A protein designed by binary patterning of polar and nonpolar amino acids displays native-like properties

Large collections of de novo α-helical proteins can be constructed by using combinatorial methods based on a 'binary code' for protein design, in which the sequence locations of polar and nonpolar amino acids are specified explicitly, but the precise identities of these residues are varied extensively. We demonstrate that a 75-residue protein chosen from such a binary code collection displays several properties similar to those of native proteins: (i) Both the chemically induced and thermally induced denaturations are cooperative; (ii) addition of the hydrophobic dye 1-analinonaphthalene- 8-sulfonate (ANS) yields only minimal fluorescence; (iii) the NMR spectrum shows significant chemical shift dispersion in both the amide and methyl regions; and (iv) amide protons are protected from exchange to an extent observed in some natural proteins. These results demonstrate that binary patterning of polar and nonpolar amino acids can serve as the basis for initial steps toward the design of novel proteins with native-like properties.