Secondary Structure Analysis Research Articles

Structural insights of a putative β-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans

Structural and conformational insights of a putative β-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans were investigated by computational and Circular Dichroism (CD) analyses. PsGH43F was cloned and expressed in E. coli BL21 (DE3) cells and the purified enzyme gave the size ~50 kDa on SDS-PAGE analysis. Multiple Sequence Alignment of PsGH43F sequence followed by superposition of modeled structure with homologous structures displayed the presence of three conserved catalytic amino acid residues, Asp33, Asp149 and Glu212. The secondary structure analysis by CD showed 2.72 % α-helix and 36.06 % β-strands. The homology modeled structure of PsGH43F displayed a 5-bladed β-propeller fold for catalytic module at N-terminal and a β-sandwich structure for CBM6 at the C-terminal. Ramachandran plot displayed 99.5 % of residues in the allowed regions. MD simulation of PsGH43F revealed the compactness and stability of the structure. Molecular docking studies of PsGH43F with xylo-oligosaccharides revealed its maximum binding affinity for xylobiose. MD simulation of PsGH43F-xylobiose complex confirmed the increased structural and conformational stability in presence of substrate. The Hydrodynamic diameter analysis of PsGH43F by DLS was in the range, 0.25–0.28 μm.

Screening of Single-Stranded DNA Aptamer Specific for Florfenicol and Application in Detection of Food Safety.

In this work, the single-stranded DNA (ssDNA) aptamers specific to florfenicol (FF) and having a high binding affinity were prepared using the magnetic bead-based systematic evolution of ligands by the exponential enrichment technique (MB-SELEX). After 10 rounds of the MB-SELEX screening, aptamers that can simultaneously recognize FF and its metabolite florfenicol amine (FFA) were obtained. The aptamer with the lowest dissociation constant (Kd) was truncated and optimized based on a secondary structure analysis. The optimal aptamer selected was Apt-14t, with a length of 43 nt, and its dissociation constant was 4.66 ± 0.75 nM, which was about 7 times higher than that of the full-length sequence. The potential binding sites and interactions with FF were demonstrated by molecular docking simulations. In addition, a colorimetric strategy for nanogold aptamers was constructed. The linear detection range of this method was 0.00128–500 ng/mL and the actual detection limit was 0.00128 ng/mL. Using this strategy to detect florfenicol in actual milk and eggs samples, the spiked recoveries were 88.9–123.1% and 84.0–112.2%, respectively, and the relative standard deviation was less than 5.6%, showing high accuracy.

Isolation and Characterization of a Novel Pathogenesis-Related Protein-1 Gene (AvPR-1) with Induced Expression in Oat (Avena sativa L.) during Abiotic and Hormonal Stresses.

Pathogenesis-related protein-1 (PR-1) plays crucial roles in regulating plant responses to biotic and abiotic stresses. This study aimed to isolate and characterize the first PR-1 (AvPR-1) gene in oat (Avena sativa L.). AvPR-1 presented conserved signal peptide motifs and core amino acid composition in the functional protein domains as the protein sequence of AvPR-1 presented 98.28%, 97.7%, and 95.4% identity with known PR1 proteins isolated from Triticum aestivum PRB1-2-like, Triticum dicoccoides PRB1-2-like, and Aegilops tauschii subsp. tauschii, respectively. Bioinformatic analysis showed that the AvPR-1 protein belongs to the CAP superfamily (PF00188). Secondary and 3D structure analyses of the AvPR-1 protein were also conducted, confirming sequence conservation of PR-1 among studied species. The AvPR-1 protein harbors a calmodulin-binding domain located in its C-terminal part as previously shown for its wheat homolog TdPR1.2. Moreover, gene expression analysis showed that AvPR-1 was induced in response to many abiotic and hormonal stresses especially in leaves after treatment for 48 h. This is the first study exhibiting the expression profiles of the AvPR-1 gene under different stresses in oat.

