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- W3201730254 abstract "The recent revolution in cryo-electron microscopy (cryo-EM) allows the determination of structures of macromolecular complexes at atomic resolution. Cryo-EM also provides information on structural heterogeneity and ensembles of macromolecules. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to liquid nitrogen temperatures. The rapid cooling preserves some information of the room temperature ensemble. However, to what extent the structural ensemble is perturbed by the cooling is currently unknown. To quantify the effects of cooling, we first estimated the temperature decay rate by solving the heat equation that suggests that cooling takes place within microseconds. Then, we started all-atom explicit-solvent molecular dynamics (MD) simulations of the ribosome from 41 snapshots taken from a room temperature ensemble with linearly decreasing temperature at 11 different cooling rates with simulation lengths ranging from 0.1 to 128 ns. The cooling leads to a marked decrease in the structural heterogeneity and the slower the cooling, the more pronounced this effect is. This observation suggests that, with slower cooling, the system is more likely to locally equilibrate into free-energy minima, thereby narrowing the room temperature ensemble. To estimate the cooling effects on the time scales of the experiment, we used a kinetic model whose parameters were obtained from MD simulations with a Bayesian approach. Finally, we used the estimated temperature decay, with the kinetic model to predict the decrease in structural heterogeneity during cryo-EM freezing. This model will allow one to quantify the heterogeneity of biologically relevant room-temperature ensembles from cryo-EM structures." @default.
- W3201730254 created "2021-10-11" @default.
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- W3201730254 date "2021-02-01" @default.
- W3201730254 modified "2023-09-28" @default.
- W3201730254 title "Effects of cryo-EM Freezing on Structural Ensembles" @default.
- W3201730254 doi "https://doi.org/10.1016/j.bpj.2020.11.926" @default.
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