title: Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep).
abstract: We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a "filtration" procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×10(9) independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties.
authors.affiliation: Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud, Orsay, France ; Unité Mixte de Recherche 8619, Centre National de Recherche Scientifique, Orsay, France.
authors.forename: Asma
authors.initials: A
authors.lastname: Guellouz
authors.forename: Marie
authors.initials: M
authors.lastname: Valerio-Lepiniec
authors.forename: Agathe
authors.initials: A
authors.lastname: Urvoas
authors.forename: Anne
authors.initials: A
authors.lastname: Chevrel
authors.forename: Marc
authors.initials: M
authors.lastname: Graille
authors.forename: Zaineb
authors.initials: Z
authors.lastname: Fourati-Kammoun
authors.forename: Michel
authors.initials: M
authors.lastname: Desmadril
authors.forename: Herman
authors.initials: H
authors.lastname: van Tilbeurgh
authors.forename: Philippe
authors.initials: P
authors.lastname: Minard
mesh_terms: D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D004797:Enzyme-Linked Immunosorbent Assay; D049452:Green Fluorescent Proteins / Q000737:chemistry; D055767:Immobilized Proteins / Q000737:chemistry; D019151:Peptide Library; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D055550:Protein Stability; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D055767:Immobilized Proteins; D019151:Peptide Library; D010455:Peptides; C485184:enhanced green fluorescent protein; D049452:Green Fluorescent Proteins