title: Recursively enriched dynamic combinatorial libraries for the self-selection of optimally stable proteins.
abstract: Even at very low template (guest) concentrations, the optimal template-assembled host from a dynamic combinatorial library (DCL) of host fragments may be unobtainable because hetero-oligomers will always be present at higher concentrations than isoenergetic homo-oligomers. Recursively enriched dynamic combinatorial libraries (REDCLs) offer a general solution to this problem that should be applicable to any self-selecting system under thermodynamic control. The utility of the REDCL strategy is demonstrated by determination of the optimal hydrophobic core packing in a template-assembled triple helical protein for which the template is a metal ion and the contributing host fragments are components of a 36-member conformationally restricted peptide library in which each peptide is augmented with a metal-binding moiety. Convergence of the 8436-member DCL to 5 optimal trimers (0.06% of the DCL) is complete after four cycles of enrichment. The core packing of the optimal sequences is shown to be native-like, and to reflect the hydrophobic amino acid preferences found in natural parallel three-stranded coiled coils. The influence of potentially critical amino acids on the outcome of the recursive enrichment is explored in a second REDCL. The same peptide sequences were returned and were shown to populate seven of the 8436 possible trimers, or 0.08% of the DCL.
authors.affiliation: Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, USA.
authors.forename: Liton
authors.initials: L
authors.lastname: Roy
authors.forename: Martin A
authors.initials: MA
authors.lastname: Case
mesh_terms: D000595:Amino Acid Sequence; D000817:Anilino Naphthalenesulfonates / Q000378:metabolism; D020650:Combinatorial Chemistry Techniques / Q000379:methods*; D057927:Hydrophobic and Hydrophilic Interactions; D007501:Iron / Q000737:chemistry; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019151:Peptide Library; D055503:Protein Multimerization; D055550:Protein Stability; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D011506:Proteins / Q000138:chemical synthesis* / Q000737:chemistry* / Q000378:metabolism
chemical_list: C515594:8-anilino-1-naphthalenesulfonic acid; D000817:Anilino Naphthalenesulfonates; D019151:Peptide Library; D011506:Proteins; D007501:Iron