Solid-phase peptide synthesis of certain sequences (commonly called “difficult sequences”) suffers from the occurrence of incomplete coupling reactions and/or partial unmaskings of Nα-protection. The underlying reasons for these problems are thought to be a structuration and/or a poor solvation of the growing peptide chains. Few methods are available to study the structural aspects of the peptide chains when still anchored to the solid support. In most cases, they rely on the incorporation of a specific label and examine therefore a modified peptide analog. We describe the complete characterization by homonuclear and heteronuclear magic angle spinning nuclear magnetic resonance (MAS NMR) of the solid-phase synthesis of a 10-residue peptide. A detailed secondary structure determination of the growing peptide on the resin beads, based on the NOE analysis and the 1H and 13C chemical shift deviations, indicated an extended structure on the whole length of the sequence. At critical synthesis steps, a correlation between the coupling difficulties and the aggregation of the peptide chains was established by chemical measurements and MAS NMR. Upon titration with the hydrogen bond-accepting solvent DMSO, the mobility of the peptide chains on the resin beads increased, resulting in a significant line narrowing of the MAS NMR spectra. This increased mobility is linked to an enhanced peptidyl-resin solvation as reflected by the better coupling efficiency at the critical synthesis steps.

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