A PROTEIN DESIGNED BY BINARY PATTERNING OF POLAR AND NONPOLAR AMINO-ACIDS DISPLAYS NATIVE-LIKE PROPERTIES

Large collections of de novo alpha-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 a cids are specified explicitly, but the precise identities of these res idues 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 chemic al shift dispersion in both the amide and methyl regions; and (iv) ami de protons are protected from exchange to an extent observed in some n atural proteins. These results demonstrate that binary patterning of p olar and nonpolar amino acids can serve as the basis for initial steps toward the design of novel proteins with native-like properties.