I am trying to express and isolate a protein in E. coli. The protein is supposed to have high prevalence of non-polar residues. Would that create problems in isolating the protein using a His tag column? If yes, are there other ways we can isolate proteins which are rich in non-polar residues?
In principle possible - the main problem is to find conditions under which your protein is soluble and does not form soluble aggregates. For example, for membrane proteins you need detergents to extract the proteins and keep them in solution, but as long as the his tag is not obstructed by the detergent micelle, it can be used for purification (see https://www.sigmaaldrich.com/technical-documents/protocols/biology/purifying-challenging-proteins/purification-his-tagged-proteins.html)
High prevalence of non-polar residue in protein (his-tagged) is not going to affect its purification by affinity chromatography. Membrane proteins have a high percentage of non-polar amino acids. You can purify the protein under non-denaturing conditions & run on an SDS-PAGE to check the presence of desired protein. If your protein is a membrane one, do not boil your sample before SDS-PAGE as it can form aggregates. Heat it to 70c for 15mins.
If the protein is not soluble, then you have to purify the protein under denaturing conditions & refold it.
You can purify it bt it might get into to the solution and has a high chance of forming inclusion bodies..
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