Amino Acid Residues Research Articles

Design and Analytical Evaluation of Novel Cardiac Troponin Assays Targeting Multiple Forms of the Cardiac Troponin I-Cardiac Troponin T-Troponin C Complex and Fragmentation Forms.

Current studies suggest that cardiac troponin (cTn) forms in the circulation may vary in different clinical scenarios. Our aim was to design a combination of cTn assays specific to the main cTn forms and to evaluate their analytical performance. We developed immunoassays specific for measuring (1) long-cTnT cTnI-cTnT-TnC (ITC) ternary complex, with cTnT in long form without cleavage at the C-terminal amino acids residue 189-223, designated "long-cTnT ITC complex assay;" (2) both the long-cTnT ITC complex plus short-cTnT ITC complex, designated "hs-total ITC complex assay;" (3) the central part of cTnT of both the long-cTnT ITC complex and free cTnT, designated "hs-cTnT assay." Sex-specific 99th percentile upper reference limits (URLs) were determined. High-sensitivity performance was assessed by examining the imprecision and detectable results above limit of detection (LoD) in the healthy population. Both complex immunoassays exhibited excellent analytical sensitivity, precision, and specificity. The 99th percentile URLs were as follows: long-cTnT ITC complex: male 0.90 ng/L, female 0.87 ng/L; hs-total ITC complex: male 16.15 ng/L, female 10.08 ng/L; hs-cTnT: male 15.57 ng/L, female 14.28 ng/L. The total imprecision at or below the sex-specific 99th percentile URLs was <5% for all assays. The hs-total ITC complex and the hs-cTnT assays showed >50% of measurable concentrations above the LoD. However, <20% were measurable for the long-cTnT ITC complex assay. The cTn assays detected concentrations of major cTn forms in the circulation with high sensitivity, precision, and specificity, supporting their use for monitoring cTn complex and fragmentation forms during myocardial injuries.

CBFβ Regulates RUNX3 ADP-Ribosylation to Mediate Homologous Recombination Repair.

RUNX3 is a master developmental transcriptional factor that has been implicated as a tumor suppressor in many cancers. However, the exact role of RUNX3 in cancer pathogenesis remains to be completely elucidated. Recently, it has emerged that RUNX3 is involved in the DNA damage response. Here, we demonstrate that heterodimerization of RUNX3 with CBFβ is necessary for its stability by protecting RUNX3 from RUNX3 ADP-ribosylation-dependent ubiquitination and degradation. We further identify new amino acid residues that are targets for PARylation and demonstrate that RUNX3 PARylation at these residues is necessary for localization of RUNX3 to DNA double strand break sites (DBSs). We also demonstrate that both RUNX3 PARylation and CBFβ heterodimerization with RUNX3 positively regulates homologous recombination (HR) repair, in part by promoting the recruitment of CtIP and phospho-RPA2 to the DBSs to mediate HR repair. In summary, we provide evidence that RUNX3 regulates HR repair activity in a PARylation-dependent manner.

Comprehensive analysis of lysine lactylation and its potential biological significance in clear cell renal cell carcinoma

BackgroundClear cell renal cell carcinoma (ccRCC) is a common histological subtype of malignant renal neoplasm. Protein lysine lactylation (Kla) plays a crucial role in tumor metabolic reprogramming. However, little is known regarding the distribution and potential biological functions of Kla in ccRCC. This study aimed to systematically investigate the role of Kla in ccRCC.MethodsA total of 12 ccRCC samples were collected from 6 patients. Western blotting was performed to determine the trend of Kla-modified proteins in ccRCC. Liquid chromatography–tandem mass spectrometry was used to quantitatively analyze Kla in ccRCC. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) network analyses were conducted to clarify the biological functions and interactional relationships of differentially lactylated proteins (DLPs).ResultsIn total, 239 DLPs, including 441 lactylated sites, were identified by comparing ccRCC tissues with adjacent normal tissues. Kla-related enzymes have a higher affinity for alanine than for other amino acid residues in ccRCC. Subcellular localization analysis revealed that most DLPs were localized in the cytoplasm and mitochondria. GO enrichment analysis showed that most of the DLPs were enriched in metabolism-associated biological processes, including the purine ribonucleotide, monocarboxylic acid, ribonucleoside triphosphate, purine nucleoside triphosphate, and ATP metabolic processes. KEGG analysis indicated that most DLPs were also enriched in metabolism-related pathways, including glycolysis, amino acid (valine, leucine, and isoleucine) degradation, pyruvate metabolism, fatty acid degradation, and the citrate cycle. The top 20 hub proteins were screened from the PPI network based on their degree ranks.ConclusionsThis study revealed the role of Kla in ccRCC, which will extend our understanding of the potential molecular mechanisms underlying ccRCC formation and progression. These key Kla-modified proteins may be promising therapeutic targets for the treatment of ccRCC. However, further molecular experiments are required to validate these findings.

