Nature Structural Biology9, 621 - 627 (2002)
Published online: 24 June 2002; | doi:10.1038/nsb815
Computer-aided design of a PDZ domain to recognize new target sequences
Jose Reina1, Emmanuel Lacroix2, Scott D. Hobson3, Gregorio Fernandez-Ballester2, Vladimir Rybin3, Markus S. Schwab3, Luis Serrano2
& Cayetano Gonzalez1
1
Cell Biology and Biophysics Program and EMBL, 69117 Heidelberg, Germany.
2
Structural Biology and Biocomputing Program, EMBL, 69117 Heidelberg, Germany.
PDZ domains are small globular domains that recognize the last 4−7 amino acids at the C-terminus of target proteins. The specificity of the PDZ−ligand recognition is due to side chain−side chain interactions, as well as the positioning of an -helix involved in ligand binding. We have used computer-aided protein design to produce mutant versions of a Class I PDZ domain that bind to novel Class I and Class II target sequences both in vitro and in vivo, thus providing an alternative to primary antibodies in western blotting, affinity chromatography and pull-down experiments. Our results suggest that by combining different backbone templates with computer-aided protein design, PDZ domains could be engineered to specifically recognize a large number of proteins.
-helix involved in ligand binding. We have used computer-aided protein design to produce mutant versions of a Class I PDZ domain that bind to novel Class I and Class II target sequences both in vitro and in vivo, thus providing an alternative to primary antibodies in western blotting, affinity chromatography and pull-down experiments. Our results suggest that by combining different backbone templates with computer-aided protein design, PDZ domains could be engineered to specifically recognize a large number of proteins.