Isolation, Computational Characterization and Structure Prediction of Chitinase Gene-Bbchit of Beauveria bassiana

Beauveria bassiana is an entomopathogenic fungus that is used as a biopesticide for the control of many insect pests in agriculturally important crops. B. bassiana produces many extracellular hydrolytic enzymes that degrade the insect cuticle. Among them, the fungal exochitinase mainly assists in the infection by degrading the chitin present in the insect cuticle. To characterize the exochitinase from B. bassiana, the chitinase gene (Bbchit) of 1050bp was amplified from the genomic DNA through PCR using gene-specific primers. This chitinase gene was cloned into the pJET1.2 cloning vector, confirmed through sequencing. The sequence (GI; OP114061) has been deposited in the NCBI database and used for bioinformatics analysis. The various Physico-chemical properties of chitinase protein such as pI, EC, AI, GRAVY and instability index were predicted using primary structure analysis. Using MEGA11 software, the translated chitinase protein- Bbchit showed that it closely resembles with the QJE37897.1 (chitinase Chit37). Primary and secondary structure analysis helps to characterize the functionality of chitinase protein (Bbchit). The 3D structure of B. bassiana was predicted using Robetta, an abinitio prediction method and confirmed through in-silico using the SAVESv6.0 (PROCHECK) server. The isolated exochitinase gene from B. bassiana has been characterized for use as a bio-control agent for the control of insect pests in crop plants.

Reduced Graphene Oxide-Extracellular Matrix Scaffolds as a Multifunctional and Highly Biocompatible Nanocomposite for Wound Healing: Insights into Characterization and Electroconductive Potential.

The development of novel regenerative technologies based on the implementation of natural extracellular matrix (ECM), or individual components of ECM combined with multifunctional nanomaterials such as graphene oxide and reduced graphene oxide, has demonstrated remarkable results in wound healing and tissue engineering. However, the synthesis of these nanocomposites involves great challenges related to maintaining the biocompatibility with a simultaneous improvement in their functionalities. Based on that, in this research we developed novel nanoengineered ECM-scaffolds formed by mixing small intestinal submucosa (SIS) with graphene oxide (GO)/reduced graphene oxide (rGO) to improve electrical conductivity while maintaining remarkable biocompatibility. For this, decellularized SIS was combined with GO to form the scaffold precursor for subsequent lyophilization, chemically crosslinking and in situ reduction. The obtained GO and rGO were characterized via Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), X-ray diffraction (XRD), electrical conductivity testing and atomic force microscopy (AFM). The results confirm the suitable synthesis of GO, the effective reduction to rGO and the significant increase in the electrical conductivity (more than four orders of magnitude higher than bare GO). In addition, the graphene oxide/reduced graphene oxide-SIS scaffolds were characterized via Raman spectroscopy, FTIR, TGA, SEM, porosity assay (higher than 97.5% in all cases) and protein secondary structural analysis. Moreover, the biocompatibility of scaffolds was studied by standardized assays of hemolysis activity (less than 0.5%), platelet activation and deposition, and cell viability in Vero, HaCat and HFF-1 cells (higher than 90% for all evaluated cell lines on the different scaffolds). The obtained results confirm the remarkable biocompatibility, as supported by high hemocompatibility, low cytotoxicity and no negative impact on platelet activation and deposition. Finally, structural characteristics such as pore size and interconnectivity as well as superior cell attachment abilities also corroborated the potential of the developed nanoengineered ECM-scaffolds as a multifunctional nanoplatform for application in regenerative medicine and tissue engineering.

Identification and functional analysis of Tex11 and Meig1 in spermatogenesis of Hyriopsis cumingii.