Molecular modeling, synthesis and biological evaluation of caffeic acid based Dihydrofolate reductase inhibitors

Dihydrofolate reductase (DHFR) is an enzyme that plays a crucial role in folate metabolism, which is essential for cell growth and division. DHFR has been identified as a molecular target for numerous diseases due to its significance in various biological processes. DHFR inhibitors can disrupt folate metabolism by inhibiting DHFR, leading to the inhibition of cell growth. So, a series of caffeic acid derivatives were designed, synthesized, characterized and evaluated for their in vitro ability to inhibit DHFR, as well as their antimicrobial and anticancer properties. Among all synthesized compounds, compound CE11 exhibited the highest DHFR inhibitory activity, with an IC50 value of 0.048 µM, which is approximately four times more potent than methotrexate. Compound CE11 exhibited similar docking performance to methotrexate, binding to the same site and engaging key residues such as Glh30, Phe31, Phe34, and Ser59. It also fit snugly in the hydrophobic pocket of modeled protein. Moreover, substantial hydrophobic interactions were noted between the ligand and the hydrophobic amino acid residues of DHFR. This effectively secured the derivative within the restricted substrate cavity. Furthermore, compound CE11 demonstrated a significant anticancer activity against MCF-7 breast cancer cell line, with an IC50 value of 5.37 ± 0.16 µM. Compounds CE3 and CE15 displayed better antibacterial activity compared to trimethoprim and comparable to ampicillin against the gram-positive bacteria S. aureus. Moreover, compounds CE3 and CE15 have shown better antibacterial activity than standard trimethoprim, ampicillin and tetracycline against the gram-negative bacteria, particularly P. aeruginosa and E. coli. Molecular docking analysis of CE3 revealed that it firmly entrapped into the active site of enzyme through hydrophobic interaction with hydrophobic residues. Additionally, it forms hydrogen bonds with important amino acid residues Ala7, Asn18, and Thr121 with excellent docking score and binding energy (-9.9, -71.77 kcal/mol). These interactions might be contributed to the significant DHFR inhibition and antimicrobial activity. The generated model holds potential value in facilitating the development of a novel category of DHFR inhibitors as anticancer and antimicrobial agents.

CLK1 Activates YAP to Promote Intrahepatic Cholangiocarcinogenesis.

Cdc2-like kinase 1 (CLK1) has dual-specificity kinase ability to phosphorylate tyrosine and serine/threonine protein residues. CLK1 regulates many physiological processes and has been shown to contribute to multiple types of cancer. Here, we investigated the functional role of CLK1 during intrahepatic cholangiocarcinoma (ICC) development. The expression of CLK1 was elevated in ICC tumors, and patients with high expression of CLK1 demonstrated poor prognosis. In hydrodynamically transfected mouse models, CLK1 alone was insufficient to induce ICC, whereas CLK1 cooperated with AKT (AKT/CLK1) to trigger ICC initiation. In addition, overexpression of CLK1 in ICC cells facilitated proliferation in vitro and tumor growth in vivo, while loss of CLK1 elicited the opposite effects. Moreover, RNAseq analysis indicated that high levels of CLK1 corresponded with activation of the Hippo-YAP signaling pathway. Consistently, the AKT/CLK1 murine tumors displayed upregulation of YAP as well as its downstream targets. Furthermore, loss or pharmacological inhibition YAP in ICC cells inhibited CLK1-induced growth, and deletion of Yap completely retarded the induction of AKT/CLK1 tumors. Mechanistically, 4D-label free mass spectrometry and co-immunoprecipitation assays revealed WWC2 as a potential mediator of CLK1-YAP cascade. Collectively, the current findings identify a critical role for CLK1 in promoting ICC development and indicate that inhibiting YAP might be an effective approach for perturbing CLK1-mediated tumorigenesis.

