INTRODUCTION: Ligand-gated ion channels (LGICs) are thought to mediate a significant proportion of anesthetic effects. We have used molecular modeling to build atomic level models of the glycine alpha one receptor (GlyRa1) to examine its interactions with anesthetics. We have previously built models of a GlyRa1 based on a prokaryotic pentameric ion channel in the closed state from Erwinia Chrysanthemi (ELIC) and demonstrated a possible intersubunit binding site for anesthetics.(1-3) Here, we further validate such a model in the similar construction of a GlyRa1 model based on the open state structures of two new ion channels from the prokaryote Gloebacter violaceus (GLIC).(4-5) These new open state templates have become extremely relevant since anesthetics are thought to bind to and stabilize the open state of the GlyRa1. METHODS: The amino acid sequences and 3D coordinates of the torpedofish nicotinic acetylcholine receptor alpha 1 subunit (nAChRa1 from 2BG9.pdb) and two forms of GLIC (3EHZ.pdb and 3EAM.pdb) were obtained from the RCSB database. The sequence of the human GlyRa1 was obtained from the NCBI database. An initial BLAST sequence search was performed at the NCBI using the GLIC sequences. Among the best scored homologous human sequences were those of the GlyRa1. The three known structures underwent structural alignment for optimum coordinate overlap within Discovery Studio 2.0.1 (Accelrys, San Diego, CA). The amino acid sequence of each structural subunit was then aligned with the sequence of the GlyRa1 using the Align123 algorithm (a derivative of ClustalW). The Modeler module was used for assignment of coordinates for aligned amino acids, the construction of possible loops, and the initial refinement of amino acid sidechains using the averaged coordinates of 3EAM and 3EHZ. Five GlyRa1 subunits were merged to form the final homomeric pentamer.
RESULTS: The BLAST derived scores suggest a close homology between the LGICs, GLIC and ELIC. Subsequent CLUSTALW alignment of the GLIC and GlyRa1 sequences demonstrates reasonable sequence similarity. The model of the GlyRa1 is a homomer with pentameric symmetry about a central ion pore and shows significant transmembrane alpha helical and extracellular beta sheet content. Unlike our previous model based on the ELIC template, the current model based on the GLIC templates shows a continuously open pore with a partial restriction within the transmembrane region. Three of the residues notable for modulating anesthetic action are on transmembrane segments 1-3 (TM1-3) (ILE229, SER 267, ALA 288). They now line the intersubunit interface, in contrast to our previous models. However, residues from TM4 that are known to modulate a variety of anesthetic effects on this or homologous LGICs are present but could only indirectly influence an intersubunit anesthetic binding site.
CONCLUSIONS: A reasonable model of the GlyRa1 was constructed using homology modeling based on the GLIC templates. This model posits an intersubunit site for anesthetic binding that may communicate with the intrasubunit region of each TMD. However, distinct questions remain regarding an explanation for the effects of TM4 mutations on anesthetic modulation of these channels.
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