: The process of spermatogenesis is complex and controlled by many genes. In mammals, Testis-expressed gene 11 (Tex11) and meiosis expressed gene 1 (Meig1) are typical spermatogenesis-related genes. In this study, we obtained the full length cDNAs for Tex11 (3143bp) and Meig1 (1649bp) in Hyriopsis cumingii by cloning. Among them, Hc-Tex11 contains 930 amino acids and Hc-Meig1 contains 91 amino acids. The protein molecular masses (MW) of Hc-Tex11 and Hc-Meig1 were 105.63 kDa and 10.95 kDa, respectively. Protein secondary structure analysis showed that Hc-TEX11 protein has three TPR domains. The expression of Hc-Tex11 and Hc-Meig1 in different tissues showed higher levels in testes. At different ages, the expression of Hc-Tex11 and Hc-Meig1 was higher levels in 3-year-old male mussels. During spermatogenesis, the mRNA levels of Hc-Tex11, Hc-Meig1 gradually increased with the development of spermatogonia and reached a peak during sperm maturation. Hc-Tex11 and Hc-Meig1 mRNA signals were detected on spermatogonia and spermatocytes by in situ hybridization. In addition, RNA interference (RNAi) experiments of Hc-Tex11 caused a down-regulated of Dmrt1, KinaseX, Tra-2 and Klhl10 genes and an up-regulated of β-catenin gene. Based on the above experimental results, it can be speculated that Hc-Tex11 and Hc-Meig1 are important in the development of the male gonadal and spermatogenesis in H. cumingii, which can provide important clues to better comprehend the molecular mechanism of Tex11 and Meig1 in regulating spermatogenesis of bivalves.

Characterization of outcomes of amino acid modifications using a combinatorial approach to reveal physical and structural perturbations: A case study using trastuzumab biosimilar

Biopharmaceuticals, such as monoclonal antibodies, are considered as life-saving drugs for autoimmune diseases, cancer and infectious diseases. However, biotherapeutics tend to undergo chemical degradation during various stages of manufacturing. The conditions of chemical degradation, along with the physical degradation pathways, have a direct influence on the overall stability, safety and efficacy of these therapeutics. While site-specific chemical changes have been well-explored and investigated using various analytical approaches, the resulting conformational and structural changes have not been much studied. Thus, we explored various biophysical techniques for assessing the influence of three representatives forced degradation conditions viz. oxidation, deamidation, and glycation, in a model therapeutic trastuzumab biosimilar. The site-specific modifications caused by these stress conditions were analysed using high resolution mass spectrometry. While their thermodynamic and conformational consequences were investigated by using differential scanning colorimetry (Nano-DSC), circular dichroism (CD) spectroscopy, analytical ultracentrifugation (AUC), and dynamic light scattering (DLS). The investigated stress conditions resulted in reduced thermodynamic stability of mAb, as confirmed using Nano-DSC. Secondary structure analysis performed with CD spectroscopy indicated detectable structural alterations in the beta sheets of stressed samples. DLS and SV-AUC studies demonstrated an enhanced level of aggregation and fragmentation in presence of all stress conditions. Thus, the biophysical analytical toolkits, when used simultaneously, could offer deeper insights into the subtle conformational changes that result from site-specific chemical modifications in mAbs. Hence, these analytical approaches may serve as significant additions to the battery of techniques used for forced degradation analysis of biopharmaceuticals.

Molecular detection and characterization of Potato spindle tuber viroid (PSTVd) infecting Tomato (Solanum lycopersicum L.) in Karnataka State of India.

Potato Spindle Tuber Viroid (PSTVd) is a non-coding, infectious, small, circular RNA known to cause disease in agricultural and horticultural plants. In the present work, an investigation was conducted in the southern districts of Karnataka state to assess the possible pospiviroid infections on tomato plants that are considered natural hosts for viroids. A total of 83 tomato samples showing disease symptoms (virus or viroid-like) along with healthy ones were collected and subjected to viroid detection by conventional Reverse Transcriptase Polymer Chain Reaction (RT-PCR) using universal (Pospi1-RE/Pospi1-FW) and a specific set of primers (3H1/2H1). The study confirmed the presence of PSTVd in one of the samples of tomato collected from Banghatta village of Mandy District, with an expected amplicon of ~ 361bp. The bioassay conducted on tomato plants (cv. Rutgers) proved the association of PSTVd, which was further confirmed by RT-PCR. The amplicons were cloned, sequenced, and the representative sequences were deposited in the NCBI GenBank. The sequence alignment and secondary structure analysis of the isolated viroid with other reference sequences revealed the variations in the pathogenicity, central conserved region, and Terminal right domains. The variations observed between the isolated PSTVd with that of other Indian isolates support that viroid may have been transmitted among the crop plants, possibly through seed or mechanical means.

