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The results show that an ionic environment approximating that of the cell nucleus enhances the specificity of hUNG but significantly diminishes the efficiency of facilitated diffusion by the dissociative ("hopping") pathway, but not the associative ("sliding") pathway.
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Alloying Mg with Y atoms increases the range of the PES, and ultimately promotes different sliding pathways in the Mg-Y alloy.
These three pathways are categorized according to the definitions of Cymer et al. In the "channel-sliding" pathway, the TMD partially enters the channel, then crosses the lateral gate, then fully integrates into the membrane.
Figure 3 figure supplement 1 in the revised manuscript shows that the dominant cotranslational integration pathway for all four TMDs in both the EmrE and nEmrE mutants is the "channel-sliding" pathway.
However, we observe only a few CG trajectories in which TMDs exhibit the "interface-sliding" pathway.
The dominant cotranslational integration pathway is the 'channel-sliding' pathway for all TMDs in both mutants.
We find that only a small number of CG trajectories exhibit the 'interface-sliding' pathway.
It is clear that the dominant cotranslational integration pathway for all four TMDs in both the EmrE and nEmrE mutants is the 'channel-sliding' pathway.
In the 'interface-sliding' pathway, the TMD enters the cytoplasm through the gap between the translocon and ribosome, prior to undergoing membrane integration.
In the 'channel-sliding' pathway, the TMD partially enters the channel, then crosses the lateral gate (LG), then fully integrates into the membrane.
In the 'interface-sliding' pathway, the TMD enters the cytoplasm through the gap between the translocon and ribosome, prior to undergoing membrane integration; a trajectory thus exhibits this pathway if a TMD visits IS4 on the way to membrane integration.
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