Palmitoylation of γb protein directs a dynamic switch between Barley stripe mosaic virus replication and movement.

Viral replication and movement are intimately linked; however, the molecular mechanisms regulating the transition between replication and subsequent movement remain largely unknown. We previously demonstrated that the Barley stripe mosaic virus (BSMV) γb protein promotes viral replication and movement by interacting with the αa replicase and TGB1 movement proteins. Here, we found that γb is palmitoylated at Cys-10, Cys-19, and Cys-60 in Nicotiana benthamiana, which supports BSMV infection. Intriguingly, non-palmitoylated γb is anchored to chloroplast replication sites and enhances BSMV replication, whereas palmitoylated γb protein recruits TGB1 to the chloroplasts and forms viral replication-movement intermediate complexes. At the late stages of replication, γb interacts with NbPAT15 and NbPAT21 and is palmitoylated at the chloroplast periphery, thereby shifting viral replication to intracellular and intercellular movement. We also show that palmitoylated γb promotes virus cell-to-cell movement by interacting with NbREM1 to inhibit callose deposition at the plasmodesmata. Altogether, our experiments reveal a model whereby palmitoylation of γb directs a dynamic switch between BSMV replication and movement events during infection.

Barley stripe mosaic virus γb protein disrupts chloroplast antioxidant defenses to optimize viral replication.

The plant antioxidant system plays important roles in response to diverse abiotic and biotic stresses. However, the effects of virus infection on host redox homeostasis and how antioxidant defense pathway is manipulated by viruses remain poorly understood. We previously demonstrated that the Barley stripe mosaic virus (BSMV) γb protein is recruited to the chloroplast by the viral αa replicase to enhance viral replication. Here, we show that BSMV infection induces chloroplast oxidative stress. The versatile γb protein interacts directly with NADPH-dependent thioredoxin reductase C (NTRC), a core component of chloroplast antioxidant systems. Overexpression of NbNTRC significantly impairs BSMV replication in Nicotiana benthamiana plants, whereas disruption of NbNTRC expression leads to increased viral accumulation and infection severity. To counter NTRC-mediated defenses, BSMV employs the γb protein to competitively interfere with NbNTRC binding to 2-Cys Prx. Altogether, this study indicates that beyond acting as a helicase enhancer, γb also subverts NTRC-mediated chloroplast antioxidant defenses to create an oxidative microenvironment conducive to viral replication.

PKSPS: a novel method for predicting kinase of specific phosphorylation sites based on maximum weighted bipartite matching algorithm and phosphorylation sequence enrichment analysis.

With the development of biotechnology, a large number of phosphorylation sites have been experimentally confirmed and collected, but only a few of them have kinase annotations. Since experimental methods to detect kinases at specific phosphorylation sites are expensive and accidental, some computational methods have been proposed to predict the kinase of these sites, but most methods only consider single sequence information or single functional network information. In this study, a new method Predicting Kinase of Specific Phosphorylation Sites (PKSPS) is developed to predict kinases of specific phosphorylation sites in human proteins by combining PKSPS-Net with PKSPS-Seq, which considers protein-protein interaction (PPI) network information and sequence information. For PKSPS-Net, kinase-kinase and substrate-substrate similarity are quantified based on the topological similarity of proteins in the PPI network, and maximum weighted bipartite matching algorithm is proposed to predict kinase-substrate relationship. In PKSPS-Seq, phosphorylation sequence enrichment analysis is used to analyze the similarity of local sequences around phosphorylation sites and predict the kinase of specific phosphorylation sites (KSP). PKSPS has been proved to be more effective than the PKSPS-Net or PKSPS-Seq on different sets of kinases. Further comparison results show that the PKSPS method performs better than existing methods. Finally, the case study demonstrates the effectiveness of the PKSPS in predicting kinases of specific phosphorylation sites. The open source code and data of the PKSPS can be obtained from https://github.com/guoxinyunncu/PKSPS.

