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. Ribosome profiling experiments in yeast revealed that ribosomes with NNU at their aminoacyl (A) site have particularly elevated densities when NNU is immediately followed (3') by a GNN codon, indicating slower mRNA threading of the NNU codon from the ribosome's A to peptidyl (P) sites. Moreover, if the assessment was limited to ribosomes that have only recently arrived at the next codon, by examining 21-nucleotide ribosome footprints (21-nt RFPs), elevated densities were observed for multiple codon classes when followed by GNN. This striking translation slowdown at adjacent 5'-NNN GNN codon pairs is likely mediated, in part, by the ribosome's CAR surface, which acts as an extension of the A-site tRNA anticodon during ribosome translocation and interacts through hydrogen bonding and pi stacking with the GNN codon. The functional consequences of 5'-NNN GNN codon adjacency are expected to influence the evolution of protein coding sequences.

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. This approach preserves the electronic properties of the organic and QD phases and also creates an optimized interface between them. We exemplify this in two emerging applications, singlet-fission-based photon multiplication (SF-PM) and triplet-triplet annihilation-based photon upconversion (TTA-UC). Steady-state and time-resolved optical spectroscopy shows that triplet excitons can be transferred with near unity efficiently across the organic-inorganic interface, while the organic films maintain efficient SF (190% yield) in the organic phase. By changing the relative energy between organic and inorganic components, yellow upconverted emission is observed upon 790 nm NIR excitation. Overall, we provide a highly versatile approach to overcome longstanding challenges in the blending of organic semiconductors with QDs that have relevance for many optical and optoelectronic applications.

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, in situ grazing incidence X-ray scattering (GIXS) gives direct insights into how small-molecule organic semiconductors and colloidal quantum dots self-assemble during blade coating. Results show that for two blends separated only by a small difference in the structure of the small molecule forming the organic phase, crystallisation may proceed down two distinct routes. It either occurs spontaneously or is mediated by the formation of quantum dot aggregates. Irrespective of the initial crystallisation route, the small-molecule crystallisation acts to exclude the quantum dot inclusions from the growing crystalline matrix phase. These results provide important fundamental understanding of structure formation in nanocomposite films of organic small molecules and colloidal quantum dots prepared via solution processing routes. It highlights the fundamental difference to structural evolution which can be made by seemingly small changes in system composition. It provides routes for the structural design and optimisation of solution-processed nanocomposites that are compatible with the large-scale deposition manufacturing techniques that are crucial in driving their wider adoption in energy harvesting applications.

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. Here, an alternative route toward optimizing QD dispersibilities is demonstrated, which dramatically improves QD dispersibilities through blending two different OSCs to form a fully mixed OSC matrix phase.

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. We observe high exciton diffusivity (~102 cm2 s-1) in lead chalcogenide QDs within the first few hundred femtoseconds after photoexcitation followed by a transition to a slower regime (~10-1-1 cm2 s-1). QD solids with larger interdot distances exhibit higher initial diffusivity and a delayed transition to the slower regime, while higher QD packing density and heterogeneity accelerate this transition. The fast transport regime occurs only in materials with exciton Bohr radii much larger than the QD sizes, suggesting the transport of delocalized excitons in this regime and a transition to slower transport governed by exciton localization. These findings suggest routes to control the optoelectronic properties of QD solids.

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. Moreover, the CAR/+1 codon interaction is affected by the identity of nucleotide 3 of +1 GCN codons, which influences the stacking of G and C. Clustering analysis suggests that the A-site decoding center adopts different neighborhood substates that depend on the identity of the +1 codon.

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 (E. coli 16S numbering), and R146 of yeast ribosomal protein Rps3. R146 can be methylated by the Sfm1 methyltransferase which is downregulated in stressed cells. Through molecular dynamics analysis, we show here that methylation of R146 compromises the integrity of CAR by reducing the cation-pi stacking of the R146 guanidinium group with A1196, leading to reduced CAR hydrogen-bonding with the +1 codon. We propose that ribosomes assembled under stressed conditions have unmethylated R146, resulting in elevated CAR/+1 codon interactions, which tunes translation levels in response to the altered cellular context.

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. It is also found in mRNA sequences immediately following non-standard AUG start sites, located upstream or downstream of the standard annotated start sites of genes. To explore the possible influences of the ramp GCN periodicity on translation efficiency, we tested edited ramps with accentuated or depressed periodicity in two test genes, SKN7 and HMT1. Greater conformance to (GCN)n was found to significantly depress translation, whereas disrupting conformance had neutral or positive effects on translation. Our recent Molecular Dynamics analysis of a subsystem of translocating ribosomes in yeast revealed an interaction surface that H-bonds to the +1 codon that is about to enter the ribosome decoding center A site. The surface, comprised of 16S/18S rRNA C1054 and A1196 (E. coli numbering) and R146 of ribosomal protein Rps3, preferentially interacts with GCN codons, and we hypothesize that modulation of this mRNA-ribosome interaction may underlie GCN-mediated regulation of protein translation. Integration of our expression studies with large-scale reporter studies of ramp sequence variants suggests a model in which the C1054-A1196-R146 (CAR) interaction surface can act as both an accelerator and braking system for ribosome translation.

