PEDS Advance Access originally published online on June 24, 2005
Protein Engineering Design and Selection 2005 18(7):309-319; doi:10.1093/protein/gzi038
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Epitope mapping using mRNA display and a unidirectional nested deletion library
1Division of Chemistry and Chemical Engineering, California Institute of Technology, M/C 147-75, Pasadena, CA 91125, USA 2Present address: Program in Cellular and Molecular Biology, University of Wisconsin, Madison, WI 53706, USA
3 To whom correspondence should be addressed. E-mail: rroberts{at}caltech.edu
In vitro selection targeting an anti-polyhistidine monoclonal antibody was performed using mRNA display with a random, unconstrained 27-mer peptide library. After six rounds of selection, epitope-like peptides were identified that contain two to five consecutive, internal histidines and are biased for arginine residues, without any other identifiable consensus. The epitope was further refined by constructing a high-complexity, unidirectional fragment library from the final selection pool. Selection by mRNA display minimized the dominant peptide from the original selection to a 15-residue functional sequence (peptide Cmin: RHDAGDHHHHHGVRQ; KD = 38 nM). Other peptides recovered from the fragment library selection revealed a separate consensus motif (ARRXA) C-terminal to the histidine track. Kinetics measurements made by surface plasmon resonance, using purified Fab (antigen-binding fragment) to prevent avidity effects, demonstrate that the selected peptides bind with 10- to 75-fold higher affinities than a hexahistidine peptide. The highest affinity peptides (KD 
10 nM) encode both a short histidine track and the ARRXA motif, suggesting that the motif and other flanking residues make important contacts adjacent to the core polyhistidine-binding site and can contribute >2.5 kcal/mol of binding free energy. The fragment library construction methodology described here is applicable to the development of high-complexity protein or cDNA expression libraries for the identification of protein–protein interaction domains.
Keywords: anti-polyhistidine/epitope mapping/HIS-1/in vitro selection/mRNA display/nested deletion/peptide libraries
Received November 23, 2004; revised April 22, 2005; accepted May 18, 2005.
Edited by Dario Neri