Hydrothermal-induced changes in the gel properties of Mung bean proteins and their effect on the cooking quality of developed compound noodles.

Mung bean proteins (MBPs) are highly nutritious food ingredients, but their lack of gluten limits their use in staple foods such as noodles. In this study, MBPs were modified by hydrothermal treatment, and their gel properties and the major structural changes were analyzed at different heating temperatures (25, 65, 75, 85, 95, and 105°C), moisture contents (0, 15, 20, 25, 30, and 35%), and hydrothermal treatment times (0, 15, 30, 45, 60, and 75 min). Thereafter, the modified MBPs (MMBPs) were added to wheat noodles at substitution levels of 3, 6, and 9% to evaluate their effect on the quality of the noodles. The results showed that the hydrothermal treatment significantly improved the gel properties and water absorption capacity of the MBPs and slightly increased their disulfide bond content. When MBPs with a 25% moisture content were heated at 85°C for 60 min, their gel properties notably improved, and their structural changes were maximal. The structural changes revealed that the MBP molecule formed a macromolecular polymer because a significant protein band appeared at about 66.2 kDa. Secondary structure and microstructure analyses revealed that the MBP structure was significantly damaged and that the β-sheet structure increased because of changes in the degree of aggregation between the protein molecules. Compared to the untreated MBPs, the MMBPs significantly improved the cooking quality and texture properties of the noodles, and the addition amount reached more than 6%, whereas that of the untreated MBPs was less than 3%. At this time, the cooking loss and the broken rate of the untreated MBPs group were about 2 times higher than that of the 6% MMBP-treated group. An analysis of changes in the water distribution, rheological properties, and microstructure revealed that intermolecular cross-linking occurred between the MMBPs and wheat dough, which improved the quality of the MMBP-treated noodles. The findings demonstrated that the MMBPs obtained by hydrothermal treatment had a positive effect on the wheat dough properties and noodle quality. These results provide a technical foundation for incorporating novel protein supplements into staple foods.

Molecular insights into the structural and dynamical changes of calcium channel TRPV6 induced by its interaction with phosphatidylinositol 4,5-bisphosphate

Transient receptor potential vanilloid subfamily member 6 (TRPV6) is an epithelial calcium channel that regulates the initial step of the transcellular calcium transport pathway. TRPV6 is expressed in the kidney, intestine, placenta, and other tissues, and the dysregulation of the channel is implicated in several human cancers. It has been reported that phosphatidylinositol 4,5-bisphosphate (PIP2) activates TRPV6 and its close homologue TRPV5; however, the underlying molecular mechanism is less clear. Recently, a structure of rabbit TRPV5 in complex with dioctanoyl (diC8) PIP2, a soluble form of PIP2, was determined by cryo-electron microscopy. Based on this structure, the structural model of human TRPV6 with PIP2 was set up, and then molecular dynamics simulations were performed for TRPV6 with and without PIP2. Simulation results show that the positively charged residues responsible for TRPV5 binding of diC8 PIP2 are conserved in the interactions between TRPV6 and PIP2. The binding of PIP2 to TRPV6 increases the distance between the diagonally opposed residues D542 in the selectivity filter and that between the diagonally opposed M578 residues in the lower gate of TRPV6. A secondary structural analysis reveals that residues M578 in TRPV6 undergo structural and position changes during the binding of PIP2 with TRPV6. In addition, principal component analysis indicates that the binding of PIP2 increases the dynamical motions of both the selectivity filter and the lower gate of TRPV6. These changes induced by PIP2 favor the channel opening. Thus, this study provides a basis for understanding the mechanism underlying the PIP2-induced TRPV6 channel activation. Communicated by Ramaswamy H. Sarma

Roholtiella volcanica sp. nov., a New Species of Cyanobacteria from Kamchatkan Volcanic Soils

