The Research Of TREK-1 Channel Dynamic Behavior And The Discovery Of Its Ligand

Currently,depression has seriously affected human’s health and life.Treatments for depression include medication,psychotherapy and physical therapy.After drug treatment,symptoms of 70% patients with depression can be relieved.Therefore,antidepressant drugs of high efficiency and safety have become a hot spot of drug research and development.TREK-1 channel belongs to two-pore domain potassium(K2P)channels.TREK-1 channel abound in hippocampus,cortex,amygdala and other brain regions,which is highly correlated with monoamine neurotransmitter system.Anti-depression animal models and gene knockout studies have shown that inhibition of the activity of TREK-1 channel can combat depression.TREK-1 channel has become an important target for antidepressant drug.However,our understanding of the inactivation mechanism of TREK-1 channel and its binding model with small molecular is still limited.Molecular dynamics(MD)simulation is a powerful approach for exploring protein dynamic behavior and function,which can imitate the movement details of the simulated system at atomic level and provide essential information for understanding protein functions.In this thesis,we have investigated the structure and function of TREK-1 channel by using MD simulations and molecular docking,providing new insights into molecular mechanism of external pH-Induced inactivation of the TREK-1 channel,the binding model of TREK-1 external Cap domain with small molecular and the dynamic behavior of the transmembrane domain of the TREK-1 channel.TREK-1 channel is an acid sensitive potassium channel.His126,which is located in the extracellular loop of TREK-1 channel,is the main site for acid sensing.To investigate the structural basis of the external acidification-induced inactivation of TREK-1,we have performed molecular dynamics(MD)simulations involving His126 in different protonation states in POPC membrane.We found that the selectivity filter of TREK-1 channel tend to show two different conformations.The protonated His126 can stablize a non-conductive TREK-1 channel via a hydrogen-bonding network around the selectivity filter.A notable feature of K2 P channels is the extracellular cap,which consisted of four helices.The function of Cap area in K2 P channel has not been clear for a long time.Here,we identified an inhibitor,TKDC,of the TREK-1 channel.Using TKDC as a chemical probe,we conducted a combined study of computation,mutagenesis and electrophysiology,which revealed an allosteric ligand-binding site in the extracellular cap of the channels.Molecular dynamics simulations suggested that the ligand-induced allosteric conformational transitions can obstruct the ion conductive path.Many studies have shown that the gating site of TREK-1 channel is located in its selectivity filter,but its transmembrane domain is still very important for the activity.Currently,crystal structures show that there are mainly two conformations in TREK channel,including Down conformation and Up conformation.Some studies of mutations,chemical crosslinkingand pharmacological experiments have shown that the Up conformation is favorable for the channel to maintain the active state.Here,we showed the TREK-1 channel conformation transition process,from Down conformation and Up conformation,by MD simulations.We predicted the inhibitor binding site may locate between M4 helix of one subunit and M2 helix of another subunit of TREK-1 channel(Site1),or on the M2,M3 and M4 helix of the same subunit of TREK-1 channel(Site2)are.Site1 has been confirmed by TREK-2 crystal structure.Using virtual screening,we also found that some inhibitors can bind to Site2.