Peptide aptamers are engineered proteins similar to antibodies that retain their integrity within cells. Peptides are genetically inserted into the primary sequence of a simple, stable scaffold protein. The folding of the scaffold conformationally constrains the peptide, so peptide aptamers bind partners with high specificity and affinity (Woodman et al 2005; see also Figure 1). eptide aptamers are engineered proteins similar to antibodies that retain their integrity within cells. Peptides are genetically inserted into the primary sequence of a simple, stable scaffold protein. The folding of the scaffold conformationally constrains the peptide, so peptide aptamers bind partners with high specificity and affinity (1; see also Figure 1).
Figure 1 3D-model of a peptide aptamer. The functional peptide moiety is shown in a 'space filled' view (upper right hand side of the molecule) to highlight the solvent-exposed features that are likely to mediate specific interaction with a target. The stable scaffold protein is shown in a 'stick' representation
Intracellular binding of a peptide aptamer to a target protein will interfere with its function, either by destabilising it or by binding to a surface normally used for a specific interaction. Any resulting phenotype yields insights into the molecular biology of the target protein (Chattopadhyay et al, 2006). Where a peptide aptamer inhibits a cell-based model of disease, the peptide aptamer becomes a guide in drug discovery.
Peptide aptamers may also be useful in diagnostics. In collaboration with physicists, chemists and engineers we are using electrical detection of protein-peptide aptamer interactions that may lead to low-cost, disposable biochips for early detection of disease, detection of new biomarkers and population-wide health monitoring (Evans et al, 2008; Figure 2).eptide aptamers may also be useful in diagnostics. Peptide aptamer microarrays can specifically detect human papilloma virus proteins in infected cells (Figure 2).
Figure 2. Peptide aptamer microarrays can detect human cyclin-dependent protein kinase (CDK) proteins in whole yeast cell lysates. An array of 10 gold-coated electrodes, each ~10 µm wide and separated by ~15 µm, were coated with either of two peptide aptamers (pep2 or pep9) or with poly-ethylene glycol (mPEG) to prevent non-specific protein binding to the electrode. Pep2 recognises only CDK2, while Pep9 recognises CDK2 and CDK4. When the array was challenged with yeast cell lysate containing CDK2, a signal was detected at both Pep2 and Pep9 electrodes. When the array was challenged with lysate containing CDK4, only the Pep9 electrode generated a signal, indicating that there is no cross-talk between electrodes on the micron scale.
Woodman, R., Yeh, J.T-H, Laurenson, S. and Ko Ferrigno, P. Design and validation of a neutral scaffold for the presentation of peptide aptamers. Journal of Molecular Biology 352 1118-1133 (2005)
Chattophadayay, A, Tate, S., Beswick, R., Wagner, S.D. and Ko Ferrigno, P. A peptide aptamer to antagonise BCL-6 function. Oncogene, 25 2223-2233 (2006)
Evans, D.; Johnson.; Laurenson, S.; Davies, A. G.; Ko Ferrigno, P.; Walti, C. Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays. J Biol 7(1): 3 (2008)