational patterns in genomic-wide tumor screens and compare them with mutations linked to hyperekplexia (HPX), a Mendelian neuromotor disease that disrupts glycinergic currents. Our analysis highlights that cancer mutations significantly accumulate across TM1 and TM2, partially overlapping with HPX changes. Based on 3D-clustering, conservation, and phenotypic data, we select three mutations near the pore, expected to impact GlyR conformation, for further study by molecular dynamics (MD). Using principal components from experimental GlyR ensembles as framework, we explore the motions involved in transitions from the human closed and desensitized structures and how they are perturbed by mutations. Our MD simulations show that WT GlyR spontaneously explores opening and re-sensitization transitions that are significantly impaired by mutations, resulting in receptors with altered permeability and desensitization properties in agreement with HPX functional data.

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

“…One of the popular topics in ion channels is the permeation of ion and water through their pores. − MD simulations are commonly employed to study the permeation, providing atomistic insight on top of the typical static pore profile using programs like HOLE2 . For example, Mhashal et al used all-atom simulations to study water permeation in the glycine receptor pentameric ion channel . Taking advantage of statistical physics, MD simulations can also be used to calculate a permeation free energy profile and thus provide a detailed gating mechanism of ion permeation.…”

“…Taking advantage of statistical physics, MD simulations can also be used to calculate a permeation free energy profile and thus provide a detailed gating mechanism of ion permeation. The derived energy landscape helps to identify important restriction residues and energy barriers. − Mhashal et al also studied cancer mutations found in genomic-wide tumor screens . MD simulations show that mutation (R252S) leads to wider upper and lower gates than wild type, facilitating ion and water permeation (Figure B).…”

“…MD simulations show that mutation (R252S) leads to wider upper and lower gates than wild type, facilitating ion and water permeation (Figure B). Because of the ion channels’ role in the central nervous system and cell metabolism, mutations of ion channels can lead to neurological disease and other diseases such as cancers. ,− Therefore, there is a huge demand to understand how mutations affect channel conformation and ion permeation. Moreover, in the era of precision medicine, personalized structural biology becomes important to understand variants and mutants .…”

“…From the applications in the CHARMM-GUI community, we note that the membrane simulations are increasingly serving as a computational microscopy with statistical reliability . Processes occurring in or out of the membrane surface, including vesicle fusion, DNA transfection, virus infection, substrate translocation, nanopore sequencing, drug delivery, protein detergent extraction, and pollutant toxicity, as well as mutation and drug-induced protein conformational changes, can all be visualized and analyzed at the atomistic level. ,,,,,,,,,, …”

“…181 For example, Mhashal et al used allatom simulations to study water permeation in the glycine receptor pentameric ion channel. 169 Taking advantage of statistical physics, MD simulations can also be used to calculate a permeation free energy profile and thus provide a detailed gating mechanism of ion permeation. The derived energy landscape helps to identify important restriction residues and energy barriers.…”