RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates.
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ABSTRACT:
SUBMITTER: Poblete S
PROVIDER: S-EPMC8655909 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Protein translation can be affected by changes in the secondary structure of mRNA. The dinQ gene in Escherichia coli encodes a primary transcript (+1) that is inert to translation. Ribonucleolytic removal of the 44 first nucleotides converts the +1 transcript into a translationally active form, but the mechanism behind this structural change is unknown. Here we present experimental evidence for a mechanism where alternative RNA secondary structures in the two dinQ mRNA variants affect translation initiation by mediating opening or closing of the ribosome binding sequence. This structural switch is determined by alternative interactions of four sequence elements within the dinQ mRNA and also by the agrB antisense RNA. Additionally, the structural conformation of +1 dinQ suggests a locking mechanism comprised of an RNA stem that both stabilizes and prevents translation initiation from the full-length dinQ transcript. BLAST search and multiple sequence alignments define a new family of dinQ-like genes widespread in Enterobacteriaceae with close RNA sequence similarities in their 5' untranslated regions. Thus, it appears that a whole new family of genes is regulated by the same mechanism of alternative secondary RNA structures.
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Project description:The adsorption of thallium (Tl) onto phyllosilicate minerals plays a critical role in the retention of Tl in soils and sediments and the potential transfer of Tl into plants and groundwater. Especially micaceous minerals are thought to strongly bind monovalent Tl(I), in analogy to their strong binding of Cs. To advance the understanding of Tl(I) adsorption onto phyllosilicate minerals, we studied the adsorption of Tl(I) onto Na- and K-saturated illite and Na-saturated smectite, two muscovites, two vermiculites and a naturally Tl-enriched soil clay mineral fraction. Macroscopic adsorption isotherms were combined with the characterization of the adsorbed Tl by X-ray absorption spectroscopy (XAS). In combination, the results suggest that the adsorption of Tl(I) onto phyllosilicate minerals can be interpreted in terms of three major uptake paths: (i) highest-affinity inner-sphere adsorption of dehydrated Tl+ on a very low number of adsorption sites at the wedge of frayed particle edges of illite and around collapsed zones in vermiculite interlayers through complexation between two siloxane cavities, (ii) intermediate-affinity inner-sphere adsorption of partially dehydrated Tl+ on the planar surfaces of illite and muscovite through complexation onto siloxane cavities, (iii) low-affinity adsorption of hydrated Tl+, especially in the hydrated interlayers of smectite and expanded vermiculite. At the frayed edges of illite particles and in the vermiculite interlayer, Tl uptake can lead to the formation of new wedge sites that enable further adsorption of dehydrated Tl+. On the soil clay fraction, a shift in Tl(I) uptake from frayed edge sites (on illite) to planar sites (on illite and muscovite) was observed with increasing Tl(I) loading. The results from this study show that the adsorption of Tl(I) onto phyllosilicate minerals follows the same trends as reported for Cs and Rb and thus suggests that concepts to describe the retention of (radio)cesium by different types of phyllosilicate minerals in soils, sediments and rocks are also applicable to Tl(I).
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Project description:BackgroundIn modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. In particular, it supports tracing the molecular evolution. Faced with an ever-increasing amount of available structural data, researchers need a range of methods enabling comparative analysis of the structures from either global or local perspective.ResultsHerein, we present a new, superposition-independent method which processes pairs of RNA 3D structures to identify their local similarities. The similarity is considered in the context of structure bending and bonds' rotation which are described by torsion angles. In the analyzed RNA structures, the method finds the longest continuous segments that show similar torsion within a user-defined threshold. The length of the segment is provided as local similarity measure. The method has been implemented as LCS-TA algorithm (Longest Continuous Segments in Torsion Angle space) and is incorporated into our MCQ4Structures application, freely available for download from http://www.cs.put.poznan.pl/tzok/mcq/ .ConclusionsThe presented approach ties torsion-angle-based method of structure analysis with the idea of local similarity identification by handling continuous 3D structure segments. The first method, implemented in MCQ4Structures, has been successfully utilized in RNA-Puzzles initiative. The second one, originally applied in Euclidean space, is a component of LGA (Local-Global Alignment) algorithm commonly used in assessing protein models submitted to CASP. This unique combination of concepts implemented in LCS-TA provides a new perspective on structure quality assessment in local and quantitative aspect. A series of computational experiments show the first results of applying our method to comparison of RNA 3D models. LCS-TA can be used for identifying strengths and weaknesses in the prediction of RNA tertiary structures.
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Project description:The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200-8500 nt. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an internal ribosomal entry site (IRES) region towards the 5'-end. This contribution provides a comprehensive computational survey of the complete genomic RNAs and a detailed comparative analysis of the conserved structural elements in seven of the currently nine genera in the family PICORNAVIRIDAE: Compared with previous studies we find: (i) that only smaller sections of the IRES region than previously reported are conserved at single base-pair resolution and (ii) that there is a number of significant structural elements in the coding region. Furthermore, we identify potential cis-acting replication elements in four genera where this feature has not been reported so far.
| S-EPMC97546 | biostudies-literature
Project description:BackgroundAccurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches.ResultsIn this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures.ConclusionsOur new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between false negative and false positive base pair predictions. Finally, AveRNA can make use of arbitrary sets of secondary structure prediction procedures and can therefore be used to leverage improvements in prediction accuracy offered by algorithms and energy models developed in the future. Our data, MATLAB software and a web-based version of AveRNA are publicly available at http://www.cs.ubc.ca/labs/beta/Software/AveRNA.
