Design of lambda Cro fold: solution structure of a monomeric variant of the de novo protein.
One of the classical DNA-binding proteins, bacteriophage lambda Cro, forms a homodimer with a unique fold of alpha-helices and beta-sheets. We have computationally designed an artificial sequence of 60 amino acid residues to stabilize the backbone tertiary structure of the lambda Cro dimer by simulated annealing using knowledge-based structure-sequence compatibility functions. The designed amino acid sequence has 25% identity with that of natural lambda Cro and preserves Phe58, which is important for formation of the stably folded structure of lambda Cro. The designed dimer protein and its monomeric variant, which was redesigned by the insertion of a beta-hairpin sequence at the C-terminal region to prevent dimerization, were synthesized and biochemically characterized to be well folded. The designed protein was monomeric under a wide range of protein concentrations and its solution structure was determined by NMR spectroscopy. The solved structure is similar to that of a monomeric variant of natural lambda Cro with a root-mean-square deviation of the polypeptide backbones at 2.1A and has a well-packed protein core. Thus, our knowledge-based functions provide approximate but essential relationships between amino acid sequences and protein structures, and are useful for finding novel sequences that are foldable into a given target structure.
Isogai
Yasuhiro
Y
Bio-metal Science Laboratory, RIKEN Harima Institute/SPring8, Mikazuki, Sayo, Hyogo 679-5148, Japan. yisogai@riken.jp
Ito
Yutaka
Y
Ikeya
Teppei
T
Shiro
Yoshitsugu
Y
Ota
Motonori
M
D000595:Amino Acid Sequence; D010582:Bacteriophage lambda / Q000737:chemistry; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000737:chemistry*; D019281:Dimerization; D019020:Directed Molecular Evolution; D051188:Knowledge Bases; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D015202:Protein Engineering / Q000379:methods*; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012996:Solutions; D040681:Structural Homology, Protein; D014764:Viral Proteins / Q000737:chemistry*; D054334:Viral Regulatory and Accessory Proteins
D004268:DNA-Binding Proteins; D010455:Peptides; D012097:Repressor Proteins; D012996:Solutions; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins