Signal Recognition Particle Research Articles

Mutagenesis Supports AlphaFold Prediction of How Modular Polyketide Synthase Acyl Carrier Proteins Dock With Downstream Ketosynthases.

The docking of an acyl carrier protein (ACP) domain with a downstream ketosynthase (KS) domain in each module of a polyketide synthase (PKS) helps ensure accurate biosynthesis. If the polyketide chain bound to the ACP has been properly modified by upstream processing enzymes and is compatible with gatekeeping residues in the KS tunnel, a transacylation reaction can transfer it from the 18.1-Å phosphopantetheinyl arm of the ACP to the reactive cysteine of the KS. AlphaFold-Multimer predicts a general interface for these transacylation checkpoints. Half of the solutions obtained for 50 ACP/KS pairs show the KS motif TxLGDP forming the first turn of an α-helix, as in reported structures, while half show it forming a type I β-turn not previously observed. Solutions with the latter conformation may represent how these domains are relatively positioned during the transacylation reaction, as the entrance to the KS active site is relatively open and the phosphopantetheinylated ACP serine and the reactive KS cysteine are relatively closer-17.2 versus 20.9 Å, on average. To probe the predicted interface, 20 mutations were made to KS surface residues within the model triketide lactone synthase P1-P6-P7. The activities of these mutants are consistent with the proposed interface.

Decoding the TAome and computational insights into parDE toxin-antitoxin systems in Pseudomonas aeruginosa.

Toxin-antitoxin (TA) modules are widely found in the genomes of pathogenic bacteria. They regulate vital cellular functions like transcription, translation, and DNA replication, and are therefore essential to the survival of bacteria under stress. With a focus on the type II parDE modules, this study thoroughly examines TAome in Pseudomonas aeruginosa, a bacterium well-known for its adaptability and antibiotic resistance. We explored the TAome in three P. aeruginosa strains: ATCC 27,853, PAO1, and PA14, and found 15 type II TAs in ATCC 27,853, 12 in PAO1, and 13 in PA14, with significant variation in the associated mobile genetic elements. Five different parDE homologs were found by further TAome analysis in ATCC 27,853, and their relationships were confirmed by sequence alignments and precise genomic positions. After comparing these ParDE modules' sequences to those of other pathogenic bacteria, it was discovered that they were conserved throughout many taxa, especially Proteobacteria. Nucleic acids were predicted as potential ligands for ParD antitoxins, whereas ParE toxins interacted with a wide range of small molecules, indicating a diverse functional repertoire. The interaction interfaces between ParDE TAs were clarified by protein-protein interaction networks and docking studies, which also highlighted important residues involved in binding. This thorough examination improves our understanding of the diversity, evolutionary dynamics, and functional significance of TA systems in P. aeruginosa, providing insights into their roles in bacterial physiology and pathogenicity.

Insight into the fate of tolfenpyrad in tea plant (Camellia sinensis L.) from root uptake

Residual pesticides in agricultural environments, including soil and irrigation water, can be taken up by plants, and thus pose a potential risk to food safety. Although tolfenpyrad has been widely used in tea plantations, limited information is available on its root uptake and fate in tea plants (Camellia sinensis L.). Exploring the mechanisms involved is crucial for understanding the migration and accumulation of tolfenpyrad in tea plants, particularly in the edible parts. In this study, root uptake of tolfenpyrad and its subsequent translocation, distribution, and metabolism in tea seedlings were investigated. The results indicated that the passive transport and apoplastic pathway dominated the root uptake of tolfenpyrad. After uptake, tolfenpyrad distributed predominantly in the cell walls (90.8–92.0 %) of roots, resulting in limited upward translocation in water-soluble fractions through transpirational pull, with translocation factor values far <1 (TFstem/root = 0.115–0.453 and TFleaf/stem = 0.039–0.184). Similar accumulation patterns were observed for the carboxylated metabolite PT-CA as well as hydroxylated metabolite PT-OH. Interestingly, the subcellular distribution of PT-CA in stems was much different from that of the parent tolfenpyrad: PT-CA mainly distributed in the stem cell walls (41.72 %) and cell organelles (56.18 %) at 3 h, then gradually transferred into the cell-soluble fractions (33.07 %) after 120 h. Results from the present study indicated limited upward translocation of tolfenpyrad with its main metabolites to leaves. This finding helps to alleviate concerns about environmental residual tolfenpyrad in tea consumption and provides valuable information for the safety evaluation of tolfenpyrad.