Non-affinity platform for processing knob-into-hole bispecific antibody

Bispecific antibodies hold significant potential as next-generation biotherapeutics owing to their ability to simultaneously bind to two targets. However, the development of bispecific antibodies as biotherapeutics has been hindered by the high levels of byproducts produced, including both high molecular weight and low molecular weight variants. In addition, the inevitable expression of homodimers in host cells presents further obstacles to the commercial development of bispecific antibodies as therapeutics. These byproducts, which share similar physicochemical properties with the target, pose several challenges for downstream purification processes. In this study, we present a non-protein A purification platform that employ a one-step polishing chromatography to purify bispecific antibodies. Mixed-mode Capto adhere resin was used to capture the target protein at pH 7.90 ± 0.10, followed by anion exchange chromatography as a polishing step. Overall, the results of this two-step chromatography purification method demonstrated at final product purity of 98% as assessed by size-exclusion high-performance liquid chromatography (SEC-HPLC) and 98% by reversed-phase-high-performance liquid chromatography (RP-HPLC), with residual host cell proteins controlled at 10 ppm and an excellent recovery rate of approximately 60%. This study presents a non-protein A capture platform, offering a simplified, streamlined, and competitive alternative to conventional affinity chromatography.Graphical

Site directed mutagenesis reveals functional importance of conserved amino acid residues within the N-terminal domain of Dpb2 in budding yeast.

In spite of being dispensable for catalysis, Dpb2, the second largest subunit of leading strand DNA polymerase (Polymerase ε) is essential for cell survival in budding yeast. Dpb2 physically connects polymerase epsilon with the replicative helicase (CMG,Cdc45-Mcm-GINS) by interacting with its Psf1 subunit. Dpb2-Psf1 interaction has been shown to be critical for incorporating polymerase ε into the replisome. Site-directed mutagenesis studies on conserved amino acid residues within the N-terminal domain of Dpb2 led to identification of key amino acid residues involved in interaction with Psf1 subunit of GINS. These amino acid residues are found to be well conserved among Dpb2 orthologues in higher eukaryotes thereby indicating the protein-protein interaction to be evolutionarily conserved. Replicating cells are known to mount a strong replicative stress response and DNA damage response upon exposure to diverse range of stressors. Here, we show that the absence of the N-terminal domain of Dpb2 increases the vulnerability of the budding yeast cells towards the cytotoxic effects of hydroxyurea (HU) and methyl methane sulphonate (MMS). Our results illustrate the importance of N-terminal domain of Dpb2 not only during replisome assembly but also in coordinating stress response in budding yeast. Considering high degree of sequence conservation across eukaryotes, Dpb2 subunit of leading-strand DNA polymerase appears to have important implications in maintenance of genome integrity.

Oxidation of thiol groups in membrane proteins inhibits the fertilization ability and motility of sperm by suppressing calcium influx.