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. Further, the formation of a range of nanocomposite materials through the self-assembly of such acene-ligated QDs with an organic small-molecule semiconductor [5,12-bis((triisopropylsilyl)ethynyl)tetracene (TIPS-Tc)] is investigated. These materials are representative of a wider set of functional solar energy materials; here the focus is on structural studies, and their optoelectronic function is not investigated. As TIPS-Tc concentrations are increased, approaching the solubility limit, SANS data show that QD fractal-like features form, with structures possibly consistent with a diffusion limited aggregation mechanism. These, it is likely, act as heterogeneous nucleation agents for TIPS-Tc crystallization, generating agglomerates containing both QDs and TIPS-Tc. Within the TIPS-Tc crystals there seem to be three distinct QD morphologies: (i) at the crystallite centre (fractal-like QD aggregates acting as nucleating agents), (ii) trapped within the growing crystallite (giving rise to QD features ordered as sticky hard spheres), and (iii) a population of aggregate QDs at the periphery of the crystalline interface that were expelled from the growing TIPS-Tc crystal. Exposure of the QD:TIPS-Tc crystals to DMF vapour, a solvent known to be able to strip ligands from QDs, alters the spacing between PbS-hydrocinnamic acid and PbS-naphthoic acid ligated QD aggregate features. In contrast, for PbS-benzoic acid ligated QDs, DMF vapour exposure promotes the formation of ordered QD colloidal crystal type phases. This work thus demonstrates how different QD ligand chemistries control the interactions between QDs and an organic small molecule, leading to widely differing self-assembly processes. It highlights the unique capabilities of multiscale X-ray and neutron scattering in characterising such composite materials.

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. The interaction surface is comprised of the edges of two stacked rRNA bases: the Watson-Crick edge of 16S/18S rRNA C1054 and the adjacent Hoogsteen edge of A1196 (Escherichia coli 16S rRNA numbering). Also part of the interaction surface, the planar guanidinium group of a conserved Arginine (R146 of yeast ribosomal protein Rps3) is stacked adjacent to A1196. On its other side, the interaction surface is anchored to the ribosome A-site through base stacking of C1054 with the wobble anticodon base of the A-site tRNA. Using molecular dynamics simulations of a 495-residue subsystem of translocating ribosomes, we observed base pairing of C1054 to nucleotide G at position 1 of the next-in-line codon, consistent with previous cryo-EM observations, and hydrogen bonding of A1196 and R146 to C at position 2. Hydrogen bonding to both of these codon positions is significantly weakened when C at position 2 is changed to G, A or U. These sequence-sensitive mRNA-ribosome interactions at the C1054-A1196-R146 (CAR) surface potentially contribute to the GCN-mediated regulation of protein translation.

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. Complementary small-angle X-ray and neutron scattering (SAXS and SANS) studies give a complete and quantitative picture of the nanoparticle structure. We find greater-than-monolayer coverage of oleic acid and a significant proportion of ligand remaining in solution, and we demonstrate reversible thermal cycling of the oleic acid coverage. We outline the effectiveness of simple purification procedures with applications in preparing dots for efficient ligand exchange. Our method is transferrable to a wide range of colloidal nanocrystals and ligand chemistries, providing the quantitative means to enable the rational design of ligand-exchange procedures.

Does 1,8-diiodooctane affect the aggregation state of PC71BM 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 (PC71BM) 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. All three factors call into question the suitability of SAXS for measurements on these samples. By contrast, small-angle neutron scattering (SANS) measurements, performed at concentrations of 15 mg ml-1 up to and including 40 mg ml-1, show no difference in the aggregation state for PC71BM in chlorobenzene with and without 3% DIO; we find PC71BM to be molecularly dissolved in all solvent cases. In situ film thinning measurements of spin-coated PC71BM solution with the DIO additive dry much slower. Optical imaging shows that the fullerene films possess enhanced molecular mobility in the presence of DIO and it is this which, we conclude, improves the nanomorphology and consequently solar cell performance. We propose that any compatible high boiling solvent would be expected to show the same behaviour.

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. Expression of several truncated proteins from downstream initiation in the same reading frame as the full-length protein (frame 1) was verified by western analysis. To facilitate analysis of the larger proteome of Drosophila, we created a streamlined sequence library from which all duplicated trypsin fragments had been removed. OMSSA assessment using this "stripped" library revealed 171 peptides that map to downstream translation initiation sites, 76% of which are in the same reading frame as the full-length annotated proteins, although some are in different reading frames creating new protein sequences not in the annotated proteome. Sequences surrounding implicated downstream AUG start codons are associated with nucleotide preferences with a pronounced three-base periodicity N1^G2^A3.