Isolation and characterization of chromium-resistant bacteria and their effects on germination, growth, and Cr accumulation in Capsicum annum (L.) under Cr stress

Chromium (Cr) is a well-known environmental pollutant while less information is available on the role of Cr-resistant bacteria in the alleviation of Cr-stress in chili (Capsicum annum L.) plants. Effect of Cr-resistant bacterial strains on growth and Cr uptake by chili plants was investigated. The results revealed that Cr-stress showed a negative effect on germination, photosynthesis, and relative water content but the inoculation ameliorated the plant stress. Chromium-resistant bacterial strains enhanced the shoot and root growth (33% SL, 19.7% RL), shoot and root dry weight (35%, 32.9%), relative water content (32.25%), membrane stability index (46.52%) SPAD value (50.76%), Cr concentration in shoots and roots (19.87 and 18.52 mg kg−1), bioaccumulation and translocation factor (0.396 mgkg−1), and seedling vigor index (40.8%) of plants. Chromium-resistant bacterial strains enhanced the NPK uptake while reduced Cr uptake by plants. The morphological and biochemical examination of rhizobacterial strains (and NM28) resistant to Cr-stress revealed smooth, off-white colonies of bacteria composed of rod-shaped cells which are Gram positive in reaction while negative in catalase activity. High quantities of malic acid were produced by bacterial strains under study i.e. NM8 (926.12 μgmL−2) and NM28 (992.25 μgmL−2). These strains were identified as Bacillus cereus strain NM8 and Bacillus subtilis strain NM28 through 16S rRNA sequencing. Results showed that B. cereus strain NM28 is more effective than B. cereus strain NM8 in promoting the growth of Cr-stressed Chili that might be suitable to develop biofertilizer for sustainable production of vegetables under metal stress.

Design of multi-epitope vaccine against porcine rotavirus using computational biology and molecular dynamics simulation approaches

Porcine Rotavirus (PoRV) is a significant pathogen affecting swine-rearing regions globally, presenting a substantial threat to the economic development of the livestock sector. At present, no specific pharmaceuticals are available for this disease, and treatment options remain exceedingly limited. This study seeks to design a multi-epitope peptide vaccine for PoRV employing bioinformatics approaches to robustly activate T-cell and B-cell immune responses. Two antigenic proteins, VP7 and VP8*, were selected from PoRV, and potential immunogenic T-cell and B-cell epitopes were predicted using immunoinformatic tools. These epitopes were further screened according to non-toxicity, antigenicity, non-allergenicity, and immunogenicity criteria. The selected epitopes were linked with linkers to form a novel multi-epitope vaccine construct, with the PADRE sequence (AKFVAAWTLKAAA) and RS09 peptide attached at the N-terminus of the designed peptide chain to enhance the vaccine’s antigenicity. Protein-protein docking of the vaccine constructs with toll-like receptors (TLR3 and TLR4) was conducted using computational methods, with the lowest energy docking results selected as the optimal predictive model. Subsequently, molecular dynamics (MD) simulation methods were employed to assess the stability of the protein vaccine constructs and TLR3 and TLR4 receptors. The results indicated that the vaccine-TLR3 and vaccine-TLR4 docking models remained stable throughout the simulation period. Additionally, the C-IMMSIM tool was utilized to determine the immunogenic triggering capability of the vaccine protein, demonstrating that the constructed vaccine protein could induce both cell-mediated and humoral immune responses, thereby playing a role in eliciting host immune responses. In conclusion, this study successfully constructed a multi-epitope vaccine against PoRV and validated the stability and efficacy of the vaccine through computational analysis. However, as the study is purely computational, experimental evaluation is required to validate the safety and immunogenicity of the newly constructed vaccine protein.

