Towards meeting the paracelsus challenge: The design, synthesis, and characterization of paracelsin-43, an α-helical protein with over 50% sequence identity to an all-β protein

• Published in: Proteins, structure, function, and bioinformatics Vol. 24; no. 4; pp. 502 - 513
• Main Authors: Jones, David T., Moody, Claire M., Uppenbrink, Julia, Viles, John H., Doyle, Paul M., Harris, C. John, Pearl, Laurence H., Sadler, Peter J., Thornton, Janet M.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01-04-1996
• Subjects: 1H NMR; Algorithms; Amino Acid Sequence; Antimicrobial Cationic Peptides; Circular Dichroism; de novo design; ethylene glycol; genetic algorithms; Hydrogen-Ion Concentration; inverse folding; Magnetic Resonance Spectroscopy; methanol; Molecular Sequence Data; peptide; Peptides - chemical synthesis; Peptides - chemistry; Protein Conformation; protein folding; protein structure; Sequence Homology, Amino Acid
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/(SICI)1097-0134(199604)24:4<502::AID-PROT9>3.0.CO;2-F

In response to the Paracelsus Challenge (Rose and Creamer, Proteins, 19:1–3, 1994), we present here the design, synthesis, and characterization of a helical protein, whose sequence is 50% identical to that of an all‐β protein. The new sequence was derived by applying an inverse protein folding approach, in which the sequence was optimized to “fit” the new helical structure, but constrained to retain 50% of the original amino acid residues. The program utilizes a genetic algorithm to optimize the sequence, together with empirical potentials of mean force to evaluate the sequence‐structure compatibility. Although the designed sequence has little ordered (secondary) structure in water, circular dichroism and nuclear magnetic resonance data show clear evidence for significant helical content in water/ethylene glycol and in water/methanol mixtures at low temperatures, as well as melting behavior indicative of cooperative folding. We believe that this represents a significant step toward meeting the Paracelsus Challenge.