Protein de novo design is an inverse but effective approach to elucidate the relationship between protein tertiary structure and its amino acid sequence. Examples include de novo designed alpha -helical coiled coils by Hodes' group [1] and four helical bundles by DeGrado and co-workers [2]. However, de novo designed peptides usually show some characteristics of molten globule rather than the expected native-like state [3]. Particularly, some can not fold into their predicted structures [4,5]. Because of the low predictability, we have to systematically investigate the factors that dominate the formation and stability of alpha -helix structure by designing and characterizing model I peptide in our previous work [6]. In this paper, we will rpesent a rational approach to the helical protein design based on the known structures of leucine zipper peptide GCN4-p1 mutants [7,8].
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