Computational redesign of protein-protein interaction specificity.
We developed a 'computational second-site suppressor' strategy to redesign specificity at a protein-protein interface and applied it to create new specifically interacting DNase-inhibitor protein pairs. We demonstrate that the designed switch in specificity holds in in vitro binding and functional assays. We also show that the designed interfaces are specific in the natural functional context in living cells, and present the first high-resolution X-ray crystallographic analysis of a computer-redesigned functional protein-protein interface with altered specificity. The approach should be applicable to the design of interacting protein pairs with novel specificities for delineating and re-engineering protein interaction networks in living cells.
Kortemme
Tanja
T
Howard Hughes Medical Institute & Department of Biochemistry, Box 357350, University of Washington, Seattle, Washington 98195-7350, USA.
Joachimiak
Lukasz A
LA
Bullock
Alex N
AN
Schuler
Aaron D
AD
Stoddard
Barry L
BL
Baker
David
D
D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D003851:Deoxyribonucleases / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012680:Sensitivity and Specificity
D001426:Bacterial Proteins; D011506:Proteins; D003851:Deoxyribonucleases