title: Design of stable alpha-helices using global sequence optimization.
abstract: The rational design of peptide and protein helices is not only of practical importance for protein engineering but also is a useful approach in attempts to improve our understanding of protein folding. Recent modifications of theoretical models of helix-coil transitions allow accurate predictions of the helix stability of monomeric peptides in water and provide new possibilities for protein design. We report here a new method for the design of alpha-helices in peptides and proteins using AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides and the tunneling algorithm of global optimization of multidimensional functions for optimization of amino acid sequences. CD measurements of helical content of peptides with optimized sequences indicate that the helical potential of protein amino acids is high enough to allow formation of stable alpha-helices in peptides as short as of 10 residues in length. The results show the maximum achievable helix content (HC) of short peptides with fully optimized sequences at 5 degrees C is expected to be approximately 70-75%. Under certain conditions the method can be a powerful practical tool for protein engineering. Unlike traditional approaches that are often used to increase protein stability by adding a few favorable interactions to the protein structure, this method deals with all possible sequences of protein helices and selects the best one from them.
authors.affiliation: Petersburg Institute of Nuclear Physics, the Russian Academy of Sciences, 188300, Gatchina, Russia. michael.petukhov@gmail.com
authors.forename: Michael
authors.initials: M
authors.lastname: Petukhov
authors.forename: Yoshiro
authors.initials: Y
authors.lastname: Tatsu
authors.forename: Kazuyo
authors.initials: K
authors.lastname: Tamaki
authors.forename: Sachiko
authors.initials: S
authors.lastname: Murase
authors.forename: Hiroko
authors.initials: H
authors.lastname: Uekawa
authors.forename: Susumu
authors.initials: S
authors.lastname: Yoshikawa
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
authors.forename: Noboru
authors.initials: N
authors.lastname: Yumoto
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D010455:Peptides; D011506:Proteins