High cadmium-accumulating Salix ecotype shapes rhizosphere microbiome to facilitate cadmium extraction

Cadmium (Cd) contamination poses a significant threat to agricultural soils and food safety, necessitating effective remediation strategies. Salix species, with their high coverage and Cd accumulating capacity, hold promise for remediation efforts. The rhizosphere microbiome is crucial for enhancing Cd accumulating capacity for Salix. However, the mechanisms by how Salix interacts with its rhizosphere microbiome to enhance Cd extraction remains poorly understood. In this study, we compared the remediation performance of two Salix ecotypes: 51–3 (High Cd-accumulating Ecotype, HAE) and P646 (Low Cd-accumulating Ecotype, LAE). HAE exhibited notable advantages over LAE, with 10.80 % higher plant height, 43.80 % higher biomass, 20.26 % higher Cd accumulation in aboveground tissues (93.09 μg on average), and a superior Cd translocation factor (1.97 on average). Analysis of the rhizosphere bacterial community via 16S rRNA amplicon sequencing revealed that HAE harbored a more diverse bacterial community with a distinct composition compared to LAE. Indicator analysis identified 84 genera specifically enriched in HAE, predominantly belonging to Proteobacteria, Actinobacteria, and Firmicutes, including beneficial microbes such as Streptomyces, Bacillus, and Pseudomonas. Network analysis further elucidated three taxa groups specifically recruited by HAE, which were highly correlated with functional genes that associated with biosynthesis of secondary metabolites, glycan biosynthesis and metabolism, and metabolism of cofactors and vitamins. These functions contribute to enhancing plant growth, Cd uptake, and resistance to Cd in Salix. Overall, our findings highlight the importance of the rhizosphere microbiome in facilitating Cd extraction and provide insights into microbiome-based strategies for sustainable agricultural practices.

Evaluating phytoremediation potential and nutrients status of Bassia indica (Wight) A. J. Scott (Indian Bassia) in a cadmium-contaminated saline soil.

Bassia indica (Wight) A. J. Scott is a fast-growing halophyte suitable for the remediation of saline lands on a large scale. However, no information is available regarding its phytoremediation potential for cadmium (Cd) alone or in combination with salinity. Besides evaluating phytoremediation, assessing micronutrient hemostasis as a crucial physiological insight into the mechanism involved in the tolerance of B. indica under saline soil contaminated with Cd was subjected. Under salinity stress, a considerable amount of sodium accumulates in the plant. Moreover, the accumulation of sodium increased by Cd stress levels. The increase in the exchangeable form of Cd in the rhizosphere in the presence of NaCl ions further elevated the Cd content in the plant tissues. For instance, compared to non-saline conditions, applying 2.5 and 5 g NaCl kg-1 to soil treated with 60 mg Cd kg-1 increased exchangeable Cd by 28.4 and 49.5% in rhizosphere soil, which led to increased cadmium content by 16.1 and 29.6% in the root (as amainpart of Cd accumulation), respectively. Under most stress conditions, potassium homeostasis in the shoot remained undisturbed. It was observed that this plant could transfer an optimal level of potassium from the roots to the shoots at a moderate salinity level. Changes and the distribution of Cu and Zn levels followed a similar pattern in the plant, indicating a common regulation mechanism for these nutrients. Generally, the plant could maintain an appropriate level of Fe, Zn, and Cu ions under most stressed conditions. However, the level of Mn decreased significantly under severe stress levels. Growth parameters, tolerance index, and the values of translocation factor < 1 and shoot bioconcentration factor > 1 under 5 mg Cd kg-1 soil treatment at different salinity levels indicated that B. indica could mitigate the detrimental effect of Cd toxicity and tolerate the NaCl stress via a phytostabilizer mechanism. However, the shoot bioconcentration factor values were very close to one at other Cd levels. Therefore, considering the obtained evidence and the innate ability of B. indica to remediation salinity, this plant is still recommended, even for higher Cd levels (even until 30 mg kg-1), in the presence of salinity.

