Synthetic antibodies for specific recognition and crystallization of structured RNA.
Antibodies that bind protein antigens are indispensable in biochemical research and modern medicine. However, knowledge of RNA-binding antibodies and their application in the ever-growing RNA field is lacking. Here we have developed a robust approach using a synthetic phage-display library to select specific antigen-binding fragments (Fabs) targeting a large functional RNA. We have solved the crystal structure of the first Fab-RNA complex at 1.95 A. Capability in phasing and crystal contact formation suggests that the Fab provides a potentially valuable crystal chaperone for RNA. The crystal structure reveals that the Fab achieves specific RNA binding on a shallow surface with complementarity-determining region (CDR) sequence diversity, length variability, and main-chain conformational plasticity. The Fab-RNA interface also differs significantly from Fab-protein interfaces in amino acid composition and light-chain participation. These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology.
Ye
Jing-Dong
JD
Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
Tereshko
Valentina
V
Frederiksen
John K
JK
Koide
Akiko
A
Fellouse
Frederic A
FA
Sidhu
Sachdev S
SS
Koide
Shohei
S
Kossiakoff
Anthony A
AA
Piccirilli
Joseph A
JA
D000595:Amino Acid Sequence; D000818:Animals; D000906:Antibodies / Q000737:chemistry; D000941:Antigens / Q000737:chemistry; D001483:Base Sequence; D001671:Biochemistry / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods; D007700:Kinetics; D008274:Magnesium / Q000737:chemistry; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D019151:Peptide Library; D012313:RNA / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D013768:Tetrahymena / Q000378:metabolism
D000906:Antibodies; D000941:Antigens; D019151:Peptide Library; D012313:RNA; D008274:Magnesium