First Results from a Broadband Search for Dark Photon Dark Matter in the 44 to 52 µeV Range with a Coaxial Dish Antenna.

We present first results from a dark photon dark matter search in the mass range from 44 to 52 µeV (10.7-12.5 GHz) using a room-temperature dish antenna setup called GigaBREAD. Dark photon dark matter converts to ordinary photons on a cylindrical metallic emission surface with area 0.5 m^{2} and is focused by a novel parabolic reflector onto a horn antenna. Signals are read out with a low-noise receiver system. A first data taking run with 24 days of data does not show evidence for dark photon dark matter in this mass range, excluding dark photon photon mixing parameters χ≳10^{-12} in this range at 90% confidence level. This surpasses existing constraints by about 2 orders of magnitude and is the most stringent bound on dark photons in this range below 49 µeV.

PhosAF: An integrated deep learning architecture for predicting protein phosphorylation sites with AlphaFold2 predicted structures.

Phosphorylation is indispensable in comprehending biological processes, while biological experimental methods for identifying phosphorylation sites are tedious and arduous. With the rapid growth of biotechnology, deep learning methods have made significant progress in site prediction tasks. Nevertheless, most existing predictors only consider protein sequence information, that limits the capture of protein spatial information. Building upon the latest advancement in protein structure prediction by AlphaFold2, a novel integrated deep learning architecture PhosAF is developed to predict phosphorylation sites in human proteins by integrating CMA-Net and MFC-Net, which considers sequence and structure information predicted by AlphaFold2. Here, CMA-Net module is composed of multiple convolutional neural network layers and multi-head attention is appended to obtaining the local and long-term dependencies of sequence features. Meanwhile, the MFC-Net module composed of deep neural network layers is used to capture the complex representations of evolutionary and structure features. Furthermore, different features are combined to predict the final phosphorylation sites. In addition, we put forward a new strategy to construct reliable negative samples via protein secondary structures. Experimental results on independent test data and case study indicate that our model PhosAF surpasses the current most advanced methods in phosphorylation site prediction.

Efficacy and Safety of Huangqi Guizhi Wuwu Decoction for Oxaliplatin-Induced Peripheral Neurotoxicity: A Systematic Review and Meta-Analysis.

Objective: Oxaliplatin is a first-line chemotherapy drug for the treatment of colorectal cancer, but its induced oxaliplatin-induced peripheral neurotoxicity (OIPN) affect the chemotherapy process and quality of life of tumor patients. OIPN is a serious and potentially permanent side effect of cancer treatment. Currently, no unified standard has been established for preventing and treating OIPN in Western medicine. Therefore, it is very important to seek effective prevention and treatment measures. Many clinical trials have reported that Huangqi Guizhi Wuwu decoction can effectively prevent OIPN, but substantial evidence base to support this treatment is lacking. We collected existing literature and evaluated the clinical efficacy and safety of Huangqi Guizhi Wuwu decoction for OIPN by performing a meta-analysis. Methods: We systematically searched China National Knowledge Internet (CNKI), VIP, Wan Fang Database, Pubmed, EMBASE, and Cochrane Library from inception through to Oct 2022 to identify only randomized controlled trials examining the prevention of OIPN using Huangqi Guizhi Wuwu decoction. This search was supplemented by manual retrieval, including dissertations and conference papers. All data were analyzed using RevMan 5.3 software. Results: A total of 18 papers involving 564 patients in the treatment group and 523 patients in the control group were included. A total of 17 articles reported the overall incidence of peripheral neurotoxicity (I² = 0%), and the overall incidence of peripheral neurotoxicity in the treatment group was 0.27 times higher than in the control group (95% CI: 0.20-0.36). A total of 16 articles reported the incidence of level III-IV severe peripheral neurotoxicity (I² = 0%), which was 0.16 times higher in the treatment group than in the control group (95% CI: 0.09-0.32). In the Huangqi Guizhi Wuwu VS no-interference subgroup, it showed that the incidence of severe peripheral neurotoxicity in the treat group was significantly lower than in the control group (OR:0.13, 95% CI:0.06-0.28). But in the Huangqi Guizhi Wuwu VS west medicine therapy subgroup, no significant difference between Huangqi Quizhi Wuwu and conventional Western medicine was observed for the prevention and treatment of severe OIPN (OR:0.37, 95% CI:0.09-1.53). A total of 2 articles were reported median nerve conduction velocity (I² = 51.2%); and no significant difference was found between the treatment and control groups (SMD: 1.43; 95% CI: 0.80-2.08); 4 studies showed Huangqi Guizhi Wuwu decoction did not increase the incidence of chemotherapy-related adverse reactions and was safe. Conclusions: Our current findings support the application of Huangqi Guizhi Wuwu decoction for the clinical prevention and treatment of patients with OIPN. However, high-quality RCT research is still needed to further exploration. The potential impact of Huangqi Guizhi Wuwu decoction on the quality of life or treatment compliance of cancer patients needs further research.

