scholarly journals The formation of intramolecular secondary structure brings mRNA ends in close proximity

2018 ◽  
Author(s):  
Wan-Jung C. Lai ◽  
Mohammad Kayedkhordeh ◽  
Erica V. Cornell ◽  
Elie Farah ◽  
Stanislav Bellaousov ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Random Coil ◽  
Untranslated Regions ◽  
Rna Sequences ◽  
Sequence Complexity ◽  
Translation Factors ◽  
Close Proximity ◽  
End To End ◽  
Regulate Protein ◽  
Mrna Length

ABSTRACTA number of protein factors regulate protein synthesis by bridging mRNA ends or untranslated regions (UTRs). Using experimental and computational approaches, we show that mRNAs from various organisms, including humans, have an intrinsic propensity to fold into structures in which the 5’ end and 3’ end are ≤ 7 nm apart irrespective of mRNA length. Computational estimates performed for ∼22,000 human transcripts indicate that the inherent proximity of the ends is a universal property of most, if not all, mRNA sequences. Only specific RNA sequences, which have low sequence complexity and are devoid of guanosines, are unstructured and exhibit end-to-end distances expected for the random coil conformation of RNA. Our results suggest that the intrinsic proximity of mRNA ends may facilitate binding of translation factors that bridge mRNA 5’ and 3’ UTRs. Furthermore, our studies provide the basis for measuring, computing and manipulating end-to-end distances and secondary structure in mRNAs in research and biotechnology.

scholarly journals A method for validating the accuracy of NMR protein structures

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicholas J. Fowler ◽  
Adnan Sljoka ◽  
Mike P. Williamson
Keyword(s):  
Secondary Structure ◽  
Crystal Structures ◽  
Protein Structures ◽  
Random Coil ◽  
Local Rigidity ◽  
Correlation Score ◽  
Nmr Structures ◽  
Explicit Solvent ◽  
Structure Ensemble ◽  
Better Than

AbstractWe present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.

Partial characterization of an RNA component that copurifies with Saccharomyces cerevisiae RNase P

1989 ◽  
Vol 9 (6) ◽  
pp. 2536-2543
Author(s):  
J Y Lee ◽  
D R Engelke
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Secondary Structure ◽  
Schizosaccharomyces Pombe ◽  
Rnase P ◽  
Partial Characterization ◽  
Rna Sequences ◽  
Extensive Sequence ◽  
Sequence Similarities

Saccharomyces cerevisiae cellular RNase P is composed of both protein and RNA components that are essential for activity. The isolated holoenzyme contains a highly structured RNA of 369 nucleotides that has extensive sequence similarities to the 286-nucleotide RNA associated with Schizosaccharomyces pombe RNase P but bears little resemblance to the analogous RNA sequences in procaryotes or S. cerevisiae mitochondria. Even so, the predicted secondary structure of S. cerevisiae RNA is strikingly similar to the bacterial phylogenetic consensus rather than to previously predicted structures of other eucaryotic RNase P RNAs.

scholarly journals Epiplasts: Membrane Skeletons and Epiplastin Proteins in Euglenids, Glaucophytes, Cryptophytes, Ciliates, Dinoflagellates, and Apicomplexans

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Ursula Goodenough ◽  
Robyn Roth ◽  
Thamali Kariyawasam ◽  
Amelia He ◽  
Jae-Hyeok Lee
Keyword(s):  
Electron Microscopy ◽  
Plasma Membrane ◽  
Amino Acid ◽  
Secondary Structure ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Random Coil ◽  
Cell Cortex ◽  
Tail Domain ◽  
Membrane Skeletons