During a study of biodiversity of cyanobacteria in Gorely volcano soils (Kamchatka Peninsula), a strain of heterocytous, a false branching cyanobacterium with gradually tapered filaments, was isolated. Prominent features of the strain were purplish-grey trichomes and firm, distinct multilayered sheaths. Based on the results obtained from the morphological, ecological, and phylogenetic analysis using the 16S rRNA and 16S–23S ITS region, 16S–23S ITS secondary structure analysis, comparison of flanking regions of BoxB and V3 helices, and the p-distance between the 16S–23S ITS region, we describe our strain K7 as a novel species of the genus Roholtiella with the name Roholtiella volcanica sp. nov., in accordance with the International Code of Nomenclature for algae, fungi, and plants. This work continues the rapid expansion of the description of new taxa of cyanobacteria, and particularly demonstrates a coming phase in cyanobacterial taxonomy in which the discovery of new species in recently described genera rapidly increases our understanding of the diversity in this phylum.

Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure

RNAs perform their function by forming specific structures, which can change across cellular conditions. Structure probing experiments combined with next generation sequencing technology have enabled transcriptome-wide analysis of RNA secondary structure in various cellular conditions. Differential analysis of structure probing data in different conditions can reveal the RNA structurally variable regions (SVRs), which is important for understanding RNA functions. Here, we propose DiffScan, a computational framework for normalization and differential analysis of structure probing data in high resolution. DiffScan preprocesses structure probing datasets to remove systematic bias, and then scans the transcripts to identify SVRs and adaptively determines their lengths and locations. The proposed approach is compatible with most structure probing platforms (e.g., icSHAPE, DMS-seq). When evaluated with simulated and benchmark datasets, DiffScan identifies structurally variable regions at nucleotide resolution, with substantial improvement in accuracy compared with existing SVR detection methods. Moreover, the improvement is robust when tested in multiple structure probing platforms. Application of DiffScan in a dataset of multi-subcellular RNA structurome and a subsequent motif enrichment analysis suggest potential links of RNA structural variation and mRNA abundance, possibly mediated by RNA binding proteins such as the serine/arginine rich splicing factors. This work provides an effective tool for differential analysis of RNA secondary structure, reinforcing the power of structure probing experiments in deciphering the dynamic RNA structurome.

Monitoring the Progression of Cell-Free Expression of Microbial Rhodopsins by Surface Enhanced IR Spectroscopy: Resolving a Branch Point for Successful/Unsuccessful Folding.

The translocon-unassisted folding process of transmembrane domains of the microbial rhodopsins sensory rhodopsin I (HsSRI) and II (HsSRII), channelrhodopsin II (CrChR2), and bacteriorhodopsin (HsBR) during cell-free expression has been investigated by Surface-Enhanced Infrared Absorption Spectroscopy (SEIRAS). Up to now, only a limited number of rhodopsins have been expressed and folded into the functional holoprotein in cell free expression systems, while other microbial rhodopsins fail to properly bind the chromophore all-trans retinal as indicated by the missing visible absorption. SEIRAS experiments suggest that all investigated rhodopsins lead to the production of polypeptides, which are co-translationally inserted into a solid-supported lipid bilayer during the first hour after the in-vitro expression is initiated. Secondary structure analysis of the IR spectra revealed that the polypeptides form a comparable amount of α-helical structure during the initial phase of insertion into the lipid bilayer. As the process progressed (>1 h), only HsBR exhibited a further increase and association of α-helices to form a compact tertiary structure, while the helical contents of the other rhodopsins stagnated. This result suggests that the molecular reason for the unsuccessful cell-free expression of the two sensory rhodopsins and of CrChR2 is not due to the translation process, but rather to the folding process during the post-translational period. Taking our previous observation into account that HsBR fails to form a tertiary structure in the absence of its retinal, we infer that the chromophore retinal is an integral component of the compaction of the polypeptide into its tertiary structure and the formation of a fully functional protein.