NRP1 promotes osteo/odontogenic differentiation via shroom3 in dental pulp stem cells

Neuropilin-1 (NRP1) is a single transmembrane glycoprotein involved in a variety of physiological events. However, the exact mechanisms by which NRP1 regulates dental pulp stem cells (DPSCs) to differentiate toward an osteo/odontogenic phenotype are poorly understood. Here, we determined the significantly increased expression of full-length NRP1 and glycosaminoglycan (GAG)-modified NRP1 during osteo/odontogenesis in DPSCs. NRP1 was confirmed to promote alkaline phosphatase (ALP) activity, mineralized nodule deposition, protein and mRNA expression of Runx2, DSPP and DMP1 in DPSCs via the loss-of-function and gain-of-function approaches. Further, a non-GAG-modified NRP1 mutant (NRP1 S612A) was generated and the suppression of osteo/odontogenic differentiation was observed in the NRP1 S612A overexpression cells. Knockdown of the adaptor protein shroom3 resulted in the inhibition of osteo/odontogenesis. The protein-protein interaction network, the protein-protein docking and confocal analyses indicated the interactions between NRP1 and shroom3. Furthermore, immunoprecipitation followed by western analysis confirmed the binding of NRP1 to shroom3, but overexpression of NRP1 S612A greatly influenced the recruitment of shroom3 by NRP1. These results provide strong evidence that NRP1 is a critical regulator for osteo/odontogenesis through interacting with shroom3. Moreover, our results indicate that NRP1 S612A attenuates osteo/odontogenesis, suggesting that GAG modification is essential for NRP1 in DPSCs.

Can Current Molecular Docking Methods Accurately Predict RNA Inhibitors?

Ribonucleic acids (RNAs), particularly the noncoding RNAs, play key roles in cancer, making them attractive drug targets. While conventional methods such as high throughput screening are resource-intensive, computational methods such as RNA-ligand docking can be used as an alternative. However, currently available docking methods are fine-tuned to perform protein-ligand and protein-protein docking. In this work, we evaluated three commonly used docking methods─AutoDock Vina, HADDOCK, and HDOCK─alongside RLDOCK, which is specifically designed for RNA-ligand docking. Our evaluation was based on several criteria including cognate docking, blind docking, scoring potential, and ranking potential. In cognate docking, only RLDOCK showed a success rate of 70% for the top-scoring docked pose. Despite this, all four docking methods did not achieve an overall success rate exceeding 50% amidst our attempt to refine the top-scoring docked poses using molecular dynamics simulations. Meanwhile, all four docking methods showed poor performance in scoring potential evaluation. Although AutoDock Vina achieved an area under the receiver operating characteristic curve of 0.70, it showed poor performance in terms of Matthews' correlation coefficient, precision, enrichment factors, and normalized enrichment factors at 1, 2, and 5%. These results highlight the growing need for further optimization of docking methods to assess RNA-ligand interactions.

Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.

The determination of the three-dimensional structure of large RNA macromolecules in solution is a challenging task that often requires the use of several experimental and computational techniques. Small-angle X-ray scattering can provide insight into some geometrical properties of the probed molecule, but this data must be properly interpreted in order to generate a three-dimensional model. Here, we propose a multiscale pipeline which introduces SAXS data into modelling the global shape of RNA in solution, which can be hierarchically refined until reaching atomistic precision in explicit solvent. The low-resolution helix model (Ernwin) deals with the exploration of the huge conformational space making use of the SAXS data, while a nucleotide-level model (SPQR) removes clashes and disentangles the proposed structures, leading the structure to an all-atom representation in explicit water. We apply the procedure on four different known pdb structures up to 159 nucleotides with promising results. Additionally, we predict an all-atom structure for the Plasmodium falceparum signal recognition particle ALU RNA based on SAXS data deposited in the SASBDB, which has an alternate conformation and better fit to the SAXS data than the previously published structure based on the same data but other modelling methods.

The formation of protein coronas and its effect on the quercetin-edible dock protein nanoparticles

