When developing peptide arrays for diagnostic testing, the capability to perform focused studies to define the characteristics of the interactions that occur between the analyte(s) and the chip is essential. This capability requires a technological leap forward in the manufacture of these peptide chips and fundamental components of this technology must include, straight-forward design, rapid synthesis, compatibility with existing array detection systems, and low cost. The innovative PepArray™ peptide array synthesis technology developed at LC Sciences has achieved this level of advancement as was recently demonstrated by a study performed by the Arizona Biodesign Institute in which surface-bound peptide-arrays were used as a model to explore the range of “nonspecific” or unstructured interactions that take place at chemically complex surfaces1.
Protein-surface interactions are of critical significance in both biological and man-made systems. While the term “specific binding” is normally reserved for the description of well-structured interactions, it is often the case in biology that there are unstructured interactions that greatly favor some protein interactions over others, a necessity in the highly crowded environment of the cell. To define these unstructured interactions, the researchers designed a custom peptide array consisting of nearly 5000 different peptides with a wide range of hydrophobicity, charge and peptide length. The synthesis of these custom peptide arrays was made possible by the PepArray™ peptide array synthesis technology2.
The researchers found that:
- All three protein samples show higher binding affinity to positively charged peptides.
- α1-antitrypsin binds with higher affinity to more hydrophobic peptides.
- α1- antitrypsin increases nearly monotonically with peptide length, both in terms of apparent affinity and binding relative to other proteins.
- β-galactosidase binds poorly to very hydrophobic peptides, both in terms of absolute binding or relative to the mixture of proteins.
- β -galactosidase affinity for the surface does not simply increase with the length of the peptide, as one might expect, even when only the best binders are considered.
- Instead, β -galactosidase affinity (both absolute and relative to the protein mixture) peaks in the 4- 9 amino acid residue range and then decreases substantially by 12 amino acids.
Of particular significance, the researchers note that:
- It was possible to obtain quite specific binding for each sample.
- The identity of the 100 peptides that showed the best apparent affinity for each of the three protein samples overlapped very little.
- Using this approach, it would be straightforward to develop surfaces covered with specific short peptide sequences with relatively specific protein interaction profiles.
This study demonstrates µParaflo® technology’s potential for development of peptide microchips for various pharmaceutical and proteomic applications in routine research laboratories.
- Wang W, Woodbury N. (2013) Selective Protein/Peptide Interactions at Surfaces. Acta Biomaterialia 10(2):761-8. [abstract]
- Pellois JP, Zhou X, Srivannavit O, Zhou T, Gulari E, Gao X. (2002) Individually addressable parallel peptide synthesis on microchips. Nature Biotechnology 20, 922-926. [abstract]