title: Synthetic antibodies for specific recognition and crystallization of structured RNA.
abstract: 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.
authors.affiliation: Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
authors.forename: Jing-Dong
authors.initials: JD
authors.lastname: Ye
authors.forename: Valentina
authors.initials: V
authors.lastname: Tereshko
authors.forename: John K
authors.initials: JK
authors.lastname: Frederiksen
authors.forename: Akiko
authors.initials: A
authors.lastname: Koide
authors.forename: Frederic A
authors.initials: FA
authors.lastname: Fellouse
authors.forename: Sachdev S
authors.initials: SS
authors.lastname: Sidhu
authors.forename: Shohei
authors.initials: S
authors.lastname: Koide
authors.forename: Anthony A
authors.initials: AA
authors.lastname: Kossiakoff
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Piccirilli
mesh_terms: 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
chemical_list: D000906:Antibodies; D000941:Antigens; D019151:Peptide Library; D012313:RNA; D008274:Magnesium