Molecular Design Lab, Institute of Physical Chemistry, Peking University, Beijing 100871, China
De novo protein design is a direct way to study the principles of protein structure. At present, to simulate the fold frequently occurred in native proteins is a major method to design new protein. The key to this question is to find out the main structural stabilizing factors. According to these factors, we can design stable and foldable proteins. From the process of designing such proteins, we can not only make proteins not exist in nature, but also we can justify our current understanding of protein structure.
From the exhaustive searching of PDB, we found a unusual stable structural motif which consists of an alpha helix and a two or three strand beta-sheet. The beta-sheet can be parallel structure or antiparallel structure. This kind of motif occurred several times in peptide inhibitors and small binding proteins. This motif is designated as alpha-beta-beta motif here. The main structural stabilizing factors of this motif is the hydrophobic core formed by the alpha helix and the beta-sheet. The structural analysis and the experimental evidences showed that the alpha-beta-beta motif within these proteins plays an important role both in the protein structure stabilization and in protein folding. It is a good protein structure template can be used to design new proteins.
After extensive studying the structure characteristics of alpha-beta-beta motif, we designed a new protein containing alpha-beta-beta motif and also built the detail molecular model of it. The protein is stabilized by a hydrophobic core consist of four hydrophobic amino acids and a hydrogen bond network. The further function designs based on the alpha-beta-beta motif structure are also proposed.
Considering alpha-beta-beta motif mostly occurred in peptide inhibitors and small binding proteins. Six new inhibitors are also designed based on alpha-beta-beta motif scaffold. The way to design them is to change the loop region of a stable protein containing alpha-beta-beta motif with those of several other peptide inhibitors. The experiments according to the above designs are underway.