Discovery of Cinnamic Acid Derivatives as Potent Anti-H. pylori Agents.

Antibiotics are currently used for the treatment of Helicobacter pylori (H. pylori), which is confirmed to be the major cause of gastric disorders. However, the long-term consumption of antibiotics has already caused antibiotic resistance and side effects in vivo. Therefore, there is an emerging need for searching for safe and effective anti-H. pylori agents. Inspired by the excellent bioactivities of cinnamic acid, a series of cinnamic acid derivatives (compounds 1-30) were synthesized and determined for H. pylori inhibition. The initial screening revealed that compound 23, a 2,4-dinitro cinnamic acid derivative containing 4-methoxyphenol, showed excellent H. pylori inhibition with an MIC value of 4 µM. Further studies indicated that compound 23 showed anti-bacterial activity and had a bactericidal effect on H. pylori due to the destruction of the bacterial structure. Molecular docking analysis revealed that the 2,4-dinitro groups in cinnamic acid moiety formed hydrogen bonding with amino acid residues in an active pocket of H. pylori protein. Interestingly, the ester moiety fitted into the hydrophobic pocket, attaining additional stability to compound 23. Above all, the present study reveals that compound 23 could be considered a promising anti-H. pylori agent to treat H. pylori causing gastritis.

Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking.

MOTIVATION: Efficiently identifying genes based on gene expression level have been studied to help to classify different cancer types and improve the prediction performance. Logistic regression model based on regularization technique is often one of the effective approaches for simultaneously realizing prediction and feature (gene) selection in genomic data of high dimensionality. However, standard methods ignore biological group structure and generally result in poorer predictive models. RESULTS: In this article, we develop a classifier named Stacked SGL that satisfies the criteria of prediction, stability and selection based on sparse group lasso penalty by stacking. Sparse group lasso has a mixing parameter representing the ratio of lasso to group lasso, thus providing a compromise between selecting a subset of sparse feature groups and introducing sparsity within each group. We propose to use stacked generalization to combine different ratios rather than choosing one ratio, which could help to overcome the inadaptability of sparse group lasso for some data. Considering that stacking weakens feature selection, we perform a post hoc feature selection which might slightly reduce predictive performance, but it shows superior in feature selection. Experimental results on simulation demonstrate that our approach enjoys competitive and stable classification performance and lower false discovery rate in feature selection for varying sets of data compared with other regularization methods. In addition, our method presents better accuracy in three public cancer datasets and identifies more powerful discriminatory and potential mutation genes for thyroid carcinoma. AVAILABILITY AND IMPLEMENTATION: The real data underlying this article are available from https://github.com/huanheaha/Stacked_SGL; https://zenodo.org/record/5761577#.YbAUyciEwk2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Barley stripe mosaic virus γb protein targets thioredoxin h-type 1 to dampen salicylic acid-mediated defenses.