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. Tracking of conformance scores for spectrum matches to proteins with progressively lower expression levels revealed that conformance scores are not uniform within data sets but are significantly lower for less abundant proteins. Similarly peptides with lower algorithm peptide-spectrum match scores have lower conformance. Although peptide mass spectrometry data is typically filtered through decoy analysis to ensure a low false discovery rate, this analysis confirms that the filtered data should not be considered as having a uniform confidence. The analysis suggests that use of different algorithms and multiple standardized parameter settings of these algorithms can increase significantly the numbers of peptides identified. This data set can be used as a resource for future algorithm assessment.

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 simulated atomic concentration profiles, hydrogen bonding patterns, and mobility analyses of the water-polymer-monolayer interfaces reveal that the presence of PVP increases the atomic density near the monolayer film, improves the film stability, and reduces the mobility of interfacial waters. These observations explain the molecular basis of the improved efficacy of these monolayer/polymer systems for evaporation protection of water and can be used to guide future development of organic thin films for other applications.

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. The chosen polybase brush shows strong IR bands which can be assigned to the N-D(+) stretch, D2O, and a carbonyl group. From such FTIR data, we are able to closely monitor the degree of protonation along the polymer chain as well as revealing information concerning the D2O concentration at the interface. The neutron reflectivity data allows us to determine the physical brush profile normal to the solid/liquid interface along with the corresponding degree of hydration. This combined approach makes it possible to quantify the charge on a polymer brush alongside the morphology adopted by the polymer chains.

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. Many of the implicated genes have suboptimal sequence contexts for translation initiation near their annotated AUG, and their ribosome profiles show elevated tag densities consistent with translation initiation at downstream AUGs as well as their annotated AUGs. These data suggest that a significant fraction of the yeast proteome derives from initiation at downstream AUGs, increasing significantly the repertoire of encoded proteins and their potential functions and cellular localizations.

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. Optical ellipsometry and neutron reflectivity were used to measure changes in the profiles of the brushes in response to DC voltages applied between the brush substrate and a parallel electrode some distance away in the surrounding liquid (water or D(2)O). Positive voltages were shown to cause swelling, while negative voltages in some cases caused deswelling. Neutron reflectometry experiments were carried out on the INTER reflectometer (ISIS, Rutherford Appleton Laboratory, UK) allowing time-resolved measurements of polymer brush structure. The PDMAEMA brushes were shown to have a polymer volume fraction profile described by a Gaussian-terminated parabola both in the equilibrium and in the partially swollen states. At very high positive voltages (in this study, positive bias means positive voltage to the brush-bearing substrate), the brush chains were shown to be stretched to an extent comparable to their contour length, before being physically removed from the interface. Voltage-induced swelling was shown to exhibit a wider range of brush swelling states in comparison to pH switching, with the additional advantages that the stimulus is remotely controlled and may be fully automated.

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. The weight matrix at the core of the scoring method was optimized based on high-confidence translation initiation sites identified by using a progressive partitioning approach. Comparing the distributions of TRII scores for sites of interest with those for high-confidence translation initiation sites and random sequences provides a new methodology for assessing the quality of translation initiation sites. The optimized weight matrices can also be used to describe the consensus at translation initiation sites, providing a quantitative measure of preferred and avoided nucleotides at each position.

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 2.3 A per layer of deposited macroinitiator. Surface-initiated ATRP of a model nonionic methacrylic monomer, 2-hydroxyethyl methacrylate (HEMA) in a 1:1 methanol/water mixture was conducted at ambient temperature. Increasing the number of macroinitiator layers led to a significant increase in PHEMA brush thickness up to 110 nm, which is attributed to the greater surface grafting density. PHEMA brush thicknesses obtained after 22 h showed a linear dependence on the number of layers of deposited macro-initiator, with all layers exhibiting near-identical growth kinetics. X-ray photoelectron spectroscopy was used to monitor L-b-L assembly and also to confirm PHEMA growth. This technique indicated the loss of small counterions from the multilayers during L-b-L deposition and confirmed an increase in the surface density of bromoester initiator groups as the number of deposited macroinitiator layers was increased. For 17 macroinitiator layers, the bromoester initiator density is estimated to be approximately 4.9 +/- 0.2 nm (-2) from the DPI data. This is comparable to that calculated for ATRP initiator monolayers obtained by either thiol or silane chemistry. Ellipsometry suggested that the macroinitiator multilayers were weakly hydrated prior to the in situ HEMA polymerization. AFM studies indicated that the PHEMA brushes had appreciable surface roughness, but this roughness became negligible compared to the brush thickness with increasing macroinitiator layers.