We have observed that a soluble recombinant green fluorescent protein produced in Escherichia coli occurs in a wide conformational spectrum. This results in differently fluorescent protein fractions in which morphologically diverse soluble aggregates abound. Therefore, the functional quality of soluble versions of aggregation-prone recombinant proteins is defined statistically rather than by the prevalence of a canonical native structure.The quality of recombinant proteins produced in bacteria and other host cells represents a major matter of concern in biological protein production and determines the potential use of target proteins for functional applications or structural analysis (2, 17). In contrast to what was formerly believed, the straightforward measurement of the soluble protein yield or the ratio between the soluble and total protein yields (usually given as a percentage of solubility) is not a useful indicator of quality. Properly folded and functional polypeptides often aggregate as inclusion bodies; therefore, an important fraction of functional protein species occurs in the insoluble cell fraction (7,9,18). Thus, the specific biological activity rather than the presence of the protein species in the soluble cell fraction reveals the conformational quality of the product and, therefore, its biotechnological potential. In this regard, an increasing number of structural analyses reveal the coexistence, in the embedded protein species, of a cross--sheet-based, amyloidlike organization (3) and also that of a native secondary structure (5). In inclusion bodies formed by enzymes, the associated enzymatic activity is sufficient for efficient in situ substrate processing. The proposal of biologically active inclusion bodies being usable as catalyzers (10) has resulted in the incorporation of diverse enzymes, in the form of inclusion bodies (including -galactosidase, D-amino acid oxidase, maltodextrin phosphorylase, sialic acid aldolase, and polyphosphate kinase) (6,(11)(12)(13)(14)(15), into different types of enzymatic processes.The molecular organization and quality of the soluble protein population, which is generally believed to adopt the native, functional conformation, have been studied much less. Therefore, in this conventional view, soluble proteins are expected to show a rather narrow conformational spectrum and to be highly functional. However, the recent finding that the solubility and conformational quality in recombinant bacteria are divergently controlled (8) seriously challenges such an assumption. Moreover, several independent observations clearly argue against a model picturing the soluble protein fraction as fully functional and structurally homogeneous. First, the specific activity of a recombinant -galactosidase aggregated as inclusion bodies is, under defined production conditions, higher than that of its soluble counterpart (7). This strongly suggests that the activity of soluble protein species represents an average of the numbers of coexisting active and inactive protein forms. I...