Nanoparticles enter into the digestive tract will quickly adsorb the protein-based biomacromolecules and form protein coronas, which can affect the release characteristic of the encapsulated bioactive compounds. In this study, edible dock protein (EDP) nanoparticles were chosen as the model nanoparticles, and quercetin (Que) was chosen as the representative bioactive compound, the regulatory mechanism of protein coronas on the release characteristic of Que within the EDP nanoparticles was investigated. Results showed that the digestive enzymes can adsorb on the surface of the Que-EDP nanoparticles and form protein coronas during the simulated digestion. Herein, hydrogen bonding, van der Waals force, and hydrophobic interactions were the main adsorption forces between digestive enzymes and nanoparticles. Moreover, the protein coronas formed by α-amylase, pepsin, trypsin, and amylopsin increased the zeta potential of the Que-EDP nanoparticles from −17.9 mV to −11.2 mV, +3.8 mV to +7.0 mV, −21.9 mV to −19.2 mV, and −21.9 mV to −12.1 mV, respectively. The particle size, polydispersity index, and protein conformation of the nanoparticles were also remarkably changed after the formation of protein coronas. Besides, the activity of α-amylase and amylopsin on the surface of the Que-EDP nanoparticles was enhanced by 1.4 and 1.6 times. The simulated digestion experiments indicated that α-amylase and amylopsin coronas slowed the release of Que, while pepsin and trypsin coronas accelerated the release of Que. This study will provide a new idea and theoretical basis for the rational design of nanoparticle carriers.

Phytoremediation Characterization of Heavy Metals by Some Native Plants at Anthropogenic Polluted Sites in Jeddah, Saudi Arabia

Many anthropogenic activities have lately resulted in soil adulteration by heavy metals (HMs). The assessment of native plant species that grow in the polluted environments is of great importance for using these plants in phytoremediation techniques. This study was conducted in three industrial regions in Jeddah city, Wadi Marik, Bahra, and Khumrah, to assess the HM contamination level in them. This study also evaluated the phytoremediation ability of nine plant species collected from the studied regions. Soil physicochemical properties of the studied sites were investigated. Nine HMs, aluminum (Al), nickel (Ni), zinc (Zn), cobalt (Co), iron (Fe), lead (Pb), manganese (Mn), chromium (Cr), and barium (Ba), have been evaluated in the collected soil, plant shoots, and root samples. Total thiol concentration in the plant shoots and roots was determined. The phytoremediation indexes, such as bioaccumulation factor (BCF) and translocation factor (TF), were estimated. The results show that the soil of all the explored sites was sandy and slightly alkaline. It was found that Ni, Pb, and Cr were above the international permissible limit in all soil samples. The Wadi Marik region recorded the highest HM concentration compared to the other sites. In the Bahra region, Fe, Zn, Co, and Mn in all collected soil samples were below internationally permissible levels. In Khumrah, the highest concentration of Zn was found in the soil sample collected around F. indica plants, while Fe, Co, and Mn in all collected soil samples were below the international permissible limit. Depending on the BCF calculations, most of the investigated species showed phytostabilization ability for most of the studied HMs. Of them, E. indica, T. nubica, and P. divisum recorded the highest BCF values that ranged from 16.1 to 3.4. The BCF values of the studied HMs reduced in the order of Cr &gt; Zn &gt; Mn &gt; Co &gt; Ba &gt; Fe &gt; Al &gt; Pb. Phytoextration of Co and Cr could be achieved by P. oleracea and F. indica, which showed TF values that reached 6.7 and 6.1, respectively. These plants showed high potential for phytoremediation and can be suggested as protective belts close to the contaminated regions of Jeddah.

Phytoremediation Potential of Crotalaria pumila (Fabaceae) in Soils Polluted with Heavy Metals: Evidence from Field and Controlled Experiments.

Phytoremediation is a useful, low-cost, and environmentally friendly alternative for the rehabilitation of heavy-metal-contaminated (HM) soils. This technology takes advantage of the ability of certain plant species to accumulate HMs in their tissues. Crotalaria pumila is a herbaceous plant with a wide geographical distribution that grows naturally in environments polluted with HMs. In this work, the bioaccumulation capacity of roots and leaves in relation to five HMs (Cr, Cu, Fe, Pb, and Zn) was evaluated, as well as the morphological changes presented in C. pumila growing in control substrate (without HMs) and mine-tailing substrate (with HMs) under greenhouse conditions for 150 days. Four metals with the following concentration pattern were detected in both tissues and substrates: Fe > Pb > Cu > Zn. Fe, Pb, and Zn concentrations were significantly higher in the roots and leaves of individuals growing on mine-tailing substrate compared to the control substrate. In contrast, Cu concentration increased over time in the exposed individuals. The bioconcentration factor showed a similar pattern in root and leaf: Cu > Fe > Pb > Zn. Around 87.5% of the morphological characters evaluated in this species decreased significantly in individuals exposed to HMs. The bioconcentration factor shows that C. pumila is efficient at absorbing Cu, Fe, and Pb from the mine-tailing substrate, in the root and leaf tissue, and the translocation factor shows its efficiency in translocating Cu from the roots to the leaves. Therefore, C. pumila may be considered as a HM accumulator plant with potential for phytoremediation of polluted soils with Cu, Pb, and Fe, along with the ability to establish itself naturally in contaminated environments, without affecting its germination rates. Also, it exhibits wide geographical distribution, it has a short life cycle, exhibits rapid growth, and can retain the mine-tailing substrate, extracting HMs in a short time.

