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Microsecond-timescale simulations suggest 5-HT-mediated preactivation of the 5-HT3A serotonin receptor



Nicholas B. Guros, Arvind Balijepalli, Jeffery B. Klauda


Aided by efforts to improve their speed and efficiency, molecular dynamics (MD) simulations provide an increasingly powerful tool to study the structure-function relationship of pentameric ligand-gated ion channels (pLGICs). However, accurate reporting of the channel state and observation of allosteric regulation by agonist binding with MD remains difficult due to the timescales necessary to equilibrate pLGICs from their artificial and crystalized conformation to a native and membrane-bound conformation in silico. Here, we perform multiple all-atom MD simulations of 5HT3 for 15 μs - 20 μs to demonstrate that such timescales are critical to observe the equilibration of a pLGIC from its crystalized conformation to a native conformation in a lipid membrane. These timescales, which are an order of magnitude longer than any previous simulation of 5HT3, allow us to observe the dynamic binding and unbinding of 5HT to the binding pocket located on the extracellular domain (ECD) and allosteric regulation of the transmembrane domain (TMD) from synergistic 5HT binding. The results provide valuable insight into the regulation of channel pre-activation, i.e. ligand-mediated channel priming for activation, from a resting state. This mechanistic insight will allow a careful examination of the regulation of pLGICs at a molecular level, expanding our understanding of their function and elucidating key structural motifs that can be targeted for therapeutic regulation.
Proceedings of the National Academy of Sciences of the United States of America


Molecular Dynamics, Ligand-gated Ion Channel, Priming or Pre-activation


Guros, N. , Balijepalli, A. and Klauda, J. (2020), Microsecond-timescale simulations suggest 5-HT–mediated preactivation of the 5-HT3A serotonin receptor, Proceedings of the National Academy of Sciences of the United States of America, [online],, (Accessed April 19, 2024)
Created January 6, 2020, Updated October 12, 2021