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In each of these MM methods, the protein was parameterised using the MMFF94x force field and ligand charges calculated using AM1-BCC.
In mobility shift methods, the protein and ligand form a noncovalent complex in solution.
Using fluorescence and transmission electron microscopic immunolocalization methods, the protein was first localized in the tapetal cells at the free microspore stage.
However, in the module-assisted methods, the protein networks are first clustered into modules with similar functionality followed by annotation of modules based on the known function of its members.
While it is impractical to validate by alternative methods the protein expression measurements for all 150+ ECM proteins observed in our proteomics experiments, we have included immunoblot data (for LTBP3, EGLN1 and CYR61) and immunohistochemical staining (LTBP3) that confirm the differential expression of these proteins (see Figure 2 figure supplement 1).
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Using a combination of mass spectrometry and immunological methods, the proteins were identified as a fragment of ApoH, ApoCI, C3a-desArg, TTR, and ApoAI.
During the dialysis method, the protein was retained in the dialysis bag and the proteins would start to refold while the denatured chemicals diffused outward.
For the hanging drop method, the protein drop is suspended above the well solution from a seal and makes no contact with the crystallisation plate.
For the sitting drop method, the protein drop sits directly on a surface of the crystallisation plate above the crystallisation condition.
For the dioxane immobilization method the protein coupling yield values are significantly lower.
By using this method, the protein was determined to be annexin V. To confirm this result, we preformed a Western blot analysis with purified annexin V.
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