Phytoremediation of metals in oil sands process affected water by native wetland species

Process affected water and other industrial wastewaters are a major environmental concern. During oil sands mining, large amounts of oil sands process affected water (OSPW) are generated and stored in ponds until reclaimed and ready for surface water discharge. While much research has focused on organics in process waters, trace metals at high concentrations may also pose environmental risks. Phytoremediation is a cost effective and sustainable approach that employs plants to extract and reduce contaminants in water. The research was undertaken in mesocosm scale constructed wetlands with plants exposed to OSPW for 60 days. The objective was to screen seven native emergent wetland species for their ability to tolerate high metal concentrations (arsenic, cadmium, copper, chromium, copper, nickel, selenium, zinc), and then to evaluate the best performing species for OSPW phytoremediation. All native plant species, except Glyceria grandis, tolerated and grew in OSPW. Carex aquatilis (water sedge), Juncus balticus (baltic rush), and Typha latifolia (cattail) had highest survival and growth, and had high metal removal efficiencies for arsenic (81–87 %), chromium (78–86 %), and cadmium (74–84 %), relative to other metals; and greater than 91 % of the dissolved portions were removed. The native plant species were efficient accumulators of all metals, as demonstrated by high root and shoot bioaccumulation factors; root accumulation was greater than shoot accumulation. Translocation factor values were greater than one for Juncus balticus (chromium, zinc) and Carex aquatilis (cadmium, chromium, cobalt, nickel). The results demonstrate the potential suitability of these species for phytoremediation of a number of metals of concern and could provide an effective and environmentally sound remediation approach for wastewaters.

Macronutrients dynamics in copper-contaminated soils: Implications for hemp growth and its phytoremediation potential

Fibrous plants with higher biomass, particularly industrial hemp, have ability to withstand and accumulate significant quantities of heavy metals from contaminated environments. The present study aimed to evaluate the dynamics of different levels (ratios) of macronutrients nitrogen, phosphorus and potassium (NPK) viz., NPK1NPK (1:1:1); NPK2NPK (2:1:1); NPK3NPK (3:1:2); NPK4NPK (4:1:2) on hemp growth and Cu contents under various levels of Cu stress (100, 400 and 800 mg kg−1 on dry soil basis using CuSO4·5H2O). Results revealed that by increasing the Cu stress, growth and biomass decreased linearly and lipid per oxidation and enzymatic antioxidants increased. Balanced application of NPK improved the biomass and decreased the membrane damage by the modulation of malonaldehyde contents. Maximum concentration of Cu in roots (377.47 ± 4.90 mg kg−1), shoots (137.45 ± 5.60 mg kg−1) and (150.07 ± 3.57 mg kg−1) was recorded at Cu3NPK2 treatment as compared to control. Maximum translocation factor (TF) and bioaccumulation coefficients (BAC) in the shoots and leaves of hemp plant were noticed where Cu stress was applied at the rate of 100 mg kg−1. However, BAC and TF were below 1. The NPK2 treatment enhanced biomass and increase Cu content both in leaves and stems, rather than the roots. Our study suggests that balanced application of NPK is a practicable approach to alleviate Cu stress and improve biomass production of industrial hemp plant. These findings indicate that optimum nutrient supply, under Cu stress, can maximize the growth potential and overall health of industrial hemp, making it a viable option for phytoremediation and sustainable agriculture on contaminated soils.

Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta.

