Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids

Rutledge, Lesley R.; Campbell-Verduyn, Lachlan S.; Wetmore, Stacey D.

doi:10.1016/j.cplett.2007.06.090

Cited by 95 publications

(180 citation statements)

References 32 publications

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“…Given that His136's interaction with G530 is through base stacking, it may be that G530A ribosomes do not exhibit significant rate defects because the stacking energies of His with guanine or adenine are similar (Rutledge et al 2007). As the stacking energy between His and uracil is predicted to be substantially weaker, one might expect more of a reduction in the GTP hydrolysis rate in the G530U mutant than we observed.…”

Section: Discussioncontrasting

confidence: 53%

“…Notably, although the aromatic Phe side chain is capable of participating in base-stacking interactions, the His136Phe mutant is inactive. This loss of activity may be due to lower stacking energy, as nucleobases stack more poorly with Phe than with His or Tyr (Rutledge et al 2007). Importantly, mutation of His136 to Ala or deletion of the C-terminal tail after residue 132 does not affect the affinity of SmpB for the ribosomal A-site.…”

Section: Discussionmentioning

confidence: 99%

“…In an attempt to further disrupt the base-stacking interaction, we purified epitope-tagged ribosomes containing the G530U mutation since uracil stacks the poorest among the nucleobases (Rutledge et al 2007). As expected, this ribosome mutation has a substantial effect on normal EF-Tu activation during canonical decoding with Phe-tRNA (Fig.…”

Section: His136 In Smpb Plays a Role In Ef-tu Activationmentioning

confidence: 99%

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An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue

Miller

Buskirk

2013

RNA

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In bacteria, ribosomes stalled on truncated mRNAs are rescued by transfer-messenger RNA (tmRNA) and its protein partner SmpB. Acting like tRNA, the aminoacyl-tmRNA/SmpB complex is delivered to the ribosomal A site by EF-Tu and accepts the transfer of the nascent polypeptide. Although SmpB binding within the decoding center is clearly critical for licensing tmRNA entry into the ribosome, it is not known how activation of EF-Tu occurs in the absence of a codon-anticodon interaction. A recent crystal structure revealed that SmpB residue His136 stacks on 16S rRNA nucleotide G530, a critical player in the canonical decoding mechanism. Here we use pre-steady-state kinetic methods to probe the role of this interaction in ribosome rescue. We find that although mutation of His136 does not reduce SmpB's affinity for the ribosomal A-site, it dramatically reduces the rate of GTP hydrolysis by EF-Tu. Surprisingly, the same mutation has little effect on the apparent rate of peptide-bond formation, suggesting that release of EF-Tu from the tmRNA/SmpB complex on the ribosome may occur prior to GTP hydrolysis. Consistent with this idea, we find that peptidyl transfer to tmRNA is relatively insensitive to the antibiotic kirromycin. Taken together, our studies provide a model for the initial stages of ribosomal rescue by tmRNA.

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Section: Discussioncontrasting

confidence: 53%

Section: Discussionmentioning

confidence: 99%

Section: His136 In Smpb Plays a Role In Ef-tu Activationmentioning

confidence: 99%

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An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue

Miller

Buskirk

2013

RNA

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“…Positive values of the splitting imply that the levels of + parity under E* are lower in energy than the levels of À parity, negative values imply the opposite. One observes that this sign is the same as the parity 's' (symmetric) or 'a' (antisymmetric) 6.3811…”

Section: Vibration-rotation-tunneling States a Energy Levels Promentioning

confidence: 93%

Vibration–rotation-tunneling states of the benzene dimer: an ab initio study

Avoird

Podeszwa

Szalewicz

et al. 2010

Phys. Chem. Chem. Phys.

