{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Zeller MJ"],"funding":["NCRR NIH HHS","NIAID NIH HHS","NCI NIH HHS","National Institutes of Health","NIGMS NIH HHS","NIH HHS"],"pagination":["438-448"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8938680"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["17(2)"],"pubmed_abstract":["RNA molecules can show high levels of cooperativity in their global folding and interactions with divalent ions. However, cooperativity at individual ligand-RNA interaction sites remains poorly understood. Here, we investigated the binding of thiamine and methylene diphosphonic acid (MDP, a soluble structural analogue of pyrophosphate) to the thiamine pyrophosphate riboswitch. These ligands each bind weakly at proximal subsites, with 10 μM and 1 mM affinities, respectively. The affinity of MDP moderately improves when thiamine or thiamine-like fragments are pre-bound to the RNA. Covalent linking of thiamine and MDP substantially increases riboswitch binding to a notable high affinity of 20 nM. Crystal structures and single-molecule correlated chemical probing revealed favorable induced fit effects upon binding of individual ligands and, unexpectedly, a substantial thermodynamically unfavorable RNA structural rearrangement upon binding of the linked thiamine-MDP ligand. Thus, linking of two ligands of modest affinity, accompanied by an unfavorable structural rearrangement, still yields a potent linked RNA-binding compound. Since complex ligands often bind riboswitches and other RNAs at proximal subsites, principles derived from this work inform and support fragment-linking strategies for identifying small molecules that interact with RNA specifically and with high affinity."],"journal":["ACS chemical biology"],"pubmed_title":["Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery."],"pmcid":["PMC8938680"],"funding_grant_id":["P30 CA016086","R01-EUREKA GM098662","P30 GM124165","R01 AI068462","P30 GM133893","R01 GM098662","S10 OD021527","R01 GM112940","S10 RR029205"],"pubmed_authors":["Zeller MJ","Serganov A","Aube J","Nuthanakanti A","Li K","Weeks KM"],"additional_accession":[]},"is_claimable":false,"name":"Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery.","description":"RNA molecules can show high levels of cooperativity in their global folding and interactions with divalent ions. However, cooperativity at individual ligand-RNA interaction sites remains poorly understood. Here, we investigated the binding of thiamine and methylene diphosphonic acid (MDP, a soluble structural analogue of pyrophosphate) to the thiamine pyrophosphate riboswitch. These ligands each bind weakly at proximal subsites, with 10 μM and 1 mM affinities, respectively. The affinity of MDP moderately improves when thiamine or thiamine-like fragments are pre-bound to the RNA. Covalent linking of thiamine and MDP substantially increases riboswitch binding to a notable high affinity of 20 nM. Crystal structures and single-molecule correlated chemical probing revealed favorable induced fit effects upon binding of individual ligands and, unexpectedly, a substantial thermodynamically unfavorable RNA structural rearrangement upon binding of the linked thiamine-MDP ligand. Thus, linking of two ligands of modest affinity, accompanied by an unfavorable structural rearrangement, still yields a potent linked RNA-binding compound. Since complex ligands often bind riboswitches and other RNAs at proximal subsites, principles derived from this work inform and support fragment-linking strategies for identifying small molecules that interact with RNA specifically and with high affinity.","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Feb","modification":"2026-05-09T22:22:28.107Z","creation":"2025-04-19T02:45:28.529Z"},"accession":"S-EPMC8938680","cross_references":{"pubmed":["35060698"],"doi":["10.1021/acschembio.1c00880"]}}