Introduction to Secondary Structures

Circular dichroism and Fourier-transform infrared spectroscopy analyses revealed that the interaction with C3G did not significantly change the secondary structures of SPI/SPIHs, while the surface hydrophobicity and average particle size of proteins decreased.

In this paper, the changes of physico-chemical characteristics, microstructures and secondary structures of duck egg white (EW) gels under the action of baijiu (Chinese liquor) were studied via the texture analyzer, environmental scanning electron microscope (ESEM) and Fourier transform infrared spectroscopy (FT-IR).

Recombinant PAD2 and PAD4 citrullinated K9CATH to various extents and circular dichroism spectroscopy revealed that both native and citrullinated K9CATH exhibited similar α-helical secondary structures.

Fluorescence and circular dichroism spectroscopy confirmed the enzyme tertiary and secondary structures, respectively.

Here, we assess the utility of the nuclear Internal Transcribed Spacer 2 (ITS2) to delimit species in the eolid nudibranchs using both primary and secondary structures.

Compensatory base changes (CBCs) in the secondary structures of internal transcribed spacer 2 (ITS2) are reliable sources to predict sexual incompatibility among closely related species.

G-quadruplexes are four-stranded nucleic acid secondary structures of biological significance and have emerged as an attractive drug target.

Simple Summary Four-stranded nucleic acid secondary structures (quadruplexes) including DNA G-quadruplexes, RNA G-quadruplexes and i-Motifs display key regulatory functions in the human genome.

Our models of numerous Synuclein oligomers, annular protofibrils, tubular protofibrils, lipoproteins, and ion channels were developed to be consistent with sizes, shapes, molecular weights, and secondary structures of assemblies as determined by EM and other studies.

Our models of numerous Synuclein oligomers, annular protofibrils, tubular protofibrils, lipoproteins, and ion channels were developed to be consistent with sizes, shapes, molecular weights, and secondary structures of assemblies as determined by EM and other studies.

Structural analysis revealed conjugates obtained by Maillard reaction induced the loss of ordered secondary structures (α-helix, β-sheets) and red-shift of maximum emission wavelength of intrinsic fluorescence spectrum.

All dsRBDs have a similar structural fold: α1-L1-β1-L2-β2-L3-β3-L4-α2 (α represents an α-helix, β a β-sheet, and L a loop conformation between the well-defined secondary structures).

Here, we showed that a large training set with 95% sequence identity cutoff can improve prediction of secondary structures even for those unrelated test sequences (<25% sequence identity cutoff) compared to the use of a non-redundant training dataset with 25% sequence identity cutoff.

G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago.

While the analysis is carried on a large dataset of viral RNA structures, it can be applied more generally to other data that involve RNA secondary structures in biological agents.

The results showed that TAP oxidation produced SO4- and OH radicals which decomposed the macromolecular proteins, causing uncoiling of protein secondary structures and exposure of inner hydrophobic sites.

Starch and protein secondary structures were changed after HMT, confirming molecules reorganizations and proteins denaturation of wheat flour during treatment.

i-Motifs are DNA secondary structures present in cytosine-rich sequences.

The sequence-dependent DNA secondary structures possess structure polymorphism.

The DNA double strand opened during replication, and gene expression allows the formation of different secondary structures such as hairpin, triple, junctions, and G-quadruplex.

Characteristic spectral features in the amide I and amide II region of three representative proteins with different secondary structures could be measured at concentrations as low as 0.

All tRNAs of these 4 species exhibited cloverleaf secondary structures except that the dihydorouridine (DHU) arm of tRNASer(AGN) was absent.

All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnC, trnV, and trnS1.

Activities include an exploration of nucleic acid secondary structures and relative stabilities, identifying non-canonical interactions within RNA folds, predicting tertiary interactions, comparing predicted structures to published experimentally-determined secondary structures, and investigating how mutations in the nucleic acid sequence can affect secondary and tertiary structure.

G-quadruplexes are four-stranded nucleic acid secondary structures of biological significance and have emerged as an attractive drug target.

RNAs form secondary structures containing double-stranded base paired regions and single-stranded regions.

This primer has fulfilled good primer characteristics because it does not cause dimer structure and the resulting amplicons do not form secondary structures.

DNA repeats capable of adopting stable secondary structures are hotspots for double-strand break (DSB) formation and, hence, for homologous recombination and gross chromosomal rearrangements (GCR) in many prokaryotic and eukaryotic organisms, including humans.

Some of these fragments show specific and stable secondary structures and are found to be inserted into the introns of genes or lncRNAs.

Comparison of predicted secondary structures of the partial 16S rRNA molecule of I.

We conducted phylogenetic analyses of multiple molecular markers and predicted secondary structures of SSU rRNA and ITS regions by adding 14 new sequences.

Under slightly acidic conditions, cytosine-rich DNA sequences can form non-canonical secondary structures called i-motifs, which occur as four stretches of cytosine repeats form hemi-protonated C·C+ base pairs.

