Problematic sequences in the synthesis of G-protein peptides

Peptide synthesis is hampered by amino acid sequence-dependent aminoacylation (coupling) difficulties that are only partially understood. Analysis of coupling efficiencies in Fmoc-based, solid-phase synthesis of G-protein fragments revealed that several problematic regions included a tetrapeptide structural motif consisting of (in the order of synthesis): (1) an aliphatic amino acid residue, (2) Asp, (3) and (4) a polar, H-bonding residue each. The results suggest that interference with aminoacylation involved residue-specific interactions, probably akin to those acting in protein-protein adhesion, that occurred between functional groups at the reaction center and others located elsewhere in the peptide molecule. Difficult couplings did not correlate in any meaningful way with conformationally based predictive parameters in the literature. The present investigation points towards the occurrence of putative adhesion signals in intact G-protein alpha-subunits where their sequences are highly conserved, suggesting biological function.