Modelling the variable incorporation of aromatic amino acids in the tyrocidines and analogous cyclodecapeptides

A mathematical model of the nonribosomal synthesis of tyrocidines and analogues by Brevibacillus parabrevis was constructed using a competitive binding mechanism (CBM) for the incorporation of the three variable aromatic amino acid (Aaa) residues in their sequence. These antimicrobial peptides have a conserved structure (D-Phe¹ -Pro² -Aaa³ -D-Aaa⁴ -Asn⁵ -Gln⁶ -Aaa⁷ -Val⁸ -Orn⁹ -Leu¹⁰ ), apart from the Aaa in positions 3, 4 and 7 containing either Phe, Trp or Tyr.

Ultra-performance liquid chromatography linked mass spectrometry was used to profile peptides from extracts of cultures grown in media with various Phe : Trp ratios. The CBM model describes the production of peptides as a function of growth medium Aaa concentration. The model accounts for variable Aaa incorporation by simultaneously considering the influence of maximal incorporation rate and cooperativity, despite similar K_M' s of synthetase modules.

Our CBM model can be utilized to predict the Aaa composition of produced peptides from the concentration of Aaas in the growth medium.

Subtly exploiting the inherent promiscuity of the nontemplate coded peptide synthesis allows for external control of peptide identity, without using genetic manipulation. Such versatility is exploitable in the production of targeted peptide complexes and rare peptides where production processes are reliant on nonribosomal synthesis.