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The trajectory termination criteria are designed to examine the effects of the Sec-facilitated membrane integration process on EmrE topogenesis.
To address point (b) in the manuscript, we provide biophysical justification for the trajectory termination criteria, adding the following explanation in the subsection "Simulation protocol": "The trajectory termination criteria are designed to examine the effects of the Sec-facilitated membrane integration process on EmrE topogenesis.
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The CG model has previously been demonstrated (B. Zhang and T. F. Miller III, Cell Rep., 2012) to correctly describe membrane integration processes that are governed by both thermodynamic and/or kinetic effects.
However, many questions about the exact nature of the signals and the process of membrane integration remain open, leaving a wide field for future research.
EMC may be involved in these co-translational membrane integration or co-translational folding processes.
Together with the epistasis over ninaA, the higher susceptibility of the Rh1 to the ERAD pathway than that of the two folding mutants of Rh1, imply that the EMC complex is more likely to be involved in the earlier processes such as membrane integration or co-translational folding than in the folding of fully translated, membrane integrated Rh1-apoprotein.
These results imply that the EMC-Cnx complex is more likely to be involved in the earlier processes such as membrane integration or co-translational folding than in the folding of fully translated membrane-integrated Rh1 apoprotein.
We now think EMC complex is more likely to be involved in the earlier processes such as membrane integration or co-translational folding, than in the folding of fully-translated, membrane-integrated Rh1-apoprotein (see above for the reason of this).
From these two results with epistasis over ninaA, we now think EMC complex is more likely to be involved in the earlier processes such as membrane integration or co-translational folding than in the folding of fully-translated, membrane-integrated Rh1-apoprotein.
The hepatitis B virus L protein forms a dual topology in the endoplasmic reticulum (ER) via a process involving cotranslational membrane integration and subsequent posttranslational translocation of its preS subdomain.
Therefore, although the collagen membrane is an essential component for driving the integration process, it is clearly not sufficient for a long-term, stable outcome.
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