In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership

Aminoacyl tRNA synthetases (aaRS) are grouped into Class I and II based on primary and tertiary structure and enzyme properties suggesting two independent phylogenetic lineages. Analogously, tRNA molecules can also form two respective classes, based on the class membership of their corresponding aaRS. Although some aaRS-tRNA interactions are not extremely specific and require editing mechanisms to avoid misaminoacylation, most aaRS-tRNA interactions are rather stereospecific. Thus, class-specific aaRS features could be mirrored by class-specific tRNA features. However, previous investigations failed to detect conserved class-specific nucleotides. Here we introduce a discrete mathematical approach that evaluates not only class-specific 'strictly present', but also 'strictly absent' nucleotides. The disjoint subsets of these elements compose a unique partition, named extended consensus partition (ECP). By analyzing the ECP for both Class I and II tDNA sets from 50 (13 archaeal, 30 bacterial and 7 eukaryotic) species, we could demonstrate that class-specific tRNA sequence features do exist, although not in terms of strictly conserved nucleotides as it had previously been anticipated. This finding demonstrates that important information was hidden in tRNA sequences inaccessible for traditional statistical methods. The ECP analysis might contribute to the understanding of tRNA evolution and could enrich the sequence analysis tool repertoire.     

Determination of the proton environment of high stability Menasemiquinone intermediate in Escherichia coli nitrate reductase A by pulsed EPR

Escherichia coli nitrate reductase A (NarGHI) is a membrane-bound enzyme that couples quinol oxidation at a periplasmically oriented Q-site (Q_D) to proton release into the periplasm during anaerobic respiration. To elucidate the molecular mechanism underlying such a coupling, endogenous menasemiquinone-8 intermediates stabilized at the Q_D site (MSQ_D) of NarGHI have been studied by high-resolution pulsed EPR methods in combination with ¹H₂O/²H₂O exchange experiments. One of the two non-exchangeable proton hyperfine couplings resolved in hyperfine sublevel correlation (HYSCORE) spectra of the radical displays characteristics typical from quinone methyl protons. However, its unusually small isotropic value reflects a singularly low spin density on the quinone carbon α carrying the methyl group, which is ascribed to a strong asymmetry of the MSQ_D binding mode and consistent with single-sided hydrogen bonding to the quinone oxygen O1. Furthermore, a single exchangeable proton hyperfine coupling is resolved, both by comparing the HYSCORE spectra of the radical in ¹H₂O and ²H₂O samples and by selective detection of the exchanged deuterons using Q-band ²H Mims electron nuclear double resonance (ENDOR) spectroscopy. Spectral analysis reveals its peculiar characteristics, i.e. a large anisotropic hyperfine coupling together with an almost zero isotropic contribution. It is assigned to a proton involved in a short ∼1.6 Å in-plane hydrogen bond between the quinone O1 oxygen and the Nδ of the His-66 residue, an axial ligand of the distal heme b_D. Structural and mechanistic implications of these results for the electron-coupled proton translocation mechanism at the Q_D site are discussed, in light of the unusually high thermodynamic stability of MSQ_D.     

Mapping hidden potential identity elements by computing the average discriminating power of individual tRNA positions

The recently published discrete mathematical method, extended consensus partition (ECP), identifies nucleotide types at each position that are strictly absent from a given sequence set, while occur in other sets. These are defined as discriminating elements (DEs). In this study using the ECP approach, we mapped potential hidden identity elements that discriminate the 20 different tRNA identities. We filtered the tDNA data set for the obligatory presence of well-established tRNA features, and then separately for each identity set, the presence of already experimentally identified strictly present identity elements. The analysis was performed on the three kingdoms of life. We determined the number of DE, e.g. the number of sets discriminated by the given position, for each tRNA position of each tRNA identity set. Then, from the positional DE numbers obtained from the 380 pairwise comparisons of the 20 identity sets, we calculated the average excluding value (AEV) for each tRNA position. The AEV provides a measure on the overall discriminating power of each position. Using a statistical analysis, we show that positional AEVs correlate with the number of already identified identity elements. Positions having high AEV but lacking published identity elements predict hitherto undiscovered tRNA identity elements.     