The redox state of thiol groups derived from cysteine residues in proteins regulates cellular functions. Changes in the redox state of thiol groups in the epididymis are involved in sperm maturation. Furthermore, the redox state of thiol groups in proteins changes during the process of sperm capacitation. However, the effect of the redox state of thiol groups in sperm membrane proteins on the fertilization ability of sperm has not been studied. Therefore, in this study, we oxidized thiol groups in sperm membrane proteins using 5,5-dithiobis-(2-nitrobenzoic acid) (DTNB), which is a thiol-selective oxidizing agent, and examined the effect of oxidation of these thiol groups on the fertilization ability of sperm. Oocytes and sperm were obtained from C57BL/6J mice, and Jcl:ICR mice were used as recipients for embryo transfer. Oxidation of the thiol groups by DTNB decreased the in vitro fertilization rate, and removal of the zona pellucida recovered the fertilization rate. DTNB treatment decreased the amplitude of the lateral head, which is an indicator of hyperactivation, and suppressed an increase in the intracellular calcium ion concentration, which is essential for hyperactivation. These findings suggest that oxidation of thiol groups in sperm membrane proteins can decrease the fertility of sperm by suppressing calcium ion influx and hyperactivation.

Genome-Wide Identification and Evolutionary Analysis of Functional BBM-like Genes in Plant Species

Background/Objectives: BABY BOOM (BBM), a transcription factor from the APETALA2 (AP2) protein family, plays a critical role in somatic embryo induction and apomixis. BBM has now been widely applied to induce apomixis or enhance plant transformation and regeneration efficiency through overexpression or ectopic expression. However, the structural and functional evolutionary history of BBM genes in plants is still not well understood. Methods: The protein sequences of 10 selected plant species were used to locate the branch of BBM-Like by key domain identification and phylogenetic tree construction. The identified BBML genes were used for further conserved motif identification, gene structural analysis, miRNA binding site prediction, cis-acting element prediction, collinear analysis, protein–protein interaction network construction, three-dimensional structure modeling, molecular docking, and expression pattern analysis. Results: A total of 24 BBML proteins were identified from 10 representative plant species. Phylogenetic relationship analysis displayed that BBML proteins from eudicots and monocots were divided into two clusters, with monocots exhibiting a higher number of BBMLs. Gene duplication events indicated that whole genome/segmental duplication were the primary drivers of BBML genes’ evolution in the tested species, with purifying selection playing a key role during evolution processes. Comparative analysis of motif, domains, and gene structures revealed that most BBMLs were highly evolutionarily conserved. The expression patterns of BBML genes revealed significant tissue specificity, particularly in the root and embryo. We also constructed protein–protein interaction networks and molecular docking models to identify functional pathways and key amino acid residues of BBML proteins. The functions of BBMLs may differ between monocots and eudicots, as suggested by the functional enrichment of interacting proteins. Conclusions: Our research delved into the molecular mechanism, evolutionary relationships, functional differentiation, and expression patterns of BBML genes across plants, laying the groundwork for further investigations into the molecular properties and biological roles of BBMLs.

Characterization of Cardiac Troponin Fragment Composition Reveals Potential for Differentiating Etiologies of Myocardial Injury.

Increased cardiac troponin (cTn) concentrations occur in acute myocardial injury and chronic diseases. Characterization of cTn composition in the circulation may assist in differentiating etiologies of myocardial injury. Our goal was to study cTn composition and kinetics in patients following type 1 myocardial infraction (T1MI), cardiac procedures, and chronic heart diseases to establish the relationship between cTn composition and clinical diagnosis. Plasma samples were collected from 201 patients with T1MI, 78 undergoing cardiac surgeries, and 218 with chronic cardiomyopathy or chronic heart failure. Major cTn forms in the circulation and their ratios were analyzed using cTn composition immunoassays, targeting (a) the long-cTnT cTnI-cTnT-TnC (ITC) ternary complex, short-cTnT ITC complex cleaved at amino acids residues 189-223 of cTnT, and the binary cTnI-TnC (IC) complex, and designated the "high-sensitivity (hs)-cTnI assay;" (b) the long-cTnT ITC complex, and designated the "long-cTnT ITC complex assay;" (c) the long-cTnT ITC complex and short-cTnT ITC complex, and designated the "hs-total ITC complex assay;" and (d) the central part of cTnT of both the long-cTnT ITC complex and free cTnT, and designated the "hs-cTnT assay." Early-stage T1MI patients showed a high ratio of long-cTnT ITC complex to cTnI (long-cTnT ITC complex/cTnI, R1). Similarly, patients after acute cardiac surgery exhibited increased cTn concentrations with high R1, which decreased rapidly. In chronic disease, cTn composition exhibited stable and low R1 and high ratios of cTnT to cTnI (cTnT/cTnI, R3). Kinetic differences in multiple cTn forms contribute to the differentiation between acute injury and chronic disease, with a high proportion of long-cTnT ITC complex implying occurrence of acute injury.