152

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An improved intermolecular potential surface for the benzene dimer is constructed from interaction energies computed by symmetry-adapted perturbation theory, SAPT(DFT), with the inclusion of third-order contributions. Twelve characteristic points on the surface have been investigated also using the coupled-cluster method with single, double, and perturbative triple excitations, CCSD(T), and triple-zeta quality basis sets with midbond functions. The SAPT and CCSD(T) results are in close agreement and provide the best representation of these points to date. The potential was used in calculations of vibration-rotation-tunneling (VRT) levels of the dimer by a method appropriate for large amplitude intermolecular motions and tunneling between multiple equivalent minima in the potential. The resulting VRT levels were analyzed with the use of the permutation-inversion full cluster tunneling (FCT) group G 576 and a chain of subgroups that starts from the molecular symmetry group C s (M) of the rigid dimer at its equilibrium C s geometry and leads to G 576 if all possible intermolecular tunneling mechanisms are feasible. Further information was extracted from the calculated wave functions. It was found, in agreement with the experimental data, that for all of the 54 G 576 symmetry species (with different nuclear spin statistical weights) the lower VRT states have a tilted T-shape (TT) structure; states with the parallel-displaced structure are higher in energy than the ground state of A + 1 symmetry by at least 30 cm À1 . The dissociation energy D 0 equals 870 cm À1 , while the depth D e of the TT minimum in the potential is 975 cm À1 . Hindered rotation of the cap in the TT structure and tilt tunneling lead to level splittings on the order of 1 cm À1 . Also intermolecular vibrations with excitation energies starting at a few cm À1 were identified. A further small, but probably significant, level splitting was assigned to cap turnover, although in scans of the potential surface we could not find a plausible 'reaction path' for this process. Rotational constants were extracted from energy levels calculated for total angular momentum J = 0 and 1, and from expectation values of the inertia tensor. Although the end-over-end rotational constant B + C agrees well with the measured microwave spectra, there is disagreement with the measurements concerning the (a)symmetric rotor character of the benzene dimer. It is concluded from calculations for the 54 nuclear spin species that the microwave spectrum should show overlapping contributions from many different species. Another interesting conclusion regards the role of the quantum number K, for a prolate near-symmetric rotor the projection of the total angular momentum on the prolate axis. For the benzene dimer, K has a substantial effect on the energy levels associated with the intermolecular motions of the complex.

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“…中两个 C＝O 伸缩振动的跃迁强度值分别为 1572.0 和 97.8 km/mol, 对比更强, 直观地表明 C＝O 伸缩之间的耦合也很强. 这些都因为嘌呤 G 的叠加作用能最大 [64] , 并且极性强 [63] , G 的叠加二聚中两个 C＝O 伸缩产生的强耦合使 G-G 中一个 C＝O 出现了较大的频率兰移, …”

Section: 理论模拟 [52～54]unclassified

Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers

王桂秀¹,

王建平²

2012

Acta Chim. Sinica

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In this work, DNA base monomers, 15 B-form stacking dimers and two G-quadruplex stacking dimers were studied by quantum chemical computations. Detailed anharmonic vibrational analysis was carried out to reveal vibrational signatures for structural aspect of the base monomers and dimers. It was found that from isolated base monomers to stacking dimers, particularly those containing guanine, the interaction between the C＝O stretching is very strong, as depicted by the significant changes of their vibrational frequencies and anharmonicities. Such changes can be manifested well in simulated 1D IR and 2D IR spectra. Delocalization degree of the C＝O vibrational modes in stacking dimers, represented by the potential energy distribution and the contribution to the diagonal anharmonicity composition from the vibrators, was found to have significant variations in comparison with isolated bases, which resulted from the influences of the C＝ O stretching and the nearby vibrations of stacking bases.

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Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids

Cited by 95 publications

References 32 publications

An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue

An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue

Vibration–rotation-tunneling states of the benzene dimer: an ab initio study

Anharmonic Vibrations of Nucleobases: III, Structural Basis of Oneand Two-Dimensional Infrared Spectra for DNA Stacking Dimers

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