DYNLL/LC8: a light chain subunit of the dynein motor complex and beyond

The LC8 family members of dynein light chains (DYNLL1 and DYNLL2 in vertebrates) are highly conserved ubiquitous eukaryotic homodimer proteins that interact, besides dynein and myosin 5a motor proteins, with a large (and still incomplete) number of proteins involved in diverse biological functions. Despite an earlier suggestion that LC8 light chains function as cargo adapters of the above molecular motors, they are now recognized as regulatory hub proteins that interact with short linear motifs located in intrinsically disordered protein segments. The most prominent LC8 function is to promote dimerization of their binding partners that are often scaffold proteins of various complexes, including the intermediate chains of the dynein motor complex. Structural and functional aspects of this intriguing hub protein will be highlighted in this minireview.     

Comparative Study on the Uniform Energy Deposition Achievable via Optimized Plasmonic Nanoresonator Distributions

Plasmonic nanoresonators of core–shell composition and nanorod shape were optimized to tune their absorption cross-section maximum to the central wavelength of a short laser pulse. The number density distribution of randomly located nanoresonators along a laser pulse-length scaled target was numerically optimized to maximize the absorptance with the criterion of minimal absorption difference between neighboring layers illuminated by two counter-propagating laser pulses. Wide Gaussian number density distribution of core–shell nanoparticles and nanorods enabled to improve the absorptance with low standard deviation; however, the energy deposited until the overlap of the two laser pulses exhibited a considerable standard deviation. Successive adjustment resulted in narrower Gaussian number density distributions that made it possible to ensure almost uniform distribution of the deposited energy integrated until the maximal overlap of the two laser pulses. While for core–shell nanoparticles the standard deviation of absorptance could be preserved, for the nanorods it was compromised. Considering the larger and polarization independent absorption cross-section as well as the simultaneously achievable smaller standard deviation of absorptance and deposited energy distribution, the core–shell nanoparticles outperform the nanorods both in optimized and adjusted nanoresonator distributions. Exception is the standard deviation of deposited energy distribution considered for the complete layers that is smaller in the adjusted nanorod distribution. Optimization of both nanoresonator distributions has potential applications, where efficient and uniform energy deposition is crucial, including biomedical applications, phase transitions, and even fusion.

     

Enhancing Diamond Fluorescence via Optimized Nanorod Dimer Configurations

Light extraction from silicon (SiV) and nitrogen (NV) vacancy diamond color centers coupled to plasmonic silver and gold nanorod dimers was numerically improved. Numerical optimization of the coupled dipolar emitter—plasmonic nanorod dimer configurations was realized to attain the highest possible fluorescence enhancement by simultaneously improving the color centers excitation and emission through antenna resonances. Conditional optimization was performed by setting a criterion regarding the minimum quantum efficiency of the coupled system (cQE) to minimize losses. By comparing restricted symmetric and allowed asymmetric dimers, the advantages of larger degrees of freedom achievable in asymmetric configurations was proven. The highest 2.59?×?10⁸ fluorescence enhancement was achieved with 46.08% cQE via NV color center coupled to an asymmetric silver dimer. This is 3.17-times larger than the 8.19?×?10⁷ enhancement in corresponding symmetric silver dimer configuration, which has larger 68.52% cQE. Among coupled SiV color centers the highest 1.04?×?10⁸ fluorescence enhancement was achieved via asymmetric silver dimer with 37.83% cQE. This is 1.06-times larger than the 9.83?×?10⁷ enhancement in corresponding symmetric silver dimer configuration, which has larger 57.46% cQE. Among gold nanorod coupled configurations the highest fluorescence enhancement of 4.75?×?10⁴ was shown for SiV color center coupled to an asymmetric dimer with 21.8% cQE. The attained enhancement is 8.48- (92.42-) times larger than the 5.6?×?10³ (5.14?×?10²) fluorescence enhancement achievable via symmetric (asymmetric) gold nanorod dimer coupled to SiV (NV) color center, which is accompanied by 16.01% (7.66%) cQE.     

Enhancing Diamond Color Center Fluorescence via Optimized Plasmonic Nanorod Configuration

Plasmonics - A novel numerical methodology has been developed, which makes possible to optimize arbitrary emitting dipole and plasmonic nano-resonator configuration with an arbitrary objective...