Problems In Determining A Mechanisms Of Receptor Activation And Relating It To Structure

Abstract

Our aim is to understand receptors well enough to be able to make predictions about the activity of a new ligand or about the effect of mutations. This has yet to be achieved but it will entail knowing about both structure and function, and about the relation between them.Receptors on ion channels that mediate synaptic transmission are essentially never at equilibrium. To understand how they function in real life requires a physical mechanism to be postulated and, if verified, the rate constants in that mechanism to be estimated. The mechanism must describe states that have real physical reality (to a sufficient approximation) if the aim of achieving predictive ability is to be attained. Recent advances in single channel analysis have allowed measurement of up to 18 rate constants, far more than can be obtained from any macroscopic analysis, and it has allowed more stringent tests of proposed mechanisms too. At a limited level some predictive ability has been achieved. For example, the synaptic current produced by glycine can be predicted from steady state single channel analysis (Burzomato et al. 2004, J. Neurosci. 24, 10924-10940), but the ability to predict the effects on function of changes in structure of either the ligand or the receptor is still very limited (though this fact is often disguised by exaggerated claims). It is impossible to say what the next major step forward will be. My guess, for what it's worth, is that single molecule fluorescence methods, perhaps combined with improved NMR and molecular dynamics, may improve enough to allow a firm structural interpretation of the postulated intermediate states in channel opening, despite their brief lifetime of 10 microsec or less (Lape et al. 2008, Nature, 454, 722 - 728)