A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination
RNA crystallization and phasing represent major bottlenecks in RNA structure determination. Seeking to exploit antibody fragments as RNA crystallization chaperones, we have used an arginine-enriched synthetic Fab library displayed on phage to obtain Fabs against the class I ligase ribozyme. We solve...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2012
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| Online Access: | http://hdl.handle.net/1721.1/72384 https://orcid.org/0000-0002-3872-2856 |
| _version_ | 1826216788146257920 |
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| author | Koldobskaya, Yelena Duguid, Erica M. Shechner, David M. Suslov, Nikolai B. Ye, Jingdong Sidhu, Sachdev S. Bartel, David Koide, Shohei Kossiakoff, Anthony A. Piccirilli, Joseph A. |
| author2 | move to dc.description.sponsorship |
| author_facet | move to dc.description.sponsorship Koldobskaya, Yelena Duguid, Erica M. Shechner, David M. Suslov, Nikolai B. Ye, Jingdong Sidhu, Sachdev S. Bartel, David Koide, Shohei Kossiakoff, Anthony A. Piccirilli, Joseph A. |
| author_sort | Koldobskaya, Yelena |
| collection | MIT |
| description | RNA crystallization and phasing represent major bottlenecks in RNA structure determination. Seeking to exploit antibody fragments as RNA crystallization chaperones, we have used an arginine-enriched synthetic Fab library displayed on phage to obtain Fabs against the class I ligase ribozyme. We solved the structure of a Fab–ligase complex at 3.1-Å resolution using molecular replacement with Fab coordinates, confirming the ribozyme architecture and revealing the chaperone's role in RNA recognition and crystal contacts. The epitope resides in the GAAACAC sequence that caps the P5 helix, and this sequence retains high-affinity Fab binding within the context of other structured RNAs. This portable epitope provides a new RNA crystallization chaperone system that easily can be screened in parallel to the U1A RNA-binding protein, with the advantages of a smaller loop and Fabs′ high molecular weight, large surface area and phasing power. |
| first_indexed | 2024-09-23T16:53:27Z |
| format | Article |
| id | mit-1721.1/72384 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:53:27Z |
| publishDate | 2012 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/723842022-10-03T08:56:33Z A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination Koldobskaya, Yelena Duguid, Erica M. Shechner, David M. Suslov, Nikolai B. Ye, Jingdong Sidhu, Sachdev S. Bartel, David Koide, Shohei Kossiakoff, Anthony A. Piccirilli, Joseph A. move to dc.description.sponsorship Massachusetts Institute of Technology. Department of Biology Bartel, David Shechner, David M. Bartel, David RNA crystallization and phasing represent major bottlenecks in RNA structure determination. Seeking to exploit antibody fragments as RNA crystallization chaperones, we have used an arginine-enriched synthetic Fab library displayed on phage to obtain Fabs against the class I ligase ribozyme. We solved the structure of a Fab–ligase complex at 3.1-Å resolution using molecular replacement with Fab coordinates, confirming the ribozyme architecture and revealing the chaperone's role in RNA recognition and crystal contacts. The epitope resides in the GAAACAC sequence that caps the P5 helix, and this sequence retains high-affinity Fab binding within the context of other structured RNAs. This portable epitope provides a new RNA crystallization chaperone system that easily can be screened in parallel to the U1A RNA-binding protein, with the advantages of a smaller loop and Fabs′ high molecular weight, large surface area and phasing power. National Institutes of Health (U.S.) (GM61835) 2012-08-28T18:44:06Z 2012-08-28T18:44:06Z 2010-12 2010-10 Article http://purl.org/eprint/type/JournalArticle 1545-9993 1545-9985 http://hdl.handle.net/1721.1/72384 Koldobskaya, Yelena et al. “A Portable RNA Sequence Whose Recognition by a Synthetic Antibody Facilitates Structural Determination.” Nature Structural & Molecular Biology 18.1 (2010): 100–106. https://orcid.org/0000-0002-3872-2856 en_US http://dx.doi.org/10.1038/nsmb.1945 Nature Structural and Molecular Biology Creative Commons Attribution-Noncommercial-Share Alike 3.0 http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf Nature Publishing Group PMC |
| spellingShingle | Koldobskaya, Yelena Duguid, Erica M. Shechner, David M. Suslov, Nikolai B. Ye, Jingdong Sidhu, Sachdev S. Bartel, David Koide, Shohei Kossiakoff, Anthony A. Piccirilli, Joseph A. A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination |
| title | A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination |
| title_full | A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination |
| title_fullStr | A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination |
| title_full_unstemmed | A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination |
| title_short | A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination |
| title_sort | portable rna sequence whose recognition by a synthetic antibody facilitates structural determination |
| url | http://hdl.handle.net/1721.1/72384 https://orcid.org/0000-0002-3872-2856 |
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