Unstructured interactions between peptides and proteins: Exploring the role of sequence motifs in affinity and specificity

Unstructured interactions between proteins and other molecules or surfaces are often described as nonspecific, and have received relatively little attention in terms of their role in biology. However, despite their lack of a specific binding structure, these unstructured interactions can in fact be very selective. The lack of a specific structure for these interactions makes them more difficult to study in a chemically meaningful way, but one approach is statistical, i.e. simply looking at a large number of different ligands and using that to understand the chemistry of binding. Surface-bound peptide arrays are useful in this regard, and have been used as a model previously for this purpose (Wang and Woodbury, 2014). In that study, the binding of several proteins, including β-galactosidase, to all possible dipeptides, tripeptides and tetrapeptides (using seven selected amino acids) was performed and analyzed in terms of the charge characteristics, hydrophobicity, etc., of the binding interaction. The current work builds upon that study by starting with a representative subset of the tetrapeptides characterized previously and either extending them by adding all possible combinations of one, two and three amino acids, or by concatenating 57 of the previously characterized tetrapeptides to each other in all possible combinations (including order). The extended and concatenated libraries were analyzed by binding either labeled β-galactosidase to them or by binding a mixture of 10 different labeled proteins of various sizes, hydrophobicities and charge characteristics to the peptide arrays. By comparing the binding signals from the tetrapeptides or amino acid extensions alone to the binding signals from the complete extended or concatenated sequences, it was possible to evaluate the extent to which affinity and specificity of the whole sequence depends on the subsequences that make it up. The conclusion is that while joining two component sequences together can either greatly increase or decrease overall binding and specificity (relative to the component sequences alone), the contribution to the binding affinity and specificity of the individual binding components is strongly dependent on their position in the peptide; component sequences that bind strongly at the C-terminus of the peptide do not necessarily add substantially to binding and specificity when placed at the N-terminus.