Frameshifting of mRNA during translation provides a strategy to expand the coding repertoire of cells and viruses. How and where in the elongation cycle +1-frameshifting occurs remains poorly understood. We describe seven ~3.5-Å-resolution cryo-EM structures of 70S ribosome complexes, allowing visualization of elongation and translocation by the GTPase elongation factor G (EF-G). Four structures with a + 1-frameshifting-prone mRNA reveal that frameshifting takes place during translocation of tRNA and mRNA. Prior to EF-G binding, the pre-translocation complex features an in-frame tRNA-mRNA pairing in the A site. In the partially translocated structure with EF-G•GDPCP, the tRNA shifts to the +1-frame near the P site, rendering the freed mRNA base to bulge between the P and E sites and to stack on the 16S rRNA nucleotide G926. The ribosome remains frameshifted in the nearly post-translocation state. Our findings demonstrate that the ribosome and EF-G cooperate to induce +1 frameshifting during tRNA-mRNA translocation.
- MeSH
- Biocatalysis MeSH
- Cryoelectron Microscopy MeSH
- Peptide Chain Elongation, Translational genetics MeSH
- Peptide Elongation Factor G chemistry genetics metabolism MeSH
- Escherichia coli genetics metabolism MeSH
- Nucleic Acid Conformation MeSH
- Protein Conformation MeSH
- RNA, Messenger chemistry genetics metabolism MeSH
- Models, Molecular MeSH
- Frameshifting, Ribosomal genetics MeSH
- Escherichia coli Proteins chemistry genetics metabolism MeSH
- Ribosomes genetics metabolism ultrastructure MeSH
- RNA, Ribosomal, 16S chemistry genetics metabolism MeSH
- RNA, Transfer chemistry genetics metabolism MeSH
- tRNA Methyltransferases genetics metabolism MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
The optical activity in porphyrins can easily be induced by a chiral environment, but it is difficult to determine the underlying mechanisms purely on an experimental basis. Therefore, in this study, magnitudes of the perturbational, dipolar, and direct covalent contributions to the electronic circular dichroism (CD) are evaluated with the aid of quantum chemical computations. Electronic properties of model porphyrin chromophores are analyzed. Time-dependent density functional theory (TD DFT), particularly with the hybrid B3LYP functional, appeared suitable for estimation of the electronic excitation energies and spectral intensities. The transition dipole coupling (TDC) between chirally stacked porphyrins was determined as the most important mechanism contributing to their optical activity. This is in agreement with previous experimental observations, where chiral matrices often induce the stacking and large CD signals. About a 10 times smaller signal could be achieved by a chiral orientation of the phenyl or similar residues covalently attached to the porphyrin core. Also, this prediction is in agreement with known experiments. Perturbation models realized by a chirally arranged porphyrin and a point charge, or by a porphyrin and the methane molecule, provided the smallest CD signals. The electrically neutral methane induced similar CD magnitudes as those of the charge, but spectral shapes were different. For a complex of porphyrin and the alanine cation, a significant influence of the solvent on the resultant CD spectral shape was observed, while for the charge and methane perturbations, a negligible solvent effect was found. Detailed dependence of the induced optical activity on variations of geometrical parameters is discussed. The simulations of the induced porphyrin activity can thus bring important information about the structure and intermolecular interactions in chiral complexes.
A complete scan of the potential-energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Moller-Plesset second-order perturbation theory (RI-MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T-shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol(-1). The different behaviors of nonmethylated and methylated trimers is also discussed. The high-level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple-zeta basis set predicts 11 uracil trimer interaction energies with a root-mean-square error of 2.3 kcal mol(-1) relative to highly correlated ab initio theoretical calculations.
The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations.
- MeSH
- Chloroform chemistry MeSH
- Dimethyl Sulfoxide chemistry MeSH
- Financing, Organized MeSH
- Nucleic Acid Conformation MeSH
- Methanol chemistry MeSH
- DNA Methylation MeSH
- Models, Molecular MeSH
- Nucleotides chemistry MeSH
- Base Pairing MeSH
- Computer Simulation MeSH
- Water chemistry MeSH
- Hydrogen Bonding MeSH
- Base Composition MeSH
Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to describe stacking. The currently used simple empirical potential form, relying on atom-centered constant point charges and Lennard-Jones van der Waals terms, is entirely able to reproduce the essential features of base stacking. Thus, we can conclude that base stacking is in principle one of the best described interactions in current molecular modeling and it allows to study base stacking in DNA using large-scale classical molecular dynamics simulations. Neglect of cooperativity of stacking appears to be the most serious approximation of the currently used force field form. This review summarizes recent developments in the field. It is written for an audience that is not necessarily expert in computational quantum chemistry and follows up on our previous contribution (Sponer et. al., J. Biomol. Struct. Dyn. 14, 117, (1997)). First, the applied methodology, its accuracy, and the physical nature of base stacking is briefly overviewed, including a comment on the accuracy of other molecular orbital methods and force fields. Then, base stacking is contrasted with hydrogen bonding, the other dominant force in nucleic acid structure. The sequence dependence and cooperativity of base stacking is commented on, and finally a brief introduction into recent progress in large-scale molecular dynamics simulations of nucleic acids is provided. Using four stranded DNA assemblies as an example, we demonstrate the efficacy of current molecular dynamics techniques that utilize refined and verified force fields in the study of stacking in nucleic acid molecules.