ABSTRACTAnimals and amoebae assemble actin/spectrin-based plasma membrane skeletons, forming what is often called the cell cortex, whereas euglenids and alveolates (ciliates, dinoflagellates, and apicomplexans) have been shown to assemble a thin, viscoelastic, actin/spectrin-free membrane skeleton, here called the epiplast. Epiplasts include a class of proteins, here called the epiplastins, with a head/medial/tail domain organization, whose medial domains have been characterized in previous studies by their low-complexity amino acid composition. We have identified two additional features of the medial domains: a strong enrichment of acid/base amino acid dyads and a predicted β-strand/random coil secondary structure. These features have served to identify members in two additional unicellular eukaryotic radiations—the glaucophytes and cryptophytes—as well as additional members in the alveolates and euglenids. We have analyzed the amino acid composition and domain structure of 219 epiplastin sequences and have used quick-freeze deep-etch electron microscopy to visualize the epiplasts of glaucophytes and cryptophytes. We define epiplastins as proteins encoded in organisms that assemble epiplasts, but epiplastin-like proteins, of unknown function, are also encoded in Insecta, Basidiomycetes, andCaulobactergenomes. We discuss the diverse cellular traits that are supported by epiplasts and propose evolutionary scenarios that are consonant with their distribution in extant eukaryotes.IMPORTANCEMembrane skeletons associate with the inner surface of the plasma membrane to provide support for the fragile lipid bilayer and an elastic framework for the cell itself. Several radiations, including animals, organize such skeletons using actin/spectrin proteins, but four major radiations of eukaryotic unicellular organisms, including disease-causing parasites such asPlasmodium, have been known to construct an alternative and essential skeleton (the epiplast) using a class of proteins that we term epiplastins. We have identified epiplastins in two additional radiations and present images of their epiplasts using electron microscopy. We analyze the sequences and secondary structure of 219 epiplastins and present an in-depth overview and analysis of their known and posited roles in cellular organization and parasite infection. An understanding of epiplast assembly may suggest therapeutic approaches to combat infectious agents such asPlasmodiumas well as approaches to the engineering of useful viscoelastic biofilms.

scholarly journals Decoding the Epitranscriptional Landscape from Native RNA Sequences

2018 ◽  
Author(s):  
Thidathip Wongsurawat ◽  
Piroon Jenjaroenpun ◽  
Trudy M. Wassenaar ◽  
Taylor D Wadley ◽  
Visanu Wanchai ◽  
...  
Keyword(s):  
Growth Conditions ◽  
Untranslated Regions ◽  
Metabolic Adaptation ◽  
Rna Modifications ◽  
Rna Sequences ◽  
Rna Methylation ◽  
E Coli ◽  
Oxford Nanopore ◽  
G Quadruplex ◽  
Bioinformatic Tool

AbstractSequencing of native RNA and corresponding cDNA was performed using Oxford Nanopore Technology. The % Error of Specific Bases (%ESB) was higher for native RNA than for cDNA, which enabled detection of ribonucleotide modification sites. Based on %ESB differences of the two templates, a bioinformatic tool ELIGOS was developed and applied to rRNAs of E. coli, yeast and human cells. ELIGOS captured 91%, 95%, ∼75%, respectively, of the known variety of RNA methylation sites in these rRNAs. Yeast transcriptomes from different growth conditions were also compared, which identified an association between metabolic adaptation and inferred RNA modifications. ELIGOS was further applied to human transcriptome datasets, which identified the well-known DRACH motif containing N6-methyadenine being located close to 3’-untranslated regions of mRNA. Moreover, the RNA G-quadruplex motif was uncovered by ELIGOS. In summary, we have developed an experimental method coupled with bioinformatic software to uncover native RNA modifications and secondary-structures within transcripts.

Modified S-transform as a tool to identify secondary structure elements in RNA

2017 ◽  
Vol 13 (4) ◽  
Author(s):  
Nancy Singh ◽  
Sunil Datt Sharma ◽  
Ragothaman M. Yennamalli
Keyword(s):  
Signal Processing ◽  
Secondary Structure ◽  
Dna Sequences ◽  
Tertiary Structure ◽  
Processing Method ◽  
Rna Sequences ◽  
Signal Processing Method ◽  
S Transform ◽  
Highly Correlated ◽  
Signal Processing Methods

