Translational T-box riboswitches bind tRNA by modulating conformational flexibility.

T-box riboswitches are noncoding RNA elements involved in genetic regulation of most Gram-positive bacteria. They regulate amino acid metabolism by assessing the aminoacylation status of tRNA, subsequently affecting the transcription or translation of downstream amino acid metabolism-related genes. Here we present single-molecule FRET studies of the Mycobacterium tuberculosis IleS T-box riboswitch, a paradigmatic translational T-box. Results support a two-step binding model, where the tRNA anticodon is recognized first, followed by interactions with the NCCA sequence. Furthermore, after anticodon recognition, tRNA can transiently dock into the discriminator domain even in the absence of the tRNA NCCA-discriminator interactions. Establishment of the NCCA-discriminator interactions significantly stabilizes the fully bound state. Collectively, the data suggest high conformational flexibility in translational T-box riboswitches; and supports a conformational selection model for NCCA recognition. These findings provide a kinetic framework to understand how specific RNA elements underpin the binding affinity and specificity required for gene regulation.

Microwave Spectra and Theoretical Calculations for Two Structural Isomers of Methylmanganese Pentacarbonyl.

The first microwave rotational spectra for two structural isomers of methylmanganese pentacarbonyl were measured in the 4-9 GHz range using a pulsed-beam Fourier transform microwave spectrometer. The spectra for the two isomers, a symmetric-top structure and an asymmetric-top acyl isomeric structure, were fit to obtain rotational and centrifugal distortion constants and 55Mn quadrupole coupling parameters. The rotational constants, the manganese (55Mn) nuclear quadrupole coupling constant, the centrifugal distortion constants, and the spin-rotation constant were determined for the symmetric CH3Mn(CO)5 and have the following values: A = B = 793.153(3) MHz, DJ = 0.00040(4) MHz, DJK = 0.0018(2) MHz, Ccc = 0.183(6) MHz, and eQqcc= -87.4(3) MHz. Rotational constants and 55Mn quadruple coupling constants were determined for the isomeric acyl-CH3C(O)Mn(CO)4 and have the following values: A = 839.96(4) MHz, B = 774.20(7) MHz, C = 625.63(1) MHz, and 1.5 eQqaa= 44.9(47) MHz and 0.25(eQqbb - eQqcc) = 11.9(12) MHz. The measured rotational constants from the isomeric acyl-CH3C(O)Mn(CO)4 were compared with various theoretical computations. The calculated rotational constants for the dihapto-acyl and the agostic-acyl structures are reasonably close to the experimental values. We note that the calculated dihapto-acyl structure most closely matches the experimental data, as the calculation for the dihapto structure using the B3LYP functional with the aug-cc-pVDZ basis set closely reproduced the experimental values for A, B, and C.

Synthesis, microwave spectra, x-ray structure, and high-level theoretical calculations for formamidinium formate.

An efficient synthesis of formamidinium formate is described. The experimental x-ray structure shows both internal and external H-bonding to surrounding molecules. However, in the gas phase, this compound occurs as a doubly hydrogen bonded dimer between formamidine and formic acid. This doubly hydrogen-bonded structure is quite different from the solid state structure. Microwave spectra were measured in the 6-14 GHz range using a pulsed-beam Fourier transform microwave (MW) spectrometer. The two nonequivalent N-atoms exhibit distinct quadrupole coupling. The rotational, centrifugal distortion, and quadrupole coupling constants determined from the spectra have the following values: A = 5880.05(2), B = 2148.7710(2), C = 1575.23473(13), 1.5 χaa (N1) = 1.715(3), 0.5(χbb-χcc) (N1) = -1.333(4), 1.5 χaa (N2) = 0.381(2), 0.25(χbb-χcc) (N2) = -0.0324(2), and DJ = 0.002145(5) MHz. The experimental inertial defect, Δ = -0.243 amu Å2, is consistent with a planar structure. Accurate and precise rotational constants (A, B, and C), obtained from the MW measurements, were closely reproduced, within 1%-2% of the measured values, with the M11 DFT theoretical calculations. Detailed comparison of the measured and calculated A, B, and C rotational constants confirms the planar doubly hydrogen bonded structure. The calculated nitrogen quadrupole coupling strengths of the monomer are quite different from either of the two nitrogen sites of the dimer. The poor agreement between measured and calculated quadrupole coupling strengths shows that the dimer is not locked in the equilibrium structure but is likely undergoing large amplitude vibrational motion of the hydrogen atoms moving between the N and O atoms involved in the hydrogen bonding.

Microwave Spectra, Structure, and the Aromatic Character of 1-Chloroborepin.

High resolution microwave spectra for the somewhat unstable compound 1-chloroborepin were measured in the 5-10 GHz range using a pulsed beam Fourier transform microwave spectrometer. Transitions were assigned and measured for three isotopologues, which include the most abundant isotopologue, 11B35Cl, and the less abundant 10B35Cl and 11B37Cl isotopologues. The molecular parameters (MHz) determined for the 11B35Cl isotopologue are A = 3490.905(35), B = 1159.38520(79), C = 870.59492(56), 1.5χaa (11B) = -0.220(22), 0.25(χbb - χcc) (11B) = -1.5300(99), 1.5χaa (35Cl) = -54.572(33), and 0.25(χbb - χcc) (35Cl) = 4.7740(79). The inertial defect is calculated to be Δ = -0.174 amu Å2 from the experimental rotational constants, indicating a planar structure with some out of plane vibrational motion. An extended Townes-Dailey analysis was performed on the 11B and 35Cl nuclei to determine the electron occupations in the valence hybridized orbitals using the experimental quadrupole coupling strengths. From the analysis it was determined that Cl is sharing some electron density with the empty p-orbital on B. The B-Cl bond length determined from the data is 1.798(1) Å, and the B-C bond lengths are 1.533(10) Å. The structural parameters and electronic structure properties of 1-chloroborepin are consistent with an aromatic boron-containing molecule.