Why are some recombinant proteins expressed more solubly than others?

Well I guess it's because of the same reason why any chemical substance would be more soluble than other: Surface electrical charges. With higher surface polarity (opposite electrical charges) on the surface of your molecule you will have higher solubility in water. For solubility in lipids you'll need the opposite , i.e.: non-polar molecules.

Now interestingly the strategies for making recombinant proteins more or less soluble are by changing their 3-dimensional structures. In other words changing the way in which the protein folds or unfolds will change its surface properties, the exposure of electrical charges, etcetera, therefore changing the solubility of the molecule.

Now if you asked "why" as in What's the function of that?? or the evolutionary advantage? Maybe its because that's a mechanism to keep certain proteins within the nucleus (those soluble in lipids) and some other proteins highly soluble in the cytoplasm so that they can travel easily and do whatever they have to do.

Strategies for improving the expression level of active and soluble protein:

1.Expression vectors design consideration,Codon usage/bias,Protein folding,Protein phosphorylation and glycosylation,Stability of mRNA,Promoter strength

2. Expression of soluble proteins can be regulated through many factors that the host cell normally use in controlling of toxic protein expression.

3. The strain or genetic background of host strain is important for recombinant protein expression(http://www.biologicscorp.com/recombinant-protein-s... ). Expression strains should be deficient in harmful proteases, but should stably maintain the expression plasmid and confer the relevant genetic elements to the expression system. E. coli BL21( DE3) is an example of the most common host and it has been proven outstanding in application for standard recombinant expression. It can grow efficiently in minimal media as nonpathogenic bacterium that cannot survive to cause diseases in host tissues.

4. Production of recombinant protein requires nutrients for bacterial growth and there is a limited control on the growth parameters. This process often leads to changes in substrate depletion, pH, and concentration of dissolved oxygen as well as accumulation of inhibitory substances from various metabolic pathways. These changes are not beneficial for the production of either soluble or correctly folded active protein. Proper and efficient protein folding might require specific cofactors in the growth media such as metal ions.Addition of these essential factors to the culture media could considerably increase the yield as well as the folding rate of the soluble proteins.

5. Inclusion bodies are intracellular protein aggregates which were observed when the target gene is over expressed in the cytoplasm of E. coli. Formation of inclusion bodies in recombinant expression systems occurs as a result of erroneous equilibrium between in vitro protein solubilization and aggregation and might lead to unfavorable protein folding.

6. The methods normally used for solubilization of inclusion body could lead to non-native conformation of the expressed protein. This problem could be resolved by proper refolding procedures of target protein at low denaturant concentrations. Higher concentration of the unfolded protein often leads to decreased refolding yields, regardless of refolding method. So, it is desirable to keep the concentration of the initial un-folded protein to a minimum level if higher and correct refolding proteins are expected.

More detail you can refer to: http://www.biologicscorp.com/protein-expression-pu...

to prevent genetic mutation and permutation some proteins evolved with different cell structures to inhibit variance .....(but don't quote me on that)....