AbstractIn this article, we describe the applicability of a signal processing method, specifically the modified S-transform (MST) method, on RNA sequences to identify periodicities between 2 and 11. MicroRNAs (miRNA) are associated with gene regulation and gene silencing and thus have wide applications in biological sciences. Also, the functionality of miRNA is highly associated with its secondary structures (stem, bulge and loop). Signal processing methods have been previously applied on genomic data to reveal the periodicities that determine a wide variety of biological functions, ranging from exon detection to microsatellite identification in DNA sequences. However, there has been less focus on RNA-based signal processing. Here, we show that the signal processing method can be successfully applied to miRNA sequences. We observed that these periodicities are highly correlated with the secondary structure of miRNA and such methods could possibly be used as indicators of secondary and tertiary structure formation.

scholarly journals Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range

2019 ◽  
Vol 73 (12) ◽  
pp. 713-725 ◽  
Author(s):  
Ruth Hendus-Altenburger ◽  
Catarina B. Fernandes ◽  
Katrine Bugge ◽  
Micha B. A. Kunze ◽  
Wouter Boomsma ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Random Coil ◽  
Disordered Proteins ◽  
Phosphoryl Group ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Secondary Chemical

Abstract Phosphorylation is one of the main regulators of cellular signaling typically occurring in flexible parts of folded proteins and in intrinsically disordered regions. It can have distinct effects on the chemical environment as well as on the structural properties near the modification site. Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins (IDPs) and the reliability of the analysis depends on an appropriate choice of random coil model. Random coil chemical shifts and sequence correction factors were previously determined for an Ac-QQXQQ-NH2-peptide series with X being any of the 20 common amino acids. However, a matching dataset on the phosphorylated states has so far only been incompletely determined or determined only at a single pH value. Here we extend the database by the addition of the random coil chemical shifts of the phosphorylated states of serine, threonine and tyrosine measured over a range of pH values covering the pKas of the phosphates and at several temperatures (www.bio.ku.dk/sbinlab/randomcoil). The combined results allow for accurate random coil chemical shift determination of phosphorylated regions at any pH and temperature, minimizing systematic biases of the secondary chemical shifts. Comparison of chemical shifts using random coil sets with and without inclusion of the phosphoryl group, revealed under/over estimations of helicity of up to 33%. The expanded set of random coil values will improve the reliability in detection and quantification of transient secondary structure in phosphorylation-modified IDPs.

Circular Dichroism of C-Phycoerythrin: A Conformational Analysis

1980 ◽  
Vol 35 (5-6) ◽  
pp. 367-375 ◽  
Author(s):  
Elisabeth Langer ◽  
Harald Lehner ◽  
Wolfhart Rüdiger ◽  
Barbara Zickendraht-Wendelstadt
Keyword(s):  
Circular Dichroism ◽  
Secondary Structure ◽  
Conformational Changes ◽  
Spectral Region ◽  
Protein Unfolding ◽  
Extensive Study ◽  
Random Coil ◽  
Linear Superposition ◽  
Thermally Induced ◽  
Circular Dichroïsm

Abstract An extensive study of the chiroptical properties of C-phycoerythrin and the α-and β-subunits in the spectral region from 700 -200 nm is presented. Based on the VIS-circular dichroism inherently chiral conform ations are proposed for the co­ valently linked chromophores. By means of mean residue ellipticities and the experimental circular dichroism spectra in the region of the n → π* peptide transition the a-helix contents of the apoproteins of the ac-and ß-subunits are estimated to amount to 60% and 40%, respectively. The circular dichroism spectrum of native C-phycoerythrin is congruent with a linear superposition of the α-and β-subspectra, in the whole spectral region studied. Since a-and β-subunits are associated in native C-phycoery-thrin as revealed by sedim entation analysis the interactions between the subunits in the native chromoprotein are not accom panied by substantial conform ational changes. In the temperature range 0°-40°C the thermally induced changes of the chrom ophores in native C-phycoerythrin are not associated with changes of the secondary structure of the apoprotein. Unfolding occurs at 60°-70°C but slowly leads to irreversible denaturation. Protein unfolding starts at 3 M urea. The random coil secondary structure of the apoproteins is reached at 8 M urea. At this concentration the absorbance and the optical activity of the chrom o­ phores are reduced by a factor 3 and 10, respectively. The conformational changes in the peptide with increasing denaturant concentration are not synchronous with those induced in the Chromo­ phore indicating that a m ultistep process is operative during unfolding. The C D results on dena­ turation are supplem ented by absorption and em ission spectroscopy.

