Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment.

TitleSpecific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment.
Publication TypeJournal Article
Year of Publication2016
AuthorsShao, Yaming, Huang Hao, Qin Daoming, Li Nan-Sheng, Koide Akiko, Staley Jonathan P., Koide Shohei, Kossiakoff Anthony A., and Piccirilli Joseph A.
JournalJ Mol Biol
Volume428
Issue20
Pagination4100-4114
Date Published2016 Oct 09
ISSN1089-8638
KeywordsCrystallography, X-Ray, Immunoglobulin Fab Fragments, Immunologic Factors, Kinetics, Models, Molecular, Nucleic Acid Conformation, Peptide Library, Protein Binding, Protein Conformation, RNA, RNA-Binding Proteins
Abstract

<p>Antibodies that bind RNA represent an unrealized source of reagents for synthetic biology and for characterizing cellular transcriptomes. However, facile access to RNA-binding antibodies requires the engineering of effective Fab libraries guided by the knowledge of the principles that govern RNA recognition. Here, we describe a Fab identified from a minimalist synthetic library during phage display against a branched RNA target. The Fab (BRG) binds with 20nM dissociation constant to a single-stranded RNA (ssRNA) sequence adjacent to the branch site and can block the action of debranchase enzyme. We report the crystal structure in complex with RNA target at 2.38Å. The Fab traps the RNA in a hairpin conformation that contains a 2-bp duplex capped by a tetraloop. The paratope surface consists of residues located in four complementarity-determining regions including a major contribution from H3, which adopts a helical structure that projects into a deep, wide groove formed by the RNA. The amino acid composition of the paratope reflects the library diversity, consisting mostly of tyrosine and serine residues and a small but significant contribution from a single arginine residue. This structure, involving the recognition of ssRNA via a stem-loop conformation, together with our two previous structures involving the recognition of an RNA hairpin loop and an RNA tertiary structure, reveals the capacity of minimalist libraries biased with tyrosine, serine, glycine, and arginine to form binding surfaces for specific RNA conformations and distinct levels of RNA structural hierarchy.</p>

DOI10.1016/j.jmb.2016.08.029
Alternate JournalJ. Mol. Biol.
PubMed ID27593161
PubMed Central IDPMC5178103
Grant ListS10 RR029205 / RR / NCRR NIH HHS / United States
R01 GM102489 / GM / NIGMS NIH HHS / United States
P41 GM103403 / GM / NIGMS NIH HHS / United States
R01 GM117372 / GM / NIGMS NIH HHS / United States
R21 HG005262 / HG / NHGRI NIH HHS / United States

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