The molecular mechanisms of general anesthesia remain unknown. The goal of the proposed studies is to elucidate the important role of ion channel dynamics in the action of volatile anesthetics. Guided by our experimental results, mostly from NMR spectroscopy, we will use large-scale molecular dynamics (MD) simulations to investigate changes in transmembrane channel dynamics due to interaction with anesthetics and nonanesthetics (nonimmobilizers), which are structurally similar to the anesthetics but are peculiarly devoid of any anesthetic effects. Two model channels chosen for this study are gramicidin A (gA) and a homopentameric channel complex composed of the second and third transmembrane domains of the alpha-1 subunits of human glycine receptor (GlyR). The NAMD2 program, developed at the University of Illinois, will be used for parallel computing.
The specific aims are: (1) to determine the structures and properties of fluorinated volatile anesthetic and nonanesthetic molecules by ab initio quantum mechanics and MD calculations, and to simulate ion channel dynamics up to 10 ns in fully hydrated membrane systems containing linear and cyclic anesthetics and nonanesthetics; (2) to study the steered ion transport effects on the changes in channel dynamics due to anesthetics and, conversely, to qualitatively analyze the anesthetic-induced changes in the steering force; (3) to investigate the channel dynamics responses to the steered gating movement of the GlyR TM2+TM3 channel in the presence and absence of anesthetic- nonanesthetic pairs; (4) to determine GlyR channel dynamics response to the forced binding and unbinding of anesthetics at the critical anesthetic-sensitive mutation site, S267, in the TM2 of GlyR; and (5) for all the simulation results in Specific Aims 1-4, to quantify the channel and lipid dynamics by analyzing root-mean-square deviation (RMSD) and fluctuations (RMSD), the autocorrelation functions, and generalized order parameters (S2), and to investigate the effects of interfacial water, interfacial lipids, and cavity dynamics on anesthetic-induced changes in channel dynamics. The central hypothesis to be tested is that anesthetics affect transmembrane channel function by profoundly changing the channel dynamics and the channel's association with lipids and interfacial water. The results from the proposed study will significantly advance the science in the following three areas: (1) large-scale parallel computing applications to biological problems, particularly anesthetic interaction with membrane-associated proteins; (2) detailed elucidation of residual dynamic contribution (through conformational entropy change) to the interfacial association between lipids and transmembrane channels; and (3) the development of a protein theory of general anesthesia on the basis of dynamics-function relationships.
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| Mowrey, David D; Kinde, Monica N; Xu, Yan et al. (2015) Atomistic insights into human Cys-loop receptors by solution NMR. Biochim Biophys Acta 1848:307-14 |
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