Validating the EMCV IRES Secondary Structure with Structure-Function Analysis.

The encephalomyocarditis virus internal ribosome entry site (EMCV IRES) is a structured RNA sequence found in the 5' UTR of the genomic RNA of the encephalomyocarditis virus. The EMCV IRES structure facilitates efficient translation initiation without needing a 5' m7G cap or the cap-binding protein eIF4E. The secondary structure of IRES has been the subject of several previous studies, and a number of different structural models have been proposed. Though some domains of the IRES are conserved across the different secondary structure models, domain I of the IRES varies greatly across them. A literature comparison led to the identification of three regions of interest that display structural heterogeneity within past secondary structure models. To test the accuracy of the secondary structure models in these regions, we employed mutational analysis and SHAPE probing. Mutational analysis revealed that two helical regions within the identified regions of interest are important for IRES translation. These helical regions are consistent with only one of the structure predictions in the literature and do not form in EMCV IRES structures predicted using modern secondary structure prediction methods. The importance of these regions is further supported by multiple SHAPE protections when probing was performed after in vitro translation, indicating that these regions are involved in the IRES translation complex. This work validates a published structure and demonstrates the importance of domain I during EMCV IRES translation initiation.

Why is sulfuric acid a much stronger acid than ethanol? Determination of the contributions by inductive/field effects and electron-delocalization effects.

Two different and complementary computational methods were used to determine the contributions by inductive/field effects and by electron-delocalization effects toward the enhancement of the gas-phase deprotonation enthalpy of sulfuric acid over ethanol. Our alkylogue extrapolation method employed density functional theory calculations to determine the deprotonation enthalpy of the alkylogues of sulfuric acid, HOSO2-(CH2CH2)n-OH, and of ethanol, CH3CH2-(CH2CH2)n-OH. The inductive/field effect imparted by the HOSO2 group for a given alkylogue of sulfuric acid was taken to be the difference in deprotonation enthalpy between corresponding (i.e., same n) alkylogues of sulfuric acid and ethanol. Extrapolating the inductive/field effect values for the n = 1-6 alkylogues, we obtained a value of 51.0 ± 6.4 kcal mol(-1) for the inductive/field effect for n = 0, sulfuric acid, leaving 15.4 kcal mol(-1) as the contribution by electron-delocalization effects. Our block-localized wavefunction method was employed to calculate the deprotonation enthalpies of sulfuric acid and ethanol using the electron-localized acid and anion species, which were compared to the values calculated using the electron-delocalized species. The contribution from electron delocalization was thus determined to be 18.2 kcal mol(-1), which is similar to the value obtained from the alkylogue extrapolation method. The two methods, therefore, unambiguously agree that both inductive/field effects and electron-delocalization effects have significant contributions to the enhancement of the deprotonation enthalpy of sulfuric acid compared with ethanol, and that the inductive/field effects are the dominant contributor.