Molecular dynamics discrimination of the conformational states of calmodulin through solid-state nanopores.

Gang Hu, Jiye Fu, Yi Qiao, Hao Meng, Zunliang Wang, Jing Tu, Zuhong Lu

Physical chemistry chemical physics : PCCP 2020 Sep 14

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As a type of biological macromolecule, the conformation of proteins dynamically changes in a solution, which often results in a change in their function. However, traditional biological assays have significant drawbacks in detecting the conformation properties of proteins. Alternatively, nanopores have potential advantages in this area, which can detect protein in high throughput and without labelling. Herein, we investigated the translocation of calmodulins through silicon nitride nanopores using molecular dynamics (MD) simulation. Initially, the calmodulins were fixed in the nanopore. Distinguished blocked ionic currents were obtained between the two forms of calmodulin. Next, in the translocation simulations, a prominent difference in time resolution was easily found between the two states of calmodulin by using the appropriate voltage and comparable size of pore to protein, rp/rg→ 1, 4.5 nm (where rp is the protein radius and rg is the gyration radius). These simulations on the nanoscale are helpful for developing Ca2+-sensitive ion channels and nanodevices.

Citation

Gang Hu, Jiye Fu, Yi Qiao, Hao Meng, Zunliang Wang, Jing Tu, Zuhong Lu. Molecular dynamics discrimination of the conformational states of calmodulin through solid-state nanopores. Physical chemistry chemical physics : PCCP. 2020 Sep 14;22(34):19188-19194