GNN Codon Adjacency Tunes Protein Translation.

The central dogma treats the ribosome as a molecular machine that reads one mRNA codon at a time as it adds each amino acid to its growing peptide chain. However, this and previous studies suggest that ribosomes actually perceive pairs of adjacent codons as they take three-nucleotide steps along the mRNA. We examined GNN codons, which we find are surprisingly overrepresented in eukaryote protein-coding open reading frames (ORFs), especially immediately after NNU codons.

Ligand-Directed Self-Assembly of Organic-Semiconductor/Quantum-Dot Blend Films Enables Efficient Triplet Exciton-Photon Conversion.

Blends comprising organic semiconductors and inorganic quantum dots (QDs) are relevant for many optoelectronic applications and devices. However, the individual components in organic-QD blends have a strong tendency to aggregate and phase-separate during film processing, compromising both their structural and electronic properties. Here, we demonstrate a QD surface engineering approach using electronically active, highly soluble semiconductor ligands that are matched to the organic semiconductor host material to achieve well-dispersed inorganic-organic blend films, as characterized by X-ray and neutron scattering, and electron microscopies.

Insights into the kinetics and self-assembly order of small-molecule organic semiconductor/quantum dot blends during blade coating.

Organic-inorganic nanocomposite films formed from blends of small-molecule organic semiconductors and colloidal quantum dots are attractive candidates for high efficiency, low-cost solar energy harvesting devices. Understanding and controlling the self-assembly of the resulting organic-inorganic nanocomposite films is crucial in optimising device performance, not only at a lab-scale but for large-scale, high-throughput printing and coating methods. Here, grazing incidence X-ray scattering (GIXS) gives direct insights into how small-molecule organic semiconductors and colloidal quantum dots self-assemble during blade coating.

Mixed Small-Molecule Matrices Improve Nanoparticle Dispersibility in Organic Semiconductor-Nanoparticle Films.

Controlling the dispersibility of nanocrystalline inorganic quantum dots (QDs) within organic semiconductor (OSC):QD nanocomposite films is critical for a wide range of optoelectronic devices. This work demonstrates how small changes to the OSC host molecule can have a dramatic detrimental effect on QD dispersibility within the host organic semiconductor matrix as quantified by grazing incidence X-ray scattering. It is commonplace to modify QD surface chemistry to enhance QD dispersibility within an OSC host.

Ultrafast exciton transport at early times in quantum dot solids.

Quantum dot (QD) solids are an emerging platform for developing a range of optoelectronic devices. Thus, understanding exciton dynamics is essential towards developing and optimizing QD devices. Here, using transient absorption microscopy, we reveal the initial exciton dynamics in QDs with femtosecond timescales.

The CAR-mRNA Interaction Surface Is a Zipper Extension of the Ribosome A Site.

The ribosome CAR interaction surface behaves as an extension of the decoding center A site and has H-bond interactions with the +1 codon, which is next in line to enter the A site. Through molecular dynamic simulations, we investigated the codon sequence specificity of this CAR-mRNA interaction and discovered a strong preference for GCN codons, suggesting that there may be a sequence-dependent layer of translational regulation dependent on the CAR interaction surface. Dissection of the CAR-mRNA interaction through nucleotide substitution experiments showed that the first nucleotide of the +1 codon dominates over the second nucleotide position, consistent with an energetically favorable zipper-like activity that emanates from the A site through the CAR-mRNA interface.

Arginine Methylation Regulates Ribosome CAR Function.

The ribosome CAR interaction surface is hypothesized to provide a layer of translation regulation through hydrogen-bonding to the +1 mRNA codon that is next to enter the ribosome A site during translocation. The CAR surface consists of three residues, 16S/18S rRNA C1054, A1196 ( 16S numbering), and R146 of yeast ribosomal protein Rps3. R146 can be methylated by the Sfm1 methyltransferase which is downregulated in stressed cells.

GCN sensitive protein translation in yeast.

Levels of protein translation by ribosomes are governed both by features of the translation machinery as well as sequence properties of the mRNAs themselves. We focus here on a striking three-nucleotide periodicity, characterized by overrepresentation of GCN codons and underrepresentation of G at the second position of codons, that is observed in Open Reading Frames (ORFs) of mRNAs. Our examination of mRNA sequences in Saccharomyces cerevisiae revealed that this periodicity is particularly pronounced in the initial codons-the ramp region-of ORFs of genes with high protein expression.

Controlling the structures of organic semiconductor-quantum dot nanocomposites through ligand shell chemistry.

Nanocrystal quantum dots (QD) functionalised with active organic ligands hold significant promise as solar energy conversion materials, capable of multiexcitonic processes that could improve the efficiencies of single-junction photovoltaic devices. Small-angle X-ray and neutron scattering (SAXS and SANS) were used to characterize the structure of lead sulphide QDs post ligand-exchange with model acene-carboxylic acid ligands (benzoic acid, hydrocinnamic acid and naphthoic acid). Results demonstrate that hydrocinnamic acid and naphthoic acid ligated QDs form monolayer ligand shells, whilst benzoic acid ligated QDs possess ligand shells thicker than a monolayer.

