Designing Repeat Proteins: Modular Leucine-rich Repeat Protein Libraries Based on the Mammalian Ribonuclease Inhibitor Family

• Published in: Journal of molecular biology Vol. 332; no. 2; pp. 471 - 487
• Main Authors: Stumpp, Michael T., Forrer, Patrik, Binz, H.Kaspar, Plückthun, Andreas
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 12-09-2003
• Subjects: Amino Acid Sequence; Animals; Base Sequence; combinatorial library; consensus sequence; Cysteine - metabolism; Databases, Protein; Humans; Leucine - chemistry; leucine-rich repeat; Models, Molecular; Molecular Sequence Data; Molecular Structure; protein design; Protein Engineering; Protein Structure, Tertiary; Proteins - chemistry; Repetitive Sequences, Amino Acid; ribonuclease inhibitor; Ribonucleases - antagonists & inhibitors; Sequence Alignment; NTA, nitrilotriacetic acid; PDB, Protein Data Bank; consensus sequence; leucine-rich repeat; AR, ankyrin repeat; LRR, leucine-rich repeat; RI, ribonuclease inhibitor; TBS, Tris-buffered saline; protein design; IMAC, immobilized metal-ion affinity chromatography; combinatorial library; ribonuclease inhibitor
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/S0022-2836(03)00897-0

We present a novel approach to design repeat proteins of the leucine-rich repeat (LRR) family for the generation of libraries of intracellular binding molecules. From an analysis of naturally occurring LRR proteins, we derived the concept to assemble repeat proteins with randomized surface positions from libraries of consensus repeat modules. As a guiding principle, we used the mammalian ribonuclease inhibitor (RI) family, which comprises cytosolic LRR proteins known for their extraordinary affinities to many RNases. By aligning the amino acid sequences of the internal repeats of human, pig, rat, and mouse RI, we derived a first consensus sequence for the characteristic alternating 28 and 29 amino acid residue A-type and B-type repeats. Structural considerations were used to replace all conserved cysteine residues, to define less conserved positions, and to decide where to introduce randomized amino acid residues. The so devised consensus RI repeat library was generated at the DNA level and assembled by stepwise ligation to give libraries of 2–12 repeats. Terminal capping repeats, known to shield the continuous hydrophobic core of the LRR domain from the surrounding solvent, were adapted from human RI. In this way, designed LRR protein libraries of 4–14 LRRs (equivalent to 130–415 amino acid residues) were obtained. The biophysical analysis of randomly chosen library members showed high levels of soluble expression in the
Escherichia coli cytosol, monomeric behavior as characterized by gel-filtration, and α-helical CD spectra, confirming the success of our design approach.