Separate protein

There are many different means to separate two different kinds of proteins. As you mentioned, one property you can use to separate proteins is the difference in their isoelectric point or their charge. Isoelectric focusing is a good means to do this on a small scale and ion-exchange chromatography is a good way to do this on a large scale. However, your proteins have very similar isoelectric points, so I don't think this is the best way of separating the two proteins.

Another property that can be used for separation in the shape/size of the proteins. If the two proteins have different sizes, they can be easily separated on a small-scale by gel electrophoresis or on the large-scale by size-exclusion chromatography.

There are many other ways of separating proteins, which are probably too numerous to list out completely. Here's a good page to read to get you started: http://en.wikipedia.org/wiki/Protein_purification