In silico analysis of enzymes involved in mycosporine-like amino acids biosynthesis in Euhalothece sp.: Structural and functional characterization

Mycosporine-like amino acids (MAAs) are ultraviolet-absorbing compounds synthesized by photoautotrophic microorganisms such as cyanobacteria. They have applications as UV protectants and antioxidants in the cosmetic and pharmaceutical sectors. To date, >30 different types of MAAs have been identified, having an absorption range between 310 and 365 nm that covers most of the UVR spectrum (~295–400 nm). In the study, MAAs were extracted and partially purified from a euryhaline Euhalothece sp. Thereafter, in silico analysis of the MAAs biosynthetic genes was conducted to determine the physicochemical characteristics, structural properties, functional analysis and homology model. High salinity stress (120 g L−1) significantly enhanced the production of MAAs (~56 %) in Euhalothece sp. Bioinformatics analysis of the genome of Euhalothece sp. revealed a distinctive mys gene cluster that contained six genes (mysA to mysE), compared to four genes commonly found in MAA-producing cyanobacteria. Interestingly, both EEVS and DHQ synthase were present, indicating the potential to synthesize MAAs via both the shikimate and sedoheptulose 7-phosphate pathways. Secondary structure analysis confirmed that in all the biosynthetic enzymes, the major components were the alpha-helices with random coils. This study emphasized the unique genes for MAAs in Euhalothece sp. as well as highlighted the potential metabolite pathways for commercial production. Elucidation of the protein structure, physicochemical properties, and interactions provides scientific insight into the biosynthesis of MAAs from hypersaline cyanobacteria. Additionally, it is essential for determining the applications of these novel photoprotective compounds.

Improving the solubility of myofibrillar proteins in water by destroying and suppressing myosin molecular assembly via glycation

Filamentous myosin is a self-assembling polymer that prevents myofibrillar proteins (MPs) from functioning in low ionic strength media. This study was aimed at investigating if glycation has the potential to improve the solubility of MPs in water. MPs were conjugated with monosaccharides, oligosaccharides, and polysaccharides under wet reaction conditions at 37 °C. The conjugation was verified by SDS-PAGE, FT-IR and amino acid analyses. MPs conjugated with dextran (DX) exhibited a higher solubility and dispersion stability in water, which corresponded to smaller particle size and more uniform distribution (P < 0.05). According to secondary and tertiary structure analyses, the loss of α-helix structures and unfolding of the MPs appear to be the main reasons for MP solubilization. Additionally, according to the zeta-potential, confocal laser scanning microscopy, and atomic force microscopy observation results, glycation can provide electrostatic repulsion or steric hindrance to disintegrate existing filamentous myosin aggregates and inhibit further self-assembly behavior.

Exploring magnetic field treatment into solid-state fermentation of organic waste for improving structural and physiological properties of keratin peptides

This study systematically investigated the effects of a low-intensity magnetic field on the influence of keratinase activity, peptide yield, and structural and functional properties of peptides produced during solid-state fermentation (SSF) of mixed organic substrates (chicken feather powder and okara) using a mutant strain of Bacillus licheniformis. Initially, the magnetic field-assisted SSF (MSSF) conditions were optimized, which provided the optimized conditions as the number of treatments 3 at every 24 h (24, 48, and 72 h) with 4 h holding time at 120 Gs of magnetic intensity (mI). Under the optimum conditions, keratinase activity and peptide production increased by 10.31% and 13.77%, respectively. Further, in order to evaluate the influence of magnetic field treatment on the peptides, MSSF experiments were done under different mI conditions (40, 80, 120, and 160 Gs), followed by the evaluation of the structural changes of the extracted peptides. The structural analysis revealed that mI had a significant impact on the keratin surface. In contrast, secondary structure analysis confirmed the unfolding of the peptide with decreased α-keratin and increased β-keratin, thereby boosting the bioactive properties of the peptides. The highest hydroxyl free radical (.OH), 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging and Fe2+ chelating rates (56.55, 71.36, and 50.72%, respectively) were found at 120 Gs, which were insignificant with the results at 160 Gs. Therefore, MSSF has a positive effect on the proteolysis mechanism, which can increase bioactive peptide production from keratin.

RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources.

