Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase–RNA complexes
RNases are varied in the RNA structures and sequences they target for cleavage and are an important type of enzyme in cells. Despite the numerous examples of RNases known, and of those with determined three-dimensional structures, relatively few examples exist with the RNase bound to intact cognate...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Journal of Structural Biology: X |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2590152422000071 |
| _version_ | 1811201762788376576 |
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| author | Seth P. Jones Christian Goossen Sean D. Lewis Annie M. Delaney Michael L. Gleghorn |
| author_facet | Seth P. Jones Christian Goossen Sean D. Lewis Annie M. Delaney Michael L. Gleghorn |
| author_sort | Seth P. Jones |
| collection | DOAJ |
| description | RNases are varied in the RNA structures and sequences they target for cleavage and are an important type of enzyme in cells. Despite the numerous examples of RNases known, and of those with determined three-dimensional structures, relatively few examples exist with the RNase bound to intact cognate RNA substrate prior to cleavage. To better understand RNase structure and sequence specificity for RNA targets, in vitro methods used to assemble these enzyme complexes trapped in a pre-cleaved state have been developed for a number of different RNases. We have surveyed the Protein Data Bank for such structures and in this review detail methodologies that have successfully been used and relate them to the corresponding structures. We also offer ideas and suggestions for future method development. Many strategies within this review can be used in combination with X-ray crystallography, as well as cryo-EM, and other structure-solving techniques. Our hope is that this review will be used as a guide to resolve future yet-to-be-determined RNase–substrate complex structures. |
| first_indexed | 2024-04-12T02:27:21Z |
| format | Article |
| id | doaj.art-fd30c019bf5b48bb9a4bbbde0bd4ffd9 |
| institution | Directory Open Access Journal |
| issn | 2590-1524 |
| language | English |
| last_indexed | 2024-04-12T02:27:21Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Structural Biology: X |
| spelling | doaj.art-fd30c019bf5b48bb9a4bbbde0bd4ffd92022-12-22T03:51:56ZengElsevierJournal of Structural Biology: X2590-15242022-01-016100066Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase–RNA complexesSeth P. Jones0Christian Goossen1Sean D. Lewis2Annie M. Delaney3Michael L. Gleghorn4School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United StatesSchool of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States; Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Lothrop St, Pittsburgh, PA 15261, United StatesSchool of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States; Mayo Clinic, 200 1st St SW, Rochester, MN 5590, United StatesSchool of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United StatesSchool of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States; Corresponding author.RNases are varied in the RNA structures and sequences they target for cleavage and are an important type of enzyme in cells. Despite the numerous examples of RNases known, and of those with determined three-dimensional structures, relatively few examples exist with the RNase bound to intact cognate RNA substrate prior to cleavage. To better understand RNase structure and sequence specificity for RNA targets, in vitro methods used to assemble these enzyme complexes trapped in a pre-cleaved state have been developed for a number of different RNases. We have surveyed the Protein Data Bank for such structures and in this review detail methodologies that have successfully been used and relate them to the corresponding structures. We also offer ideas and suggestions for future method development. Many strategies within this review can be used in combination with X-ray crystallography, as well as cryo-EM, and other structure-solving techniques. Our hope is that this review will be used as a guide to resolve future yet-to-be-determined RNase–substrate complex structures.http://www.sciencedirect.com/science/article/pii/S2590152422000071RNase–RNA complexPre-cleavageScissile-phosphateStructure determinationEnzymatic inhibitionNucleic acid recognition |
| spellingShingle | Seth P. Jones Christian Goossen Sean D. Lewis Annie M. Delaney Michael L. Gleghorn Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase–RNA complexes Journal of Structural Biology: X RNase–RNA complex Pre-cleavage Scissile-phosphate Structure determination Enzymatic inhibition Nucleic acid recognition |
| title | Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase–RNA complexes |
| title_full | Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase–RNA complexes |
| title_fullStr | Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase–RNA complexes |
| title_full_unstemmed | Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase–RNA complexes |
| title_short | Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase–RNA complexes |
| title_sort | not making the cut techniques to prevent rna cleavage in structural studies of rnase rna complexes |
| topic | RNase–RNA complex Pre-cleavage Scissile-phosphate Structure determination Enzymatic inhibition Nucleic acid recognition |
| url | http://www.sciencedirect.com/science/article/pii/S2590152422000071 |
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