Salicylic acid (SA) acts as a signaling molecule to perceive and defend against pathogen infections. Accordingly, pathogens evolve versatile strategies to disrupt the SA-mediated signal transduction, and how plant viruses manipulate the SA-dependent defense responses requires further characterization. Here, we show that barley stripe mosaic virus (BSMV) infection activates the SA-mediated defense signaling pathway and upregulates the expression of Nicotiana benthamiana thioredoxin h-type 1 (NbTRXh1). The γb protein interacts directly with NbTRXh1 in vivo and in vitro. The overexpression of NbTRXh1, but not a reductase-defective mutant, impedes BSMV infection, whereas low NbTRXh1 expression level results in increased viral accumulation. Similar with its orthologs in Arabidopsis (Arabidopsis thaliana), NbTRXh1 also plays an essential role in SA signaling transduction in N. benthamiana. To counteract NbTRXh1-mediated defenses, the BSMV γb protein targets NbTRXh1 to dampen its reductase activity, thereby impairing downstream SA defense gene expression to optimize viral cell-to-cell movement. We also found that NbTRXh1-mediated resistance defends against lychnis ringspot virus, beet black scorch virus, and beet necrotic yellow vein virus. Taken together, our results reveal a role for the multifunctional γb protein in counteracting plant defense responses and an expanded broad-spectrum antibiotic role of the SA signaling pathway.

Casein Kinase 1 Regulates Cytorhabdovirus Replication and Transcription by Phosphorylating a Phosphoprotein Serine-Rich Motif.

Casein kinase 1 (CK1) family members are conserved Ser/Thr protein kinases that regulate important developmental processes in all eukaryotic organisms. However, the functions of CK1 in plant immunity remain largely unknown. Barley yellow striate mosaic virus (BYSMV), a plant cytorhabdovirus, infects cereal crops and is obligately transmitted by the small brown planthopper (SBPH; Laodelphax striatellus). The BYSMV phosphoprotein (P) exists as two forms with different mobilities corresponding to 42 kD (P42) and 44 kD (P44) in SDS-PAGE gels. Mass spectrometric analyses revealed a highly phosphorylated serine-rich (SR) motif at the C-terminal intrinsically disordered region of the P protein. The Ala-substitution mutant (PS5A) in the SR motif stimulated virus replication, whereas the phosphorylation-mimic mutant (PS5D) facilitated virus transcription. Furthermore, PS5A and PS5D associated preferentially with nucleocapsid protein-RNA templates and the large polymerase protein to provide optimal replication and transcription complexes, respectively. Biochemistry assays demonstrated that plant and insect CK1 protein kinases could phosphorylate the SR motif and induce conformational changes from P42 to P44. Moreover, overexpression of CK1 or a dominant-negative mutant impaired the balance between P42 and P44, thereby compromising virus infections. Our results demonstrate that BYSMV recruits the conserved CK1 kinases to achieve its cross-kingdom infection in host plants and insect vectors.

Identification of genetic susceptibility in preterm newborns with bronchopulmonary dysplasia by whole-exome sequencing: BIVM gene may play a role.

Bronchopulmonary dysplasia (BPD) is a common chronic respiratory disease in preterm infants caused by multifactorial etiology. Genetic factors are involved in the occurrence of BPD, but studies have found that candidate genes have poor reproducibility and are influenced by ethnic heterogeneity; therefore, more exploration is still needed. We performed whole-exon sequencing in 34 preterm infants with BPD and 32 non-BPD control neonates. The data were analyzed and interpreted by Fisher difference comparison, PLINK and eQTL association analysis, KEGG and GO enrichment analysis, STRING tool, Cytoscape software, ProtParam tool, HOPE online software, and GEOR2 analysis on NCBI GEO dataset. BPD has a highly heterogeneity in different populations, and we found 35 genes overlapped with previous whole-exon sequencing studies, such as APOB gene. Arterial and epithelial cell development and energy metabolism pathways affect BPD. In this study, 24 key genes were identified, and BIVM rs3825519 mutation leads to prolonged assisted ventilation in patients with BPD. A novel DDAH1 mutation site (NM_012137: exon1: c.89 T > G: p.L30R) was found in 9 BPD patients. CONCLUSION: BIVM gene rs3825519 mutation may play a role in the pathogenesis of BPD by affecting cilia movement, and the DDAH1 and APOB genes mutations may have a pathogenic role in BPD. WHAT IS KNOWN: • Genetic factors are involved in the occurrence of bronchopulmonary dysplasia. • The candidate genes have poor reproducibility and are influenced by ethnic heterogeneity, therefore, more exploration is still needed. WHAT IS NEW: • We identified the role of susceptible SNPs in BPD in Shenzhen, China, and identified 24 key genes that influence the pathogenesis of BPD, and also found 35 genes overlapped with previous whole exon sequencing studies, such as APOB gene. • We found that BIVM and DDAH1 genes may play a pathogenic role in the pathogenesis of BPD.

