Protein Core Packing by Dynamic Combinatorial Chemistry

We describe the first example of the recursive selection of biologically relevant macromolecules from a dynamic combinatorial library (DCL). A small library of 36 peptides was allowed to undergo self-association in aqueous solution to form 8436 trimers. The stability of each of these trimers was governed by the formation of a well-packed hydrophobic core. The DCL allowed variation of the hydrophobic residues comprising this core over all combinations of glycine, alanine, valine, leucine, isoleucine, and phenylalanine at six positions. The study leads to three important conclusions: (i) fewer than 0.2% of all possible core packing arrangements have high folding stabilities; (ii) these arrangements are stabilized by intimate jigsaw packing, not by sequestration of maximum hydrophobic surface area; (iii) a well-defined rule for packing of stable cores exists, but this rule is nuanced by the presence of two unexpected amino acid sequences and the absence of one expected amino acid sequence.