By using two different synthetic techniques several polypeptides interacting with Class B
type G-protein coupled receptors were prepared. These polypeptides of different lengths (20 ≤ amino
acids ≤ 40), structural and aggregation properties, were prepared both by solid phase peptide synthesis
(SPPS) and E.coli bacterial expression. Their purity, synthetic yields, by-products and 15N/13Clabelling
characteristics were compared as function of i) the applied method, ii) amino acid length and
iii) folding propensities. Their tentative yields, costs and “environmental footprints” were analyzed and found as follows.
For unlabelled and short polypeptides (n= 20 aa.) the method of choice is the less environmentally friendly however,
quick and effective SPPS. If the polypeptide is (un)folded and/or has no aggregation propensity, then SPPS gives relatively
good yield (e.g. 14±4%) and a pure product (>97%). For aggregating polypeptides production yields drop for both
methods 4±2% (SPPS) and 2±1% (E. coli), respectively. For longer (n≥ 30 aa.) macromolecules (e.g. miniproteins) bacterial
expression efficacy gets higher. Moreover biotechnology is “greener”, the resulting in raw material is purer (2.8±1.5
mg). All these advantages for at a lower cost: ~4 €/aa. If isotopic labelling is needed for heteronuclear NMR measurements,
bacterial expression is the sole option, due to the high cost of 15N/13C labelled Fmoc(Boc)-L-aa-OH starting materials
needed for SPPS. In E.coli uniformly double-labelled, pure polypeptides can be obtained for less than 5-700 €/mg,
regardless of the length of the polypeptide chain. Thus, chemists are encouraged to use E.coli expression systems when
adequate to make not only proteins but polypeptides and miniproteins as well.