A Ribosome Interaction Surface Sensitive to mRNA GCN Periodicity.

A longstanding challenge is to understand how ribosomes parse mRNA open reading frames (ORFs). Significantly, GCN codons are over-represented in the initial codons of ORFs of prokaryote and eukaryote mRNAs. We describe a ribosome rRNA-protein surface that interacts with an mRNA GCN codon when next in line for the ribosome A-site.

Ligand Shell Structure in Lead Sulfide-Oleic Acid Colloidal Quantum Dots Revealed by Small-Angle Scattering.

Nanocrystal quantum dots are generally coated with an organic ligand layer. These layers are a necessary consequence of their chemical synthesis, and in addition they play a key role in controlling the optical and electronic properties of the system. Here we describe a method for quantitative measurement of the ligand layer in 3 nm diameter lead sulfide-oleic acid quantum dots.

Does 1,8-diiodooctane affect the aggregation state of PCBM in solution?

1,8-Diiodooctane (DIO) is an additive used in the processing of organic photovoltaics and has previously been reported, on the basis of small-angle X-ray scattering (SAXS) measurements, to deflocculate nano-aggregates of [6,6]-phenyl-C71-butyric acid methyl ester (PCBM) in chlorobenzene. We have critically re-examined this finding in a series of scattering measurements using both X-rays and neutrons. With SAXS, we find that the form of the background solvent scattering is influenced by the presence of DIO, that there is substantial attenuation of the X-rays by the background solvent and that there appears to be beam-induced aggregation.

N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries.

We identified tryptic peptides in yeast cell lysates that map to translation initiation sites downstream of the annotated start sites using the peptide-spectrum matching algorithms OMSSA and Mascot. To increase the accuracy of peptide-spectrum matching, both algorithms were run using several standardized parameter sets, and Mascot was run utilizing a, b, and y ions from collision-induced dissociation. A large fraction (22%) of the detected N-terminal peptides mapped to translation initiation downstream of the annotated initiation sites.

Assessment of MS/MS search algorithms with parent-protein profiling.

Peptide mass spectrometry relies crucially on algorithms that match peptides to spectra. We describe a method to evaluate the accuracy of these algorithms based on the masses of parent proteins before trypsin endoprotease digestion. Measurement of conformance to parent proteins provides a score for comparison of the performances of different algorithms as well as alternative parameter settings for a given algorithm.

Molecular mechanism of stabilization of thin films for improved water evaporation protection.

All-atom molecular dynamics simulations and experimental characterization have been used to examine the structure and dynamics of novel evaporation-suppressing films where the addition of a water-soluble polymer to an ethylene glycol monooctadecyl ether monolayer leads to improved water evaporation resistance. Simulations and Langmuir trough experiments demonstrate the surface activity of poly(vinyl pyrrolidone) (PVP). Subsequent MD simulations performed on the thin films supported by the PVP sublayer show that, at low surface pressures, the polymer tends to concentrate at the film/water interface.

The relationship between charge density and polyelectrolyte brush profile using simultaneous neutron reflectivity and in situ attenuated total internal reflection FTIR.

We report on a novel experimental study of a pH-responsive polyelectrolyte brush at the silicon/D2O interface. A poly[2-(diethylamino)ethyl methacrylate] brush was grown on a large silicon crystal which acted as both a substrate for a neutron reflectivity solid/liquid experiment but also as an FTIR-ATR spectroscopy crystal. This arrangement has allowed for both neutron reflectivities and FTIR spectroscopic information to be measured in parallel.

Amino termini of many yeast proteins map to downstream start codons.

Comprehensive knowledge of proteome complexity is crucial to understanding cell function. Amino termini of yeast proteins were identified through peptide mass spectrometry on glutaraldehyde-treated cell lysates as well as a parallel assessment of publicly deposited spectra. An unexpectedly large fraction of detected amino-terminal peptides (35%) mapped to translation initiation at AUG codons downstream of the annotated start codon.

Voltage-induced swelling and deswelling of weak polybase brushes.

We have investigated a novel method of remotely switching the conformation of a weak polybase brush using an applied voltage. Surface-grafted polyelectrolyte brushes exhibit rich responsive behavior and show great promise as "smart surfaces", but existing switching methods involve physically or chemically changing the solution in contact with the brush. In this study, high grafting density poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) brushes were grown from silicon surfaces using atom transfer radical polymerization.

TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites.

Relative individual information is a measurement that scores the quality of DNA- and RNA-binding sites for biological machines. The development of analytical approaches to increase the power of this scoring method will improve its utility in evaluating the functions of motifs. In this study, the scoring method was applied to potential translation initiation sites in Drosophila to compute Translation Relative Individual Information (TRII) scores.

Layer-by-layer deposition of polyelectrolyte macroinitiators for enhanced initiator density in surface-initiated ATRP.

The layer-by-layer (L-b-L) deposition of oppositely charged polyelectrolytic macroinitiators has been demonstrated on planar silica substrates. The build-up of the macroinitiator multilayers was monitored by ellipsometry (up to 21 layers) and dual polarization interferometry (up to 17 layers) and good agreement was found between these techniques. The increase in L-b-L thickness was approximately linear, with an average thickness of 2.