Selective protein–peptide interactions at surfaces

Abstract

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. In this study, surface-bound peptide arrays were used as a model to explore the range of protein–surface interactions and to better understand the kinds of “nonspecific” or unstructured interactions that take place at chemically complex surfaces. Three samples, β-galactosidase, α1-antitrypsin and a mixture of nine different proteins, were bound to arrays of nearly 5000 different peptides with a wide range of hydrophobicity, charge and peptide length. All three protein samples show higher binding affinity to positively charged peptides. While β-galactosidase binds poorly to very hydrophobic peptides, in terms of either absolute binding or relative to the mixture of proteins, α1-antitrypsin binds with higher affinity to more hydrophobic peptides. More surprising is the observation that 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, its affinity (both absolute and relative to the protein mixture) peaks in the four-to-nine amino acid residue range and then decreases substantially by 12 amino acids. In contrast, α1-antitrypsin increases nearly monotonically with peptide length, in terms of both apparent affinity and binding relative to other proteins. Of particular significance in a practical sense, it was possible to obtain quite specific binding; the identity of the 100 peptides that showed the best apparent affinity for each of the three protein samples overlapped very little. Thus, using this approach it would be straightforward to develop surfaces covered with specific short peptide sequences with relatively specific protein interaction profiles.