LncRNA NR_003508 Suppresses Mycobacterium tuberculosis-Induced Programmed Necrosis via Sponging miR-346-3p to Regulate RIPK1.

Emerging evidence suggests that long non-coding RNAs (LncRNAs) are involved in Mtb-induced programmed necrosis. Among these LncRNAs, LncRNA NR_003508 is associated with LPS-induced acute respiratory distress syndrome. However, whether LncRNA NR_003508 contributes to Mtb-induced programmed necrosis remains undocumented. Firstly, the expression of LncRNA NR_003508 was determined using RT-qPCR and FISH. The protein expression of RIPK1, p-RIPK1, RIPK3, p-RIPK3, MLKL, and p-MLKL was measured by Western blot in RAW264.7 and mouse lung tissues. Furthermore, luciferase reporter assays and bioinformatics were used to predict specific miRNA (miR-346-3p) and mRNA (RIPK1) regulated by LncRNA NR_003508. In addition, RT-qPCR was used to detect the RIPK1 expression in TB patients and healthy peripheral blood. The flow cytometry assay was performed to detect cell necrosis rates. Here we show that BCG infection-induced cell necrosis and increased LncRNA NR_003508 expression. si-NR_003508 inhibited BCG/H37Rv-induced programmed necrosis in vitro or in vivo. Functionally, LncRNA NR_003508 has been verified as a ceRNA for absorbing miR-346-3p, which targets RIPK1. Moreover, RIPK1 expression was elevated in the peripheral blood of TB patients compared with healthy people. Knockdown of LncRNA NR_003508 or miR-346-3p overexpression suppresses cell necrosis rate and ROS accumulation in RAW264.7 cells. In conclusion, LncRNA NR_003508 functions as a positive regulator of Mtb-induced programmed necrosis via sponging miR-346-3p to regulate RIPK1. Our findings may provide a promising therapeutic target for tuberculosis.

Computational prediction and analysis of species-specific fungi phosphorylation via feature optimization strategy.

Protein phosphorylation is a reversible and ubiquitous post-translational modification that primarily occurs at serine, threonine and tyrosine residues and regulates a variety of biological processes. In this paper, we first briefly summarized the current progresses in computational prediction of eukaryotic protein phosphorylation sites, which mainly focused on animals and plants, especially on human, with a less extent on fungi. Since the number of identified fungi phosphorylation sites has greatly increased in a wide variety of organisms and their roles in pathological physiology still remain largely unknown, more attention has been paid on the identification of fungi-specific phosphorylation. Here, experimental fungi phosphorylation sites data were collected and most of the sites were classified into different types to be encoded with various features and trained via a two-step feature optimization method. A novel method for prediction of species-specific fungi phosphorylation-PreSSFP was developed, which can identify fungi phosphorylation in seven species for specific serine, threonine and tyrosine residues (http://computbiol.ncu.edu.cn/PreSSFP). Meanwhile, we critically evaluated the performance of PreSSFP and compared it with other existing tools. The satisfying results showed that PreSSFP is a robust predictor. Feature analyses exhibited that there have some significant differences among seven species. The species-specific prediction via two-step feature optimization method to mine important features for training could considerably improve the prediction performance. We anticipate that our study provides a new lead for future computational analysis of fungi phosphorylation.

