Affinity chromatographic screening of soluble combinatorial peptide libraries

Affinity chromatography using immobilized S-protein was used for the screen ing of affinity peptide ligands from two soluble peptide libraries. Peptide library consisted of octamers with glycine (G) at both termini of each pep tide, i.e. GXXXXXXG. The six center positions were constructed using random sequences of six L-amino acids (Y, N, F, E, V, and L). Peptide library II also consisted of octamers but with glycine and valine (V) at both termini of each peptide (GVZZZZVG). The four variable center positions of peptide l ibrary II were random sequences of 18 L-amino acids. Peptides that were ret ained specifically on the immobilized S-protein column were eluted by 2% ac etic acid. The peptides in the acid eluate were further separated using rev ersed-phase HPLC. Each separated peptide fraction was collected and the pep tide sequences deconvoluted by mass spectrometry (MS/MS). The screenings of peptide libraries I and II resulted in 12 and 7 affinity peptides, respect ively. Eight out of the twelve peptides from peptide library I contained th e clear consensus sequence NFEV. Peptide library II resulted in affinity pe ptides with the sequences GVNFEVVG, GVNFTVVG and GVFFEL(I)VG. The advantage s and limitations of affinity chromatography in peptide library screening a re discussed. (C) 1999 John Wiley & Sons, Inc.