The oligomerization of protein macromolecules on cell membranes plays a fundamental role in regulating cellular function. From modulating signal transduction to directing immune response, membrane proteins (MPs) play a crucial role in biological processes and are often the target of many pharmaceutical drugs. Despite their biological relevance, the challenges in experimental determination have hampered the structural availability of membrane proteins and their complexes. Computational docking provides a promising alternative to model membrane protein complex structures. Here, we present Rosetta-MPDock, a flexible transmembrane (TM) protein docking protocol that captures binding-induced conformational changes. Rosetta-MPDock samples large conformational ensembles of flexible monomers and docks them within an implicit membrane environment. We benchmarked this method on 29 TM-protein complexes of variable backbone flexibility. These complexes are classified based on the root-mean-square deviation between the unbound and bound states (RMSDUB) as: rigid (RMSDUB <1.2 Å), moderately-flexible (RMSDUB ∈ [1.2, 2.2) Å), and flexible targets (RMSDUB > 2.2 Å). In a local docking scenario, i.e. with membrane protein partners starting ≈10 Å apart embedded in the membrane in their unbound conformations, Rosetta-MPDock successfully predicts the correct interface (success defined as achieving 3 near-native structures in the 5 top-ranked models) for 67% moderately flexible targets and 60% of the highly flexible targets, a substantial improvement from the existing membrane protein docking methods. Further, by integrating AlphaFold2-multimer for structure determination and using Rosetta-MPDock for docking and refinement, we demonstrate improved success rates over the benchmark targets from 64% to 73%. Rosetta-MPDock advances the capabilities for membrane protein complex structure prediction and modeling to tackle key biological questions and elucidate functional mechanisms in the membrane environment. The benchmark set and the code is available for public use at github.com/Graylab/MPDock.

Development of a subunit vaccine against the cholangiocarcinoma causing Opisthorchis viverrini: a computational approach.

Opisthorchis viverrini is the etiological agent of the disease opisthorchiasis and related cholangiocarcinoma (CCA). It infects fish-eating mammals and more than 10 million people in Southeast Asia suffered from opisthorchiasis with a high fatality rate. The only effective drug against this parasite is Praziquantel, which has significant side effects. Due to the lack of appropriate treatment options and the high death rate, there is a dire need to develop novel therapies against this pathogen. In this study, we designed a multi-epitope chimeric vaccine design against O. viverrini by using immunoinformatics approaches. Non-allergenic and immunogenic MHC-1, MHC-2, and B cell epitopes of three candidate proteins thioredoxin peroxidase (Ov-TPx-1), cathepsin F1 (Ov-CF-1) and calreticulin (Ov-CALR) of O. viverrini, were predicted to construct a potent multiepitope vaccine. The coverage of the HLA-alleles of these selected epitopes was determined globally. Four vaccine constructs made by different adjuvants and linkers were evaluated in the context of their physicochemical properties, antigenicity, and allergenicity. Protein-protein docking and MD simulation found that vaccines 3 was more stable and had a higher binding affinity for TLR2 and TLR4 immune receptors. In-silico restriction cloning of vaccine model led to the formation of plasmid constructs for expression in a suitable host. Finally, the immune simulation showed strong immunological reactions to the engineered vaccine. These findings suggest that the final vaccine construct has the potential to be validated by in vivo and in vitro experiments to confirm its efficacy against the CCA causing O. viverrini.

Comprehensive study of chiral herbicide flusulfinam uptake, translocation, degradation, and subcellular distribution in rice (Oryza sativa L.)

The biological behavior of flusulfinam, a potential commercial chiral herbicide for rice, has not been well explored. Herein, the uptake of chiral flusulfinam by rice and its transport, degradation, and subcellular distribution in rice (Oryza sativa L.) were investigated. The enantiomeric fraction (EF) in roots was 0.54 during 0 d to 7 d in hydroponic laboratory conditions. The bioconcentration factor of flusulfinam enantiomers was 2.1, suggesting an absence of observed enantioselectivity in the absorption process. Notably, the EF in the shoots decreased to 0.35 on the 7th day. The translocation factors of R- and S-flusulfinam were 0.12 and 0.27, respectively, indicating a preferential transfer of the S-flusulfinam from the root to the shoot. Flusulfinam was identified in the root after spraying. The translocation factors of R- and S-flusulfinam were consistently similar, signifying the capacity for downward movement without enantioselectivity. Interestingly, the degradation half-lives of R- and S-flusulfinam in the total plant were 5.50 and 5.06 d (p < 0.05), respectively, supporting the preferential degradation of S-flusulfinam throughout the total plant. Flusulfinam primarily entered the roots via the apoplastic pathway and was subsequently transported within the plant through aquaporins and ion channels. The subcellular distribution experiment revealed the predominant accumulation of flusulfinam enantiomers in soluble components (84%) with no enantioselectivity in these processes. There was upregulation lipid transfer protein-2 and carboxylesterases15 genes, which could explain the preferential transport and degradation of S-flusulfinam. This study is important in assessing the environmental risk associated with flusulfinam and ensuring food safety.

