Not all scFV fragments are produced equally well in E.coli. As Lars Nieba showed, hydrophobic residues on the surface of the native structure can have a marked influence on the distribution of newly synthesized scFv fragment between native, soluble fraction and periplasmic inclusion bodies. This is not a function of thermodynamic stability nor a function of the solubility of the native fragment, but an effect on the speed with which unfolded or misfolded molecules aggregate and precipitate.

In particular, the hydrophobic residues of the V/C interface of the original Fab fragment become solvent accessible in scFV constructs. However, in the scFV fragment they are not needed to stabilize an interface.