Natural Gomesin-like Peptides with More Selective Antifungal Activities

Background: Antimicrobial peptides are generally considered promising drug candidates for combating resistant bacterial infections. However, the selectivity of their action may vary significantly. Natural gomesin, isolated from haemocytes of the tarantula Acanthoscurria gomesiana, demonstrates a broad spectrum of antimicrobial activities, being the most effective against pathogenic fungi. Methods: Here, we searched for variants of natural gomesin-like peptides and produced their recombinant analogs in the bacterial expression system. The antimicrobial activities of the obtained peptides were tested against a panel of bacterial and yeast strains, and their toxicity towards human cells was examined. Results: Most of the new analogs of gomesin have primary structures homologous to that of the natural gomesin; however, they have fewer amino acid residues and post-translational modifications. One of the discovered analogs, the His-rich shorter peptide from the spider Dysdera sylvatica, designated as DsGom, displays antifungal activity comparable with that of natural gomesin. In the process of the structural–functional study of DsGom, it was shown that this analog retains a basic mechanism of action similar to that of natural gomesin. The DsGom analog has a significantly better toxicity profile as compared to gomesin. At the same time, the loss of the first Arg residue reduces, but does not annul, the antifungal activity of DsGom. Moreover, the acidification of the growth medium reduces the loss of the antifungal activity of this analog. Conclusions: The discovered natural gomesin-like peptides display more selective antifungal activities as compared to gomesin. The low cytotoxicity of DsGom, combined with its high antifungal activity and stability, allows us to consider it a promising drug candidate for the treatment of fungal infections, especially those caused by fungi of the Candida genus.

Protein Modeling with DEER Spectroscopy.

Double electron-electron resonance (DEER) combined with site-directed spin labeling can provide distance distributions between selected protein residues to investigate protein structure and conformational heterogeneity. The utilization of the full quantitative information contained in DEER data requires effective protein and spin label modeling methods. Here, we review the application of DEER data to protein modeling. First, we discuss the significance of spin label modeling for accurate extraction of protein structural information and review the most popular label modeling methods. Next, we review several important aspects of protein modeling with DEER, including site selection, how DEER restraints are applied, common artifacts, and the unique potential of DEER data for modeling structural ensembles and conformational landscapes. Finally, we discuss common applications of protein modeling with DEER data and provide an outlook.

Beneficial Soil Fungus Kills Predatory Nematodes with Dehydropeptides Translocating into the Animal Gut.

Mortierella alpina is a mold fungus that has gained attention for its positive correlation with soil health, plant growth, and applications as a crop biocontrol agent to suppress the threats of nematode pests. To date, the mechanisms underlying the protective traits of M. alpina against these plant parasites have remained elusive. Here we report that abundantly produced peptidic biosurfactants, malpinin A-D, exhibit robust inhibitory activity against nematodes. Nematode assays with malpinin congeners and chemically synthesized analogues revealed that the dehydro amino acid is critical for activity, whereas the N-terminal amino acid residues modulate the lipophilicity. Complementary imaging by fluorescence microscopy and Raman microspectroscopy, using externally fluorescence-labeled, semisynthetic malpinin or a biosynthetically alkyne-tagged probe generated by precursor-directed biosynthesis, visualized the translocation and enrichment of malpinin in the gut of the model nematode Caenorhabditis elegans. Our findings provide valuable insight into the use of M. alpina as a biocontrol agent, emphasizing the ecologically significant role of malpinins as a protective trait. In addition to solving a long-standing riddle, these findings have translational value for applications in agriculture.

Organophosphate Hydrolysis by a Designed Metalloenzyme: Impact of Mutations Explained.

