Trudell, JR1, Bertaccini, ED1, Borghese2, C., Lindahl, E3, Harris, RA2
1 Department of Anesthesia, Stanford University, Stanford, CA
2 Waggoner Center for Alcohol and Addiction Research, University of Texas Austin
3 Science for Life Laboratory, Stockholm University, Stockholm, Sweden
Two of the important questions about the effects of alcohols on ion channels are: (1) How could the energy of agonist binding be transmitted to the ion channel pore? (2) How could alcohols potentiate the opening of ion channels if they bind or interact at sites distant from agonist binding?
There are many global analyses of coupling and conductance pathways (Auerbach, 2016). However, in the case of small molecules such as ethanol, we propose that we must change our concepts about the effects of ligand binding on receptor function. In contrast to traditional ligands, such as morphine or diazepam, which are bound to sites of action for minutes or hours, we suggest that ethanol might interact by more distributed mechanisms. Our speculations about ‘binding sites’ or ‘sites of interaction’ are constrained by our studies and those of others (Murail et al., 2011;Yoluk et al., 2015). These studies show that the occupancy time of ligands is very transient (nanoseconds). Thus small ligands, such as ethanol, butanol, and isoflurane, will not reside in a single site during the course of an action potential (microseconds to milliseconds). As a result, we are likely viewing an ensemble average of the interactions of these ligands with GLRA1.
This point leads us to the question: What are the most distributed interactions that alcohols could be involved with to cause potentiation? Here we examine the possible interactions of alcohols with electrostatic interactions at the interface of the ligand-binding to transmembrane domains.
METHODS: We use two approaches: (1) In collaboration with Dr. R. Adron Harris (U. Texas Austin), we express and test mutations in GABAaR and GlyR receptors. (2) We perform molecular dynamics simulations of the effects of alcohol on the receptors using the GROMACS program in collaboration with Dr. Erik Lindahl (Stockholm University). However, binding studies of small molecules, such as ethanol, sometimes require much slower algorithms in which the immediate docking region is treated with quantum mechanics while the outlying regions are treated with molecular mechanics (QM-MM). Although much slower, QM-MM may be required to understand some of the interactions of ethanol with receptors.