Conformational Ensemble of TteAdoCbl Riboswitch Provides Stable Structural Elements for Conformation Selection and Population Shift in Cobalamin Recognition

Abstract

Cobalamin riboswitch is a cis-regulatory element widely found in the 5′-UTRs of the vitamin B12-associated genes in bacteria, resulting in modulation and production of a particular protein. Thermoanaerobacter tengcongensis (Tte) AdoCbl riboswitches are the largest of the known riboswitches with 210 nucleotides, partially due to its long peripheral P6-extension, which enable high affinity of AdoCbl. Two structural elements, T-loop/T-looplike motif and kissing loop are key to the global folding of the RNA. While the structure of the TteAdoCbl riboswitch complex is known, we still do not understand the structure and conformation before AdoCbl ligand recognition. In order to delineate the conformational changes and the stabilities of long-range interactions, we have performed extensive all-atom replica-exchange molecular dynamics simulations of the TteAdoCbl riboswitch with a total simulation time of 2296 ns. We found that both the T-loop/T-looplike motif and kissing loop are very stable with ligand binding. The gating conformation changes of P6-extension allow the ligand to bind to the preorganized kissing loop binding pocket. The T-loop/T-looplike motif has much more hydrogen bonds than observed in TteAdoCbl riboswitch complex crystal structure, indicating an allosteric response of the T-loop/T-looplike motif. Our study demonstrated that the conformational ensemble of TteAdoCbl riboswitch provides stable structural elements for conformation selection and population shift in cobalamin recognition.

Short Oligonucleotides Facilitate Co-transcriptional Labeling of RNA at Specific Positions

“…The labeled sites, 47 and 185, are close to the hairpins L5 and L13 (Figure A). Based on crystallographic data and molecular dynamics simulations on riboC, a stable kissing loop (KL) is formed between the two hairpins. , Cy3Cy5-riboC was immobilized onto quartz via hybridization to a biotin-labeled DNA for investigating the dynamics of the KL at the single-molecule level by smFRET (Figure C,D). Dynamic changes of Cy3Cy5-RNA upon addition of Mg 2+ and AdoCbl were monitored by smFRET.…”

Cobalamin Riboswitches Are Broadly Sensitive to Corrinoid Cofactors to Enable an Efficient Gene Regulatory Strategy

“…4 and 5 ). Recent molecular dynamics simulations of the T. tengcongensis Cbl-riboswitch suggest that the kissing loop structure may form prior to effector binding, which would place even greater constraints on the corrinoid tail orientation to achieve shape complementarity with its binding site ( 92 ). Additionally, some Cbl-riboswitches may in fact bind base-off corrinoids but disrupt subsequent formation of downstream regulatory structures of the expression platform, perhaps by interfering with the kissing loop ( Fig.…”

Cobalamin riboswitches are broadly sensitive to corrinoid cofactors to enable an efficient gene regulatory strategy

“…In this case, Cbl-riboswitches only indirectly sense the chemical composition of the variable lower ligand group, with differential binding largely determined by steric effects and shape complementarity (Figures 4-5). Recent molecular dynamics simulations of the T. tengcongensis Cbl-riboswitch suggest that the kissing loop structure may form prior to effector binding, which would place even greater constraints on the corrinoid tail orientation to achieve shape complementarity with its binding site (Ma et al, 2021). Additionally, some Cbl-riboswitches may in fact bind base-off corrinoids but disrupt subsequent formation of downstream regulatory structures of the expression platform, perhaps by interfering with the kissing loop (Figure S9).…”