The serine/threonine/tyrosine kinase STY46 defends against hordeivirus infection by phosphorylating γb protein.

Protein phosphorylation is a common post-translational modification that frequently occurs during plant-virus interaction. Host protein kinases often regulate virus infectivity and pathogenicity by phosphorylating viral proteins. The Barley stripe mosaic virus (BSMV) γb protein plays versatile roles in virus infection and the coevolutionary arms race between plant defense and viral counter-defense. Here, we identified that the autophosphorylated cytosolic serine/threonine/tyrosine (STY) protein kinase 46 of Nicotiana benthamiana (NbSTY46) phosphorylates and directly interacts with the basic motif domain (aa 19-47) of γb in vitro and in vivo. Overexpression of wild-type NbSTY46, either transiently or transgenically, suppresses BSMV replication and ameliorates viral symptoms, whereas silencing of NbSTY46 leads to increased viral replication and exacerbated symptom. Moreover, the antiviral role of NbSTY46 requires its kinase activity, as the NbSTY46T436A mutant, lacking kinase activity, not only loses the ability to phosphorylate and interact with γb but also fails to impair BSMV infection when expressed in plants. NbSTY46 could also inhibit the replication of Lychnis ringspot virus, another chloroplast-replicating hordeivirus. In summary, we report a function of the cytosolic kinase STY46 in defending against plant viral infection by phosphorylating a viral protein in addition to its basal function in plant growth, development, and abiotic stress responses.

P. aeruginosa biofilm activates the NLRP3 inflammasomes in vitro.

The ability of P.aeruginosa to form biofilms renders common treatments inefficient, thereby promoting chronic infection. Inflammasomes activate caspase-1, which is important for the maturation of IL-1ß and IL-18 and evoke an inflammatory response. We aimed to investigate the activation of inflammasomes induced by P.aeruginosa biofilm. THP-1 cells were mock-infected or infected with PAO1 biofilms. Protein levels of caspase-1 p20, pro-caspase-1, caspase-4 p20, and pro-caspase-4 in THP-1 macrophages were determined by Western blotting. The expression of NLRC4 and NLRP3 was measured by RT-PCR. The production of IL-1ß and IL-18 was monitored using ELISA. P. aeruginosa biofilm significantly elevated caspase-1 levels, and decreased NLRC4 levels. Additionally, caspase-4 and NLRP3 levels were significantly increased. P.aeruginosa biofilm significantly enhanced IL-1ß and IL-18 production. We concluded that P. aeruginosa biofilm induced the production of IL-1ß and IL-18, possibly via NLRP3 inflammasomes, rather than NLRC4 inflammasomes.

A risk scoring system to predict the individual incidence of early-onset colorectal cancer.

BACKGROUND: The incidence of early-onset colorectal cancer (EOCRC) is increasing at an alarming rate and further studies are needed to identify risk factors and to develop prevention strategies. METHODS: Risk factors significantly associated with EOCRC were identified using meta-analysis. An individual risk appraisal model was constructed using the Rothman-Keller model. Next, a group of random data sets was generated using the binomial distribution function method, to determine nodes of risk assessment levels and to identify low, medium, and high risk populations. RESULTS: A total of 32,843 EOCRC patients were identified in this study, and nine significant risk factors were identified using meta-analysis, including male sex, Caucasian ethnicity, sedentary lifestyle, inflammatory bowel disease, and high intake of red meat and processed meat. After simulating the risk assessment data of 10,000 subjects, scores of 0 to 0.0018, 0.0018 to 0.0036, and 0.0036 or more were respectively considered as low-, moderate-, and high-risk populations for the EOCRC population based on risk trends from the Rothman-Keller model. CONCLUSION: This model can be used for screening of young adults to predict high risk of EOCRC and will contribute to the primary prevention strategies and the reduction of risk of developing EOCRC.

