In search of proteins interacting with PKS4 (PKS4 works in salt stress), I want to know the proteins for protein interaction study (Pull down assay and Yeast two hybrid assay). Gene accession number is NM_001248880.2 in soybean.
There are several ways to do this, both experimentally and computationally. Experimentally, you can run a native (non-denaturing) gel electrophoresis assay, or UV-crosslinking. Computationally, you can use any of the software available in the internet that perform protein-protein or protein-ligand predictions. HTH.
In addition to Vicente's recommendations, you can try affinity chromatography: crosslinking your protein to a resin using EDC etc. Proteins that bind your protein will remain in the column attached to the protein and can be eluted with chaotropic agents and analyzed by SDS-PAGE. Purified proteins can then be subjected to other assays/ techniques to ensure that the binding was not non-specific.
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