No abstract

Functional RNA molecules such as ribosomal RNAs frequently contain highly conserved internal loops with a 5’-UAA/5’-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt distinctive structure inconsistent with secondary structure predictions. The structure has a narrow major groove and forms a trans Hoogsteen/Sugar edge (tHS) A/G base pair followed by an unpaired stacked adenine, a trans Watson-Crick/Hoogsteen (tWH) U/A base pair and finally by a bulged nucleotide (N). The structure is further stabilized by a three-adenine stack and base-phosphate interaction. In the ribosome, the UAA/GAN internal loops are involved in extensive tertiary contacts, mainly as donors of A-minor interactions. Further, this sequence can adopt an alternative 2D/3D pattern stabilized by a four-adenine stack involved in a smaller number of tertiary interactions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (cWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 µs of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by MM-PBSA free energy calculations, locally enhanced sampling (LES) runs, targeted MD (TMD) and nudged elastic band (NEB) analysis. We compared parm99 and parmbsc0 force fields and net-neutralizing Na+ vs. excess salt KCl ion environments. Both force fields provide a similar description of the simulated structures, with the parmbsc0 leading to modest narrowing of the major groove. The excess salt simulations also cause a similar effect. While the NMR structure is entirely stable in simulations, the simulated X-ray structure shows considerable widening of the major groove, loss of base-phosphate interaction and other instabilities. The alternative X-ray geometry even undergoes conformational transition towards the solution 2D structure. Free energy calculations confirm that the X-ray arrangement is less stable than the solution structure. LES, TMD and NEB provide a rather consistent pathway for interconversion between the X-ray and NMR structures. In simulations, the incomplete cWS A/U base pair of the NMR structure is water mediated and alternates with the canonical A–U base pair, which is not indicated by the NMR data. Completion of full cWS A/U base pair is prevented by the overall internal loop arrangement. In summary, the simulations confirm that the UAA/GAN internal loop is a molecular switch RNA module that adopts its functional geometry upon specific tertiary contexts.

The wide compositional differences between conventional and alternative fuels have resulted in much research aimed at determining which alternative fuels can be used, and in what proportions, in conventional engines. Atomic-scale modeling is uniquely positioned to lend insight into this question without extensive large-scale tests. The predictive power such modeling affords could narrow the phase space that must be examined experimentally. This study utilizes molecular dynamics (MD) simulations to predict the properties of a set of pure hydrocarbons, as well as binary and multicomponent surrogate fuel mixtures for alternative fuels created from these pure components. The accuracy and transferability of the modified Lennard-Jones adaptive intermolecular reactive empirical bond-order potential (mod-LJ AIREBO) [J. Comput. Chem.200829601611] was assessed by calculating densities, heats of vaporization, and bulk moduli of pure hydrocarbons and the mixtures of these hydrocarbons, i.e., surrogate fuels. Calculated results were compared to experimentally determined values and to values obtained with the nonreactive, all-atom version of the optimized potential for liquid simulations (OPLS-AA) [J. Am. Chem. Soc.19961181122511236]. The mod-LJ AIREBO potential quantitatively predicts the densities of the pure hydrocarbons and binary mixtures of n-dodecane and 2,2,4,4,6,8,8-heptamethylnonane (isocetane). It is interesting to note, that despite doing an excellent job predicting the densities of the pure hydrocarbons, the performance of the mod-LJ AIREBO potential degrades when predicting the densities of the multicomponent surrogates and mixtures of n-hexadecane and isocetane, implying that it is not straightforward to extend potentials fit with pure compounds to mixtures. The OPLS-AA potential also has difficulty quantitatively predicting the densities of mixtures, although a new parameter set for long-chain hydrocarbons (L-OPLS) [J. Chem. Theory Comput.2012814591470] yields some improvement for binary mixtures. Heat of vaporization predictions using both potentials also agree reasonably well with experiment. Bulk moduli predictions using the mod-LJ AIREBO potential are consistently higher than, and do not quantitatively agree with, the experimental values. In contrast, bulk moduli predictions using the OPLS-AA potential are generally in good agreement with experimental values. Despite the success of the OPLS-AA potential predicting the bulk moduli of individual hydrocarbons, it is unable to quantitatively predict the bulk moduli of the multicomponent surrogates. Interestingly, the use of the L-OPLS parameter set improves density predictions but not predicted bulk moduli values.