Computer-aided design of a PDZ domain to recognize new target sequences.
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 alpha-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.
Reina
Jose
J
Cell Biology and Biophysics Program, EMBL, 69117 Heidelberg, Germany.
Lacroix
Emmanuel
E
Hobson
Scott D
SD
Fernandez-Ballester
Gregorio
G
Rybin
Vladimir
V
Schwab
Markus S
MS
Serrano
Luis
L
Gonzalez
Cayetano
C
D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D017076:Computer-Aided Design; D015195:Drug Design; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D011485:Protein Binding; D015202:Protein Engineering; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D020798:Two-Hybrid System Techniques
D008024:Ligands; D011506:Proteins