Biological systems possess a highly complex and dynamic cellular RNA population, collectively known as the transcriptome. Many RNAs fold into complex three-dimensional structures, both intrinsically and as ribonucleoprotein (RNP) complexes, and play fundamental roles in nearly every aspect of gene expression. Understanding cell biology, health, and disease requires knowledge of how RNA structure mediates biological function. X-ray crystallography provides a powerful method for structure determination, but RNA crystallization represents a major bottleneck in the process, reflecting in part the limited surface chemistry for mediating lattice interactions and repulsion among the phosphates. Considering the rapid pace of new RNA discovery, there remains an acute need to develop methods to facilitate RNA structure acquisition. For difficult protein targets, antibody fragments (Fab or scFv) have served as effective chaperones for crystallization, and we hypothesized that the large size, conformational properties and surface chemistry of Fabs will facilitate RNA crystallization as well. Using phage-display library selections we demonstrated that Fabs can bind RNA with high affinity and specificity, mediate the majority of lattice interactions in Fab-RNA co-crystals, and provide a molecular replacement model for solving the structures. The long-term goal of this project is to facilitate resolution of the RNA crystallization bottleneck through development of a high-throughput pipeline for antibody production against RNA. The objective of this application is to enable facile access to RNA- binding Fabs and pursue them as reagents for RNA and RNP crystallization and structure determination. To attain this objective we will (a) improve Fab libraries using phage display and molecular evolution approaches to identify amino acid types that tailor complementary determining regions (CDRs) for RNA binding, (b) develop general use crystallization modules with surface and conformational properties adjusted to facilitate crystallization, and (c) use these techniques to create and use Fab complexes of RNA and RNP targets for crystallization and structure determination. Completion of the research will allow facile access to RNA binding Fabs, provide structural biologists with a suite of portable modules for generalized use in RNA/RNP crystallization, and provide important new structural knowledge for understanding biological function.

Public Health Relevance

Our understanding of human health and disease and our capacity to develop disease treatment hinges critically on knowledge of the three-dimensional architectures of cellular macromolecules and macromolecular complexes. RNAs and RNA-protein complexes (RNPs) play a major role in human health and disease, but difficulties in obtaining high quality crystals of RNA and RNP complexes have severely limited our knowledge of the structural basis for RNA and RNP function. We propose to unleash the power of synthetic antibodies as crystallization chaperones for obtaining structures of RNA and RNP complexes.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM102489-06
Application #
9610651
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Preusch, Peter
Project Start
2013-04-01
Project End
2021-11-30
Budget Start
2018-12-01
Budget End
2019-11-30
Support Year
6
Fiscal Year
2019
Total Cost
Indirect Cost
Name
University of Chicago
Department
Biochemistry
Type
Schools of Medicine
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637
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