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Project description:Trimethylphosphine(hexafluoroacetylacetonato)silver(I) was used as a precursor to deposit silver onto silicon surfaces. The deposition was performed on silicon-based substrates including silica, H-terminated Si(100), and OH-terminated (oxidized) Si(100). The deposition processes at room temperature and elevated temperature (350 °C) were compared. The successful deposition resulted in nanostructures or nanostructured films as confirmed by atomic force microscopy (AFM) and scanning electron microscopy (SEM) with metallic silver being the majority deposited species as confirmed by X-ray photoelectron spectroscopy (XPS). The reactivity of the precursor depends drastically not only on the temperature of the process but also on the type of substrate. Density functional theory (DFT) was used to explain these differences and to propose the mechanisms for the initial deposition steps.
| S-EPMC5482543 | biostudies-literature
Project description:Nanomaterials are good candidates for the design of novel components with biomedical applications. For example, nano-patterned substrates may be used to immobilize protein molecules in order to integrate them in biosensing units. Here, we perform long MD simulations (up to 200 ns) using an explicit solvent and physiological ion concentrations to characterize the adsorption of bovine serum albumin (BSA) onto a nano-patterned graphite substrate. We have studied the effect of the orientation and step size on the protein adsorption and final conformation. Our results show that the protein is stable, with small changes in the protein secondary structure that are confined to the contact area and reveal the influence of nano-structuring on the spontaneous adsorption, protein-surface binding energies, and protein mobility. Although van der Waals (vdW) interactions play a dominant role, our simulations reveal the important role played by the hydrophobic lipid-binding sites of the BSA molecule in the adsorption process. The complex structure of these sites, that incorporate residues with different hydrophobic character, and their flexibility are crucial to understand the influence of the ion concentration and protein orientation in the different steps of the adsorption process. Our study provides useful information for the molecular engineering of components that require the immobilization of biomolecules and the preservation of their biological activity.
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Project description:Carbonate rock strengthening using chemical techniques is a strategy to prevent excessive fines migration during oil and gas production. We provide herein a study of the adsorption of three types of hydrolysed polyacrylamide (HPAM) of different molecular weight (F3330S, 11-13 MDa; F3530 S, 15-17 MDa; F3630S, 18-20 MDa) onto calcium carbonate (CaCO3) particles via spectrophotometry using a Shimadzu UV-2600 spectrometer. The results are compared to different adsorption isotherms and kinetic models. The Langmuir isotherm shows the highest correlation coefficient (R2 > 0.97) with equilibrium parameters (RL) ranging between 0 and 1 for all three HPAMs, suggesting a favorable monolayer adsorption of HPAM onto CaCO3. The adsorption follows pseudo-second order kinetics, indicating that the interaction of HPAM with CaCO3 is largely dependent on the adsorbate concentration. An adsorption plot reveals that the amount of HPAM adsorbed onto CaCO3 at equilibrium increases with higher polymer molecular weight; the equilibrium adsorbed values for F3330S, F3530S and F3630S are approximately 0.24 mg/m2, 0.31 mg/m2, and 0.43 mg/m2, respectively. Zeta potential analysis shows that CaCO3 has a zeta potential of +12.32 mV, which transitions into negative values upon introducing HPAM. The point of zero charge (PZC) is observed at HPAM dosage between 10 to 30 ppm, in which the pH here lies between 9-10.
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Project description:BACKGROUND: Current RNA secondary structure prediction approaches predict prevalent pseudoknots such as the H-pseudoknot and kissing hairpin. The number of possible structures increases drastically when more complex pseudoknots are considered, thus leading to computational limitations. On the other hand, the enormous population of possible structures means not all of them appear in real RNA molecules. Therefore, it is of interest to understand how many of them really exist and the reasons for their preferred existence over the others, as any new findings revealed by this study might enhance the capability of future structure prediction algorithms for more accurate prediction of complex pseudoknots. METHODOLOGY/PRINCIPAL FINDINGS: A novel algorithm was devised to estimate the exact number of structural possibilities for a pseudoknot constructed with a specified number of base pair stems. Then, topological classification was applied to classify RNA pseudoknotted structures from data in the RNA STRAND database. By showing the vast possibilities and the real population, it is clear that most of these plausible complex pseudoknots are not observed. Moreover, from these classified motifs that exist in nature, some features were identified for further investigation. It was found that some features are related to helical stacking. Other features are still left open to discover underlying tertiary interactions. CONCLUSIONS: Results from topological classification suggest that complex pseudoknots are usually some well-known motifs that are themselves complex or the interaction results of some special motifs. Heuristics can be proposed to predict the essential parts of these complex motifs, even if the required thermodynamic parameters are currently unknown.
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Project description:A class of wedge-shaped small molecules has been designed, synthesized, and shown to bind bulged RNA secondary structures. These minimally cationic ligands exhibit good affinity and selectivity for certain RNA bulges as demonstrated in a fluorescent intercalator displacement assay.
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