Binding proteins from alternative scaffolds

The use of so-called protein scaffolds for the generation of novel binding proteins via combinatorial engineering has recently emerged as a powerful alternative to natural or recombinant antibodies. This concept requires an extraordinary stable protein architecture tolerating multiple substitutions or insertions at the primary structural level. With respect to broader applicability it should involve a type of polypeptide fold which is observed in differing natural contexts and with distinct biochemical functions, so that it is likely to be adaptable to novel molecular recognition purposes. The quickly growing number of approaches can be classified into three groups: carrier proteins for the display of single variegated loops, scaffolds providing rigid elements of secondary structure, and protein frameworks supporting a group of conformationally variable loops in a fixed spatial arrangement. Generally, such artificial receptor proteins should be based on monomeric and small polypeptides that are robust, easily engineered, and efficiently produced in inexpensive prokaryotic expression systems. Today, progress in protein library technology allows for the parallel development of immunoglobulin (Ig) as well as scaffold-based affinity reagents. Both biomolecular tools have the potential to complement each other, thus expanding the possibility to find an affinity reagent suitable for a given application. The repertoire of protein scaffolds hitherto recruited for combinatorial protein engineering purposes will probably be further expanded in the future, including both additional natural proteins and de novo designed proteins, contributing to the collection of libraries available at present. In this review both the structural features and the practical use of scaffold proteins will be discussed and exemplified. (C) 2004 Elsevier B.V. All rights reserved.