Hi,

There is no straight answer to your question: in your case, you'll probably have to try a series of chromatographic steps, thereby hoping that your protein of interest has some distinctive physicochemical properties that allows for its separation from the majority of background proteins. 

Depending on the size and pI of your protein, you could start with combining SEC and some form of ion exchange (cation/anion). If your protein has a certain binding partner or substrate, you might be able to use that for purification.

Is it expressed in a certain part of the plant?

Good luck!

We frequently perform native protein purification, albeit from E. coli. We begin with a series of ammonium sulfate cuts to purify the protein as best as possible after cell lysis. Then we use a series of chromatographic steps - hydrophobic, anion/cation exchange, affinity, etc. Depending on your protein's function/behavior, it is possible to use a wide variety of chromatographic steps to achieve a pure yield of protein.

Hi there,

If your protein binds a ligand spontaneously then you may consider affinity chromatography step using resin bearing the immobilized ligand  (or analog structure).

This question is very broad ?

First you have to lyse the protein. Than isolate or wash your aggregated protein with Tween, Triton, Nacl buffer. after ward extraction of protein (depend on your behavior may require Urea/GuHCl some concentration) 

Refold the protein (to achieve Native conformation) see in HPLC refolding method. Than depend on protein isoelectric point and hydrophobicity you can choose capturing column steps (Cation/Anion best choice) here you can achieve maximum purity (near to 80 %) intermediate purification is also requires to achive more purity for that you can go with HIC or Capto type resin for better separation. (here may got near to 90-95% Purity) depend on protein elution pattern, if you want to improve more purity you can go SEC (depend on impurities) or RP-HPLC prep column with organic solvent.

Go expasy home page and check physical parameter.