Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.
The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Mihai L
ML
Azoitei
Bruno E
BE
Correia
Yih-En Andrew
YE
Ban
Chris
C
Carrico
Oleksandr
O
Kalyuzhniy
Lei
L
Chen
Alexandria
A
Schroeter
Po-Ssu
PS
Huang
Jason S
JS
McLellan
Peter D
PD
Kwong
David
D
Baker
Roland K
RK
Strong
William R
WR
Schief
D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000911:Antibodies, Monoclonal / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D057134:Antibodies, Neutralizing / Q000737:chemistry* / Q000276:immunology* / Q000378:metabolism; D000915:Antibody Affinity; D000918:Antibody Specificity; D015704:CD4 Antigens / Q000378:metabolism; D019295:Computational Biology; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D000939:Epitopes / Q000276:immunology; D015483:HIV Antibodies / Q000737:chemistry / Q000276:immunology* / Q000378:metabolism; D015699:HIV Envelope Protein gp120 / Q000737:chemistry* / Q000276:immunology* / Q000378:metabolism; D008958:Models, Molecular; D018716:Molecular Mimicry; D008969:Molecular Sequence Data; D016296:Mutagenesis; D011487:Protein Conformation; D015202:Protein Engineering; D054730:Protein Interaction Domains and Motifs; D020349:Surface Plasmon Resonance
D000911:Antibodies, Monoclonal; D057134:Antibodies, Neutralizing; D015704:CD4 Antigens; D000939:Epitopes; D015483:HIV Antibodies; D015699:HIV Envelope Protein gp120