G-quadruplexes (G4s) are non-canonical secondary structures located in DNA and RNA which have demonstrable roles in the regulation of transcription and translation.

9% of alpha-helix and β-sheet secondary structures.

By using the biotin tag, we obtained a thixotropic lupin-derived peptide hydrogel (named BT13) with tunable mechanical properties (from 2 to 11 kPa), without impairing its spontaneous formation of β-sheet secondary structures.

These polymers combine the great solubility of OEG, and the excellent biocompatibility, biodegradability and well defined secondary structures of PAA.

The interplay and interaction between two well-defined secondary structures within one scaffold offer tremendous opportunity for the design and construction of functional supramolecular biomaterials.

We also identified structural differences in seven tRNA secondary structures between both species.

Their nucleotide composition, codon usage, features of control region, and tRNA secondary structures are similar to other members of Cicadellidae.

Secondary structure propensity analysis based on the assigned chemical shifts showed that mouse vWF-A2 forms similar secondary structures in solution to the previously determined crystal structure of human vWF-A2.

Our results indicate that each member of the JAM family has a unique tertiary structure in spite of having similar secondary structures.

A Raman spectrum of a protein provides unique signatures for various secondary structures like helices, beta-sheets, turns, random structures, etc.

Nucleic acids can adopt various secondary structures including double-, triple-, and tetra-stranded helices that differ by the specific hydrogen bond mediated pairing pattern between their nucleobase constituents.

The increase in ordered secondary structures was associated with the modified EWP gel properties.

Most AMPs function by disrupting microbial membranes because of their amphipathic properties and ordered secondary structures.

This minimizes the formation of mRNA secondary structures that could inhibit transcription and translation and also sequesters a NusG domain that promotes transcription termination.

Our findings revealed a novel facet of the RNA structurome with important functional and evolutionary implications and indicated a potential method for distinguishing the mRNA secondary structures maintained by natural selection from molecular noise.

IR measurements confirmed that all three samples were in a similar conformation, consistent with pseudo 14-helical secondary structures.

Nevertheless, ADSC cells have been proven to produce a greater amount of collagen with a lower content of helical secondary structures, at the same time showing a higher mineralization intensity compared to BMDSC cells.

DNA geometry can be altered by DNA lesions or by peculiar sequences forming secondary structures, like G-quadruplex (G4) and trinucleotide repeats (TNR) hairpins, which significantly differ from canonical B-form.

Telomeres in general pose a challenge to DNA replication owing to their repetitive nature and potential for forming secondary structures.

Intramolecular secondary structures within templates have been shown to lower PCR performance.

EF-G-induced translocation results in unwinding of the intramolecular secondary structures of mRNA by three base pairs at a time that renders the translating ribosome a processive helicase.

Protein sequence analysis showed that there were some differences in amino acid numbers and isoelectric points amongst different subfamilies, and the main secondary structures were α-helix and random coil.

Both circular dichroism and FT-IR confirmed β-sheet, α-helix and β-turn were the main secondary structures in oat proteins.

It was confirmed that the formed hydrogel had strongly crosslinked networks with β-sheet and unordered coil secondary structures.

The amount and spatial distribution of TERS bands assigned to aromatic amino acid residues (histidine, tyrosine and phenylalanine) and to parallel β-sheet and random coil secondary structures suggest that both the surface and core of Aβ(1-42) fibrils are probed, confirm the twisted nature of the fibrils and reveal the presence of several β-sheet and disordered fibril regions with different hydrophilicity.

Quaternary amino acids are important tools for the modification and stabilisation of peptide secondary structures.

In this paper, we introduce the anticancer peptide secondary structures as additional features and propose an effective computational model, CL-ACP, that uses a combined network and attention mechanism to predict anticancer peptides.

While there are extensive studies on peptide cyclisation for reinforcing regular secondary structures such as α-helices and β-sheets, there are remarkably few reports of cyclising peptides which adopt irregular conformations in their bioactive target-bound state.

Molecular dynamics simulations revealed higher overall flexibility, decreased intramolecular hydrogen bonds and lower content of regular secondary structures for both cancer driver variants G73W and F432S when compared to the wild-type structure.

Here, we reveal that the interaction between insulin and the interface destabilizes native insulin secondary structure, promoting formation of α helix secondary structures.

Octopromycin consists of 38 amino acids, (+5) net positive charge, high hydrophobic residue ratio (36%), and two α-helix secondary structures.

pH or enzyme, we have designed peptides that are capable of self-assembling into nanoscale structures with distinct secondary structures.

Our data suggest that these bacteria might have independently co-evolved thermosensing abilities with different RNA sequences but distinct secondary structures to evade the immune system.

We performed molecular dynamics simulations of LBF14 and let it fold de novo into its ensemble of native secondary structures.

Additionally, we present an updated method for generating in vitro transcribed and folded RNA that maintains native secondary structures in long RNA molecules.