The efficient design of novel enzymes has been attainable only by a combination of theoretical approaches and experimental refinement, suggesting inadequate performance of de novo design protocols. Based on the analysis of the evolutionary trajectory of a designed organophosphate hydrolase, this work aimed at developing and validating the improved theoretical models describing the catalytic activity of five enzyme variants (including wild-type as well as theoretically derived and experimentally refined enzymes) performing the hydrolysis of diethyl 7-hydroxycoumarinyl phosphate. The following aspects possibly important for enzyme design were addressed: the level of theory sufficient for a reliable description of enzyme-reactant interactions, the issue of ground state (GS) destabilization versus transition state (TS) stabilization, and the derivation of the proper side chain rotamers of amino acid residues. For enzyme variants analyzed herein, differential transition state stabilization (DTSS, i.e., preferential TS binding by an enzyme over the GS binding) calculated with a non-empirical model of the interaction energy (i.e., multipole electrostatic plus approximate dispersion terms, MED) displayed a superior performance in ranking the enzyme catalytic activity. The MED DTSS-based systematic rotamer refinement performed with an efficient scanning procedure and accounting for long-range interaction energy terms is an important step capable of unlocking the full potential impact of the given residue that could be otherwise overlooked with a conventional static approach featuring optimization to the nearby minimum. While TS stabilization is the main factor contributing to the increased catalytic activity of the de novo-designed variant studied in this work, directed evolution refinement appears to impact the catalytic activity of another enzyme variant analyzed herein via GS destabilization.

Proline-Selective Electrochemiluminescence Detecting a Single Amino Acid Variation Between A1 and A2 β-Casein Containing Milks.

The proline amino acid and prolyl residues of peptides/proteins confer unique biological and biochemical properties that motivates the development of proline-selective analysis. The study focuses on one specific class of problem, the detection of single amino acid variants involving proline, and reports a Pro-selective electrochemiluminescence (ECL) method. To develop this method, the A1-/A2- variants of milk's β-casein protein are investigated because it is a well-established example and abundant samples are readily available. Specifically, β-casein has 209 amino acids with 34 (or 35) proline residues: the A1-variant has a Pro-to-His substitution at position 67 (relative to the A2 variant). The study shows that proline's strong luminescence allows the generic discrimination of: Pro from other amino acids; an A2-oligopeptide from an A1-oligopeptide; the A2-β-casein variant from the A1-variant; and commercially-available A2 milks from A1-containing regular milks. The evidence indicates that luminescence depends on proline content and accessibility, as well as signal quenching. Compared to conventional immunoassays, the ECL method is simple, rapid, and inexpensive. Further, the ECL-method is Pro-selective (vs molecularly-selective like typical immunoassays) which should make it broadly useful for studying the role of proline in biology and especially useful for tracking the digestion of proline-rich proteins in the diet.

Neuroprotective Potential of Aminonaphthoquinone Derivatives Against Amyloid Beta-Induced Neuronal Cell Death Through Modulation of SIRT1 and BACE1

Alzheimer’s disease (AD) is characterized by the accumulation of tau protein tangles and amyloid-β (Aβ) plaques in the central nervous system (CNS), leading to progressive neurodegeneration. Hence, the discovery of disease-modifying agents capable of delaying the progression is essential for effective management. Aminonaphthoquinone (ANQ) is an attractive pharmacophore with various biological effects. This study explores the neuroprotective potentials of ANQ derivatives (1–18) using in vitro models of AD pathology (i.e., Aβ42-induced SH-SY5Y cells). Findings demonstrated that all compounds mitigated Aβ42-induced cellular damage by preserving cell viability and morphology. Among all, four compounds (10, 12, 16, and 18) showed potent antioxidant activities as well as abilities to minimize AD-related damages (i.e. decreasing intracellular reactive oxygen species (ROS) production, preserving mitochondrial membrane potential (MMP), protecting membrane damage, and modulating beta-secretase 1 (BACE1) activity) with comparable protective effects to the well-known neuroprotectant, resveratrol (RSV). A molecular docking study indicated these compounds could suitably bind to sirtuin 1 (SIRT1) protein with preferable affinity. Key amino acid residues and key functional groups essential for binding interactions were revealed. Target prediction identified a list of possible AD-related targets of these compounds offering insights into their mechanisms of action and suggesting their multifunctional potentials. Additionally, in silico predictions revealed that these candidates showed favorable drug-like properties. Overall, this study highlighted the therapeutic potential of ANQ derivatives in AD treatment, emphasizing the need for further experimental validation and comprehensive investigations to fully realize their therapeutic benefits.