SpSIZ1 from hyperaccumulator Sedum plumbizincicola orchestrates SpABI5 to fine-tune cadmium tolerance.

Sedum plumbizincicola is a renowned hyperaccumulator of cadmium (Cd), possesses significant potential for eco-friendly phytoremediation of soil contaminated with Cd. Nevertheless, comprehension of the mechanisms underpinning its Cd stress response remains constrained, primarily due to the absence of a comprehensive genome sequence and an established genetic transformation system. In this study, we successfully identified a novel protein that specifically responds to Cd stress through early comparative iTRAQ proteome and transcriptome analyses under Cd stress conditions. To further investigate its structure, we employed AlphaFold, a powerful tool for protein structure prediction, and found that this newly identified protein shares a similar structure with Arabidopsis AtSIZ1. Therefore, we named it Sedum plumbizincicola SIZ1 (SpSIZ1). Our study revealed that SpSIZ1 plays a crucial role in positively regulating Cd tolerance through its coordination with SpABI5. Overexpression of SpSIZ1 significantly enhanced plant resistance to Cd stress and reduced Cd accumulation. Expression pattern analysis revealed higher levels of SpSIZ1 expression in roots compared to stems and leaves, with up-regulation under Cd stress induction. Importantly, overexpressing SpSIZ1 resulted in lower Cd translocation factors (Tfs) but maintained relatively constant Cd levels in roots under Cd stress, leading to enhanced Cd stress resistance in plants. Protein interaction analysis revealed that SpSIZ1 interacts with SpABI5, and the expression of genes responsive to abscisic acid (ABA) through SpABI5-dependent signaling was significantly up-regulated in SpSIZ1-overexpressing plants with Cd stress treatment. Collectively, our results illustrate that SpSIZ1 interacts with SpABI5, enhancing the expression of ABA downstream stress-related genes through SpABI5, thereby increasing Cd tolerance in plants.

A study on soil remediation of hexavalent chromium pollution using nano-sized zinc oxide and Miscanthus lutarioriparius

Hexavalent chromium (Cr(VI)) pollution poses significant health and ecological risks warranting cost-effective remediation. This study investigated the efficacy of zinc oxide nanoparticles (nZnO) and Miscanthus lutarioriparius synergism for Cr(VI) immobilization and stabilization. nZnO characterized by XRD, SEM-EDS and DLS was amended to 3 mg kg−1 Cr(VI) spiked soil pots at 0.5 % and 1 %. M. lutarioriparius seedlings were then transplanted and grown for 3 months. Results showed increase in residual soil Cr(III) from negligible to 68.9 % upon 1 % nZnO indicating reduction of Cr(VI). Maximum decline of 76.3 % in total Cr(VI) confirmed immobilization. Batch adsorption experiments revealed rising Cr(VI) removal from 61.3 % to 83.7 % by increase in nZnO dose from 0.2 to 1 g L−1. M. lutarioriparius demonstrated hyperaccumulator ability uptaking 208.3 and 156.8 mg kg−1 Cr in roots and shoots respectively. Restricted root-shoot translocation factor of 0.79 aided suitability for phytostabilization. The plant-nZnO synergy enhanced remediation efficiency as confirmed by tolerance index restoration from 38.6 % to 100 %. Increased growth performance reflected mitigation of toxicity by restricted bioavailability. Overall, the nanoremediation strategy displayed high potential for effective in situ stabilization of Cr(VI) contamination combining favorable properties of nZnO and plant tolerance mechanisms.