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theses

Two main projects involving molecular dynamics simulation of GABAAR and a collaborative project involving simulations of GLIC receptor are presented in this thesis. The first project involves analyzing and comparing the conformational and functional changes between WT and K289M GABAAR receptor. The second project involves calculating binding affinity for propofol, an intravenous anesthetic, at sites identified experimentally and verified using MD simulations in GABAAR receptor. With comparatively lesser experimental knowledge for binding sites of sevoflurane, we use flooding simulation in addition to MD simulations to find exact binding sites and understand the pathway of binding. The third project involved running MD simulations of a prokaryotic pLGIC, GLIC, a bacterial proton-gated homolog, to understand how the lipid-facing M4 helix modulates channel function. Pentameric ligand-gated ion channels mediate chemical transmission of nerve signals, when an agonist binds the ECD of the channel, leading to pore opening in the TMD. While various crystal structure of these channels has provided extensive information regarding the neurotransmitter binding sites, open/close conformations, it is still challenging to understand the microscopic interaction that drives this allosteric transition between the ECD to TMD. Molecular dynamics is an effective technique in guiding us to take a closer look at the residue level interactions. Using MD, we show how the difference in electrostatic interactions at the ECD-TMD in GABAAR interface causes the channel to open in case of the WT and destabilize the open state in case of the K289M. Similar computational approaches reveal lipid penetration disrupting the interactions within the TMD helices of the 5ALA-GLIC mutant receptor which validates the reduced channel function in these receptors, as identified by experimentalists. In addition to traditional MD simulations, biased computational techniques, like AFEP helped us isolate putative binding sites, and quantify and rank binding affinities for two commonly used intravenous (Propofol) and inhalational (Sevoflurane) anesthetic, that has experimentally shown to target GABAAR receptors. Furthermore, we are able to compare and explain the protein-anesthetic interactions that cause their affinities to different binding sites in the receptor.

ETD_8980

Ph.D.

Includes bibliographical references

by Sruthi Murlidaran

doi:10.7282/T3RF5ZCT

ETD doctoral

The author owns the copyright to this work.