Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer
The thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modifies gene expression in response to TPP concentration. Its specificity is dependent upon conformational changes that take place within its aptamer domain. Here, the role of tertiary interactions in ligand bindin...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2015-12-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/12362 |
| _version_ | 1818018984183726080 |
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| author | Van K Duesterberg Irena T Fischer-Hwang Christian F Perez Daniel W Hogan Steven M Block |
| author_facet | Van K Duesterberg Irena T Fischer-Hwang Christian F Perez Daniel W Hogan Steven M Block |
| author_sort | Van K Duesterberg |
| collection | DOAJ |
| description | The thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modifies gene expression in response to TPP concentration. Its specificity is dependent upon conformational changes that take place within its aptamer domain. Here, the role of tertiary interactions in ligand binding was studied at the single-molecule level by combined force spectroscopy and Förster resonance energy transfer (smFRET), using an optical trap equipped for simultaneous smFRET. The ‘Force-FRET’ approach directly probes secondary and tertiary structural changes during folding, including events associated with binding. Concurrent transitions observed in smFRET signals and RNA extension revealed differences in helix-arm orientation between two previously-identified ligand-binding states that had been undetectable by spectroscopy alone. Our results show that the weaker binding state is able to bind to TPP, but is unable to form a tertiary docking interaction that completes the binding process. Long-range tertiary interactions stabilize global riboswitch structure and confer increased ligand specificity. |
| first_indexed | 2024-04-14T07:47:02Z |
| format | Article |
| id | doaj.art-50e615842bf24d379d6461b505b5e887 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-14T07:47:02Z |
| publishDate | 2015-12-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-50e615842bf24d379d6461b505b5e8872022-12-22T02:05:18ZengeLife Sciences Publications LtdeLife2050-084X2015-12-01410.7554/eLife.12362Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamerVan K Duesterberg0https://orcid.org/0000-0002-6036-5453Irena T Fischer-Hwang1Christian F Perez2Daniel W Hogan3Steven M Block4Biophysics Program, Stanford University, Stanford, United StatesDepartment of Electrical Engineering, Stanford University, Stanford, United StatesDepartment of Physics, Stanford University, Stanford, United StatesDepartment of Applied Physics, Stanford University, Stanford, United StatesDepartment of Applied Physics, Stanford University, Stanford, United States; Department of Biology, Stanford University, Stanford, United StatesThe thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modifies gene expression in response to TPP concentration. Its specificity is dependent upon conformational changes that take place within its aptamer domain. Here, the role of tertiary interactions in ligand binding was studied at the single-molecule level by combined force spectroscopy and Förster resonance energy transfer (smFRET), using an optical trap equipped for simultaneous smFRET. The ‘Force-FRET’ approach directly probes secondary and tertiary structural changes during folding, including events associated with binding. Concurrent transitions observed in smFRET signals and RNA extension revealed differences in helix-arm orientation between two previously-identified ligand-binding states that had been undetectable by spectroscopy alone. Our results show that the weaker binding state is able to bind to TPP, but is unable to form a tertiary docking interaction that completes the binding process. Long-range tertiary interactions stabilize global riboswitch structure and confer increased ligand specificity.https://elifesciences.org/articles/12362optical trapsmFRETsingle molecule biophysicsTPPriboswitch |
| spellingShingle | Van K Duesterberg Irena T Fischer-Hwang Christian F Perez Daniel W Hogan Steven M Block Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer eLife optical trap smFRET single molecule biophysics TPP riboswitch |
| title | Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer |
| title_full | Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer |
| title_fullStr | Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer |
| title_full_unstemmed | Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer |
| title_short | Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer |
| title_sort | observation of long range tertiary interactions during ligand binding by the tpp riboswitch aptamer |
| topic | optical trap smFRET single molecule biophysics TPP riboswitch |
| url | https://elifesciences.org/articles/12362 |
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