The Carboxyl Terminal Regions of P0 Protein Are Required for Systemic Infections of Poleroviruses.

P0 proteins encoded by poleroviruses Brassica yellows virus (BrYV) and Potato leafroll virus (PLRV) are viral suppressors of RNA silencing (VSR) involved in abolishing host RNA silencing to assist viral infection. However, other roles that P0 proteins play in virus infection remain unclear. Here, we found that C-terminal truncation of P0 resulted in compromised systemic infection of BrYV and PLRV. C-terminal truncation affected systemic but not local VSR activities of P0 proteins, but neither transient nor ectopic stably expressed VSR proteins could rescue the systemic infection of BrYV and PLRV mutants. Moreover, BrYV mutant failed to establish systemic infection in DCL2/4 RNAi or RDR6 RNAi plants, indicating that systemic infection might be independent of the VSR activity of P0. Partially rescued infection of BrYV mutant by the co-infected PLRV implied the functional conservation of P0 proteins within genus. However, although C-terminal truncation mutant of BrYV P0 showed weaker interaction with its movement protein (MP) when compared to wild-type P0, wild-type and mutant PLRV P0 showed similar interaction with its MP. In sum, our findings revealed the role of P0 in virus systemic infection and the requirement of P0 carboxyl terminal region for the infection.

Assessment of AI-Based Protein Structure Prediction for the NLRP3 Target.

The recent successes of AlphaFold and RoseTTAFold have demonstrated the value of AI methods in highly accurate protein structure prediction. Despite these advances, the role of these methods in the context of small-molecule drug discovery still needs to be thoroughly explored. In this study, we evaluated whether the AI-based models can reliably reproduce the three-dimensional structures of protein-ligand complexes. The structure we chose was NLRP3, a challenging protein target in terms of obtaining a three-dimensional model both experimentally and computationally. The conformation of the binding pockets generated by the AI models was carefully characterized and compared with experimental structures. Further molecular docking results indicated that AI-predicted protein structures combined with molecular dynamics simulations offers a promising approach in small-molecule drug discovery.

Tobacco Necrosis Virus-AC Single Coat Protein Amino Acid Substitutions Determine Host-Specific Systemic Infections of Nicotiana benthamiana and Soybean.

Plant viruses often infect several distinct host species. Sometimes, viruses can systemically infect a specific host whereas, in other cases, only local infections occur in other species. How viral and host factors interact to determine systemic infections among different hosts is largely unknown, particularly for icosahedral positive-stranded RNA viruses. The Tobacco necrosis virus-A Chinese isolate belongs to the genus Alphanecrovirus in the family Tombusviridae. In this study, we investigated variations in systemic infections of tobacco necrosis virus-AC (TNV-AC) in Nicotiana benthamiana and Glycine max (soybean) by alanine-scanning mutagenesis of the viral coat protein (CP), which is essential for systemic movement of TNV-AC. We found that three amino acids, R169, K177, and Q233, are key residues that mediate varying degrees of systemic infections of N. benthamiana and soybean. Further analysis revealed that variations in systemic trafficking of TNV-AC CP mutants in N. benthamiana and soybean are associated with virion assembly and stability. The CP amino acids K177 and Q233 are highly conserved among all TNV-A isolates and are replaced by Q and K in the TNV-D isolates. We demonstrated that systemic infectivity of either TNV-AC K177A and Q233A or K177Q and Q233K mutants are correlated with the binding affinity of the mutated CPs to the host-specific Hsc70-2 protein. These results expand our understanding of host-dependent long-distance movement of icosahedral viruses in plants.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications.

Accumulative studies have indicated that amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence protein posttranslational modifications (PTMs) and bring about a detrimental effect on protein function. Computational mutation analysis can greatly narrow down the efforts on experimental work. To increase the utilization of current computational resources, we first provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. We also discuss the challenges that are faced while developing novel in silico approaches in the future. The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine.