Modeling of Electrostatic Interactions inside Human Voltage-Gated Sodium Channels

dc.contributor.authorChen, Taoyien
dc.contributor.committeechairWelborn, Valerieen
dc.contributor.committeememberLemkul, Justin Alanen
dc.contributor.committeememberMayhall, Nicholasen
dc.contributor.committeememberCrawford, Danielen
dc.contributor.departmentChemistryen
dc.date.accessioned2025-06-10T08:03:05Zen
dc.date.available2025-06-10T08:03:05Zen
dc.date.issued2025-06-09en
dc.description.abstractIn this project, we focus on the permeation of Na+ through human voltage-gated sodium channels (Navs). Despite their biological significance, the selective permeation mechanism of Nav channels remains poorly understood at the molecular level. Here, we calculated electric fields inside the channel pore of Nav1.5, 1.6, and 1.7 to gain insights into the components that control the selectivity and permeation of Nav channels. We found that water inside the channel pore aligns vertically in response to the electric fields created by the channel residues. The regions with stronger electric field, characterized by stronger water alignment, correlate to Na+ binding sites identified by Na+ free energy profile. Residues in the P-loop, including the selectivity filter and outer ring residues, generate strong electric fields acting on pore Na+ ions, showing their significance in Na+ binding and permeation. Future study with different ions can identify their roles in ion selectivity. Overall, we have shown that electric fields computed from molecular dynamics simulations using the AMOEBA force field serve as effective indicators for identifying residues crucial to protein function.en
dc.description.abstractgeneralVoltage-gated sodium channels are essential proteins in nerve and muscle cells that transmit electrical signals. They allow Na+ to flow into the cell while rejecting other ions. Understanding the selective permeation process of these channels is crucial. In this study, we used molecular dynamics simulations to explore the electrostatic environment inside the channel pore. Our simulations reveal that water molecules align inside the channel pore. This alignment is the reaction of water dipoles to the electric fields generated by the channels' residues. We show that these residues have been shown to dictate the selective permeation process. Previous experimental alternations of these residues show disruption of channel functions, indicating their importance. The free energy profiles of Na+ along the channel pore revealed multiple Na+ binding sites situated in regions of stronger electric fields, corresponding to those residues of importance. Overall, we demonstrated that electric field can be used as an indicator for identifying key residues for protein function.en
dc.description.degreeMaster of Scienceen
dc.format.mediumETDen
dc.identifier.othervt_gsexam:44027en
dc.identifier.urihttps://hdl.handle.net/10919/135439en
dc.language.isoenen
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectHuman Sodium Channelen
dc.subjectMolecular Dynamicsen
dc.subjectElectric Fielden
dc.subjectPolarizable Force fielden
dc.subjectWater Dynamicsen
dc.titleModeling of Electrostatic Interactions inside Human Voltage-Gated Sodium Channelsen
dc.typeThesisen
thesis.degree.disciplineChemistryen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.levelmastersen
thesis.degree.nameMaster of Scienceen

Files

Original bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
Chen_T_T_2025.pdf
Size:
25.71 MB
Format:
Adobe Portable Document Format

Collections