RNA–protein complexes regulate a variety of biological functions. Thus, it is essential to explore and visualize RNA–protein structural interaction features, especially pocket interactions. In this work, we develop an easy-to-use bioinformatics resource: RPpocket. This database provides RNA–protein complex interactions based on sequence, secondary structure, and pocket topology analysis. We extracted 793 pockets from 74 non-redundant RNA–protein structures. Then, we calculated the binding- and non-binding pocket topological properties and analyzed the binding mechanism of the RNA–protein complex. The results showed that the binding pockets were more extended than the non-binding pockets. We also found that long-range forces were the main interaction for RNA–protein recognition, while short-range forces strengthened and optimized the binding. RPpocket could facilitate RNA–protein engineering for biological or medical applications.

Description of Limnomonas gen. nov., L. gaiensis sp. nov. and L. spitsbergensis sp. nov. (Chlamydomonadales, Chlorophyta)

Two novel Chlamydomonas-like species, belonging to the Moewusii clade, have been described. The first species inhabits eutrophic and neutral to basic pH waters in Sweden and England. It is easily recognizable under a light microscope due to its morphology (a small green prolate spheroidal shape with a large and truncated papilla at its anterior end, two equal flagella, a single lateral eyespot, a basal nucleus, and a well-defined pyrenoid) and to its peculiar whole-body pendulum movement while resting on surfaces or attached to floating particles. The species occurs as free-living individuals and is able to gather temporarily into groups of individual cells. No particular binding structures or palmelloid cells were observed in cultures. The second species, previously assigned to Chlamydomonas cf. proboscigera, was collected from persistent snow in Svalbard, Norway. Its morphology is revised herein. Using SSU rDNA sequence analyses, these two species formed a well-supported clade. Moreover, ITS-2 secondary structure analyses confirmed sexual incompatibility between these biological species. Considering these results, a new genus Limnomonas and its type species L. gaiensis and L. spitsbergensis are proposed.

Evaluation of pH change effects on the HSA folding and its drug binding characteristics, a computational biology investigation.

The binding of therapeutics to human serum albumin (HSA), which is an abundant protein in plasma poses a major challenge in drug discovery. Although HSA has several binding pockets, the binding site I on D2 and binding site II on D3 are the main binding pockets of HSA. To date, a few experiments have been conducted to examine the effects of the potential of hydrogen (pH) changes on HSA attributes. In the present investigation, the effect of acidic (pH7.1) and basic states (pH7.7) on HSA structure and its drug binding potency were examined in comparison with the physiological state (pH 7.4). For this purpose, molecular dynamics (MD), free energy landscape (FEL), principal component analysis (PCA), probability distribution function (PDF), tunnel-cavity investigation, secondary structure analysis, docking study, and free energy investigation were employed to investigate the effect of pH changes on the structural characteristics of HSA at the atomic level. The results obtained from this study revealed the significant effect of pH alterations on the secondary and tertiary structure of HSA. In addition, HSA stability and its drug binding ability can be severely affected following pH changes. Given that pH change frequently occurs in various diseases such as cancer, diabetes, and kidney failure, therefore, pharmaceutical companies should allocate specific consideration to this subject throughout their drug design experiments.

Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium

Enterococcus faecium is an emerging ESKAPE bacterium that is capable of causing severe public health complications in humans. There are currently no licensed treatments or vaccinations to combat the deadly pathogen. We aimed to design a potent and novel prophylactic chimeric vaccine against E. faecium through an immunoinformatics approach The antigenic Penicillin-binding protein 5 (PBP 5) protein was selected to identify B and T cell epitopes, followed by conservancy analysis, population coverage, physiochemical assessment, secondary and tertiary structural analysis. Using various immunoinformatics methods and tools, two linear B-cell epitopes, five CTL epitopes, and two HTL epitopes were finally selected for vaccine development. The constructed vaccine was determined to be highly immunogenic, cytokine-producing, antigenic, non-toxic, non-allergenic, and stable, as well as potentially effective against E. faecium. In addition, disulfide engineering, codon adaptation, and in silico cloning, were used to improve stability and expression efficiency in the host E. coli. Molecular docking and molecular dynamics simulations indicated that the structure of the vaccine is stable and has a high affinity for the TLR4 receptor. The immune simulation results revealed that both B and T cells had an increased response to the vaccination component. Conclusively, the in-depth in silico analysis suggests, the proposed vaccine to elicit a robust immune response against E. faecium infection and hence a promising target for further experimental trials.