DNA sequences containing consecutive guanines organized in 4-interspaced tandem repeats can form stable single-stranded secondary structures, called G-quadruplexes (G4).

In this paper, we review the recent progress in volumetric investigations of G-quadruplexes and i-motifs, four-stranded secondary structures of DNA that have been found in the cell and implicated in regulatory genomic functions.

All tRNAs could fold into typical clover-leaf secondary structures, with the exception of two trnS genes, lacking the dihydrouridine (DHU) stem.

The secondary structure of tRNAs shows that all the tRNAs can be folded into canonical clover-leaf secondary structures, except three trnW, trnG, and trnC.

The morphology, 16S rRNA gene phylogeny and the 16S-23S rRNA gene ITS secondary structures of three strains of marine Cyanobacteria, isolated from inter- and subtidal environments from north Portugal were studied, resulting in the description of Zarkia subtidalensis gen.

The D1-D1', Box-B and V3 ITS secondary structures showed the uniqueness of this strain, as it shared no similar pattern with closest genera within the Chroococcales.

, SFU decreased the intermolecular/intramolecular hydrogen bond force of proteins and, therefore, caused more order secondary structures and more loosen microstructures.

G-quadruplex (G4) motifs are higher-order secondary structures putatively present in the promoter region of several oncogenes and telomeric ends of chromosomes.

The preferred secondary structures, antimicrobial activities, and cell-membrane disruption activities of the synthesized peptides were evaluated.

Our results revealed many similarities in amino acid composition and preferred secondary structures between epitopes and LCRs; however, we also identified differences in evolutionary trends where LCRs exhibit overall lower sequence conservation and higher disorder.

We performed a bioinformatic analysis of the 5'-UTR secondary structures in the pool of DDX3-dependent mRNAs in silico and predicted that the length of 5'-UTRs for such mRNAs is less than the average for the genome and that there are also characteristic hairpin structures in the region of the first 50 nucleotides from the 5'-end of the mRNA.

Although GUAPV did not replicate in tested mammalian cells, 3′UTR secondary structures duplication and codon usage index were similar to pathogenic flavivirus.

Since dsRBPs require double-stranded RNA to bind, their binding affinity depends on the competition among all possible secondary structures of the target RNA molecule.

SESCA_bayes samples possible secondary structures using a Monte Carlo scheme, driven by the likelihood of estimated scaling errors and non-secondary-structure contributions of the measured spectrum.

In developing these attractive optical nanomaterials, synthesizing responsive nanostructures, and assembling them into more complex secondary structures (including both photonic crystals and plasmonic superstructures) are important.

Extensive screening identifies a rhodium(I)-catalyst that displays robust chemoselectivity toward base-unpaired guanosines in single and double-strand oligonucleotides with structurally complex secondary structures.

In our study, the screening of complete genome of Mycobacterium avium revealed six putative precursor microRNA sequences bearing typical secondary structures.

A convolutional neural network (CNN) model was trained and tested on a dataset consisting 87993 spectra computed from protein peptide segments with α-helical, β-sheet, and other typical secondary structures.

Similar to natural and synthetic porphyrins, MPPs are thought to bind DNA and stabilize secondary structures such as guanine quadruplexes (G-4) and thus potentially impact telomerase activity and DNA synthesis which are important targets for chemotherapy.

The use of RNA molecules shows several advantages since they show a very low immunogenicity, are able to penetrate the cell/nuclear membrane, and to target the desired gene even if highly expressed, they are cheap and easy to synthesize, and can be chemically modified, in order to increase their stability or to stabilize secondary structures.

Conclusion We show in silico secondary structures design of selected of 8 miRNAs over-expressed in diabetic foot ulcers healing by means of computational biology.

Conclusion In this study we show in silico secondary structures projection of selected of 12 miRNA inhibitors against miRNA over-expressed in thyroid cancer through computational biology.

Our method includes using "Enzymer," a software for designing RNA sequences with desired secondary structures that may include pseudoknots.

This chapter describes how to use the software RNARedPrint for the de novo rational design of RNA sequences adopting one or several desired secondary structures.

The problem is further compounded by the high guaninecytosine (GC) content of the region (~80%) that can form strong secondary structures impairing strand denaturation.

To improve both the selectivity and to avoid strong secondary structures, that could hinder the hybridization efficiency, a sandwich format of the A.

Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific secondary structures that are difficult to characterize with biophysical techniques.

Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, influencing protein dynamics and interactions with other molecules.

Background: G-quadruplex (G4) are nucleic secondary structures characterized by G-tetrads.

The method we developed provides a new strategy for identifying proteins that interact with nucleic secondary structures in cells and benefit the study of their biological roles.

Molecular sequence variation analysis identified the conserved secondary structures of tRNAs.

The contributions of many conserved secondary structures of Rad6 and its human homologs UBE2A and UBE2B to their biological functions are not understood.