Abstract
This thesis describes coarse-grained approaches for simulating the co-translational integration and translocation of proteins via the Sec translocon, which is a key step in the biogenesis of membrane and secretory proteins. We present a coarse-grained simulation approach that is capable of simulating minute-timescale dynamics while retaining sufficient chemical and structural detail to capture sequence-specific interactions. The model is validated through comparison to existing experimental data and applied to characterize the forces that act on nascent proteins and drive successful integration and translocation. We also apply coarse-grained simulations of the integration of multi-spanning membrane proteins to understand the effect of sequence modifications on expression levels. We uncover the link between integration efficiency and observed expression levels for membrane proteins, and utilize coarse-grained simulations to predict sequence modifications that improve heterologous overexpression.
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