TOPAS: network-based structural alignment of RNA sequences

2019 ◽  
Vol 35 (17) ◽  
pp. 2941-2948 ◽  
Author(s):  
Chun-Chi Chen ◽  
Hyundoo Jeong ◽  
Xiaoning Qian ◽  
Byung-Jun Yoon
Keyword(s):  
Computational Complexity ◽  
Secondary Structure ◽  
Large Scale ◽  
Structural Alignment ◽  
Programming Approach ◽  
Rna Sequences ◽  
Optimal Sequence ◽  
Dynamic Programming Approach ◽  
Probabilistic Network ◽  
Rna Structural Alignment

Abstract Motivation For many RNA families, the secondary structure is known to be better conserved among the member RNAs compared to the primary sequence. For this reason, it is important to consider the underlying folding structures when aligning RNA sequences, especially for those with relatively low sequence identity. Given a set of RNAs with unknown structures, simultaneous RNA alignment and folding algorithms aim to accurately align the RNAs by jointly predicting their consensus secondary structure and the optimal sequence alignment. Despite the improved accuracy of the resulting alignment, the computational complexity of simultaneous alignment and folding for a pair of RNAs is O(N6), which is too costly to be used for large-scale analysis. Results In order to address this shortcoming, in this work, we propose a novel network-based scheme for pairwise structural alignment of RNAs. The proposed algorithm, TOPAS, builds on the concept of topological networks that provide structural maps of the RNAs to be aligned. For each RNA sequence, TOPAS first constructs a topological network based on the predicted folding structure, which consists of sequential edges and structural edges weighted by the base-pairing probabilities. The obtained networks can then be efficiently aligned by using probabilistic network alignment techniques, thereby yielding the structural alignment of the RNAs. The computational complexity of our proposed method is significantly lower than that of the Sankoff-style dynamic programming approach, while yielding favorable alignment results. Furthermore, another important advantage of the proposed algorithm is its capability of handling RNAs with pseudoknots while predicting the RNA structural alignment. We demonstrate that TOPAS generally outperforms previous RNA structural alignment methods on RNA benchmarks in terms of both speed and accuracy. Availability and implementation Source code of TOPAS and the benchmark data used in this paper are available at https://github.com/bjyoontamu/TOPAS.

scholarly journals Systematic FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin under Various Denaturation Conditions

Biomolecules ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 359 ◽  
Author(s):  
Usoltsev ◽  
Sitnikova ◽  
Kajava ◽  
Uspenskaya
Keyword(s):  
Secondary Structure ◽  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Ftir Spectroscopy ◽  
Conformational Changes ◽  
Data Interpretation ◽  
Random Coil ◽  
Helical Conformation ◽  
Structure Changes

Human serum albumin (HSA) is the most abundant protein in blood plasma. HSA is involved in the transport of hormones, fatty acids, and some other compounds, maintenance of blood pH, osmotic pressure, and many other functions. Although this protein is well studied, data about its conformational changes upon different denaturation factors are fragmentary and sometimes contradictory. This is especially true for FTIR spectroscopy data interpretation. Here, the effect of various denaturing agents on the structural state of HSA by using FTIR spectroscopy in the aqueous solutions was systematically studied. Our data suggest that the second derivative deconvolution method provides the most consistent interpretation of the obtained IR spectra. The secondary structure changes of HSA were studied depending on the concentration of the denaturing agent during acid, alkaline, and thermal denaturation. In general, the denaturation of HSA in different conditions is accompanied by a decrease in α-helical conformation and an increase in random coil conformation and the intermolecular β-strands. Meantime, some variation in the conformational changes depending on the type of the denaturation agent were also observed. The increase of β-structural conformation suggests that HSA may form amyloid-like aggregates upon the denaturation.

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