Insights into the structural changes that trigger receptor binding upon proteolytic activation of Bacillus thuringiensis Vip3Aa insecticidal protein.

Bacillus thuringiensis (Bt) bacteria produce different pore forming toxins with insecticidal activity, including Cry and Vip3 proteins. While both Cry and Vip3 cause insect death by forming pores in susceptible lepidopteran larval midgut cells, their mechanisms of action differ. The Vip3Aa protoxin adopts a tetramer-structure, where each monomer has five distinct domains. Upon proteolytic activation, the Vip3 tetramer undergoes a large conformational change forming a syringe like structure that is ready for membrane insertion and pore formation. Here we show that Vip3Aa protoxin had low binding to Spodoptera frugiperda brush border membrane vesicles (BBMV) unlike the activated toxin that bound specifically in a concentration dependent way, suggesting that a structural change upon Vip3Aa proteolytic activation is required for efficient receptor binding. Consistently, the Vip3Aa protoxin showed no toxicity to Sf9 cells compared to the activated toxin. In contrast, Cry1Fa protoxin and its activated toxin, were both highly toxic to Sf9 cells. To identify the region of Vip3 involved in binding to BBMV proteins, different overlapping peptides from Vip3Aa covering domains III, IV and V were expressed, and binding analysis were performed against BBMV, showing that domain III is the primary binding domain. Additionally, domains III, IV and V amino acid residues that become exposed upon activation of Vip3Aa were identified. Mutagenesis of these exposed residues revealed three amino acids (K385, K526 and V529) located in two structural adjacent loops, domain III loop β5-β6 and loop α11-β16 that connects domains III and IV, that are crucial for binding to the midguts of S. frugiperda larvae and for toxicity. Our results demonstrate that proteolytic activation of Vip3Aa exposes a receptor binding region essential for its toxicity.

Analysis of the interaction of influenza a virus nucleoprotein with host cell nucleolin.

Targeting interactions between a virus and a host protein is one of the important approaches to developing antiviral therapies. We previously identified host nucleolin as a novel interacting partner of the influenza A virus nucleoprotein, and it was demonstrated that this interaction restricts virus replication. In the current study, we examined the interaction of nucleolin with the viral nucleoprotein at the domain and amino acid levels using in vitro and in silico approaches. Both approaches demonstrated a direct and specific interaction between these two proteins. Furthermore, it was observed that previous pandemic strains of influenza A virus had specific amino acid residues in their nucleoproteins that were predicted to be critical for interaction with nucleolin. This preliminary analysis provides insights into the binding process, which could be explored for developing antiviral strategies.

Genetic diversity of highly pathogenic avian influenza H5N6 and H5N8 viruses in poultry markets in Guangdong, China, 2020-2022.

H5 highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/96 (Gs/Gd) lineage continue to evolve and cause outbreaks in domestic poultry and wild birds, with sporadic spillover infections in mammals. The global spread of clade 2.3.4.4b viruses via migratory birds since 2020 has facilitated the introduction of novel reassortants to China, where avian influenza of various subtypes have been epizootic or enzootic among domestic birds. To determine the impact of clade 2.3.4.4b re-introduction on local HPAI dynamics, we analyzed the genetic diversity of H5N6 and H5N8 detected from monthly poultry market surveillance in Guangdong, China, between 2020 and 2022. Our findings reveal that H5N6 viruses clustered in clades 2.3.4.4b and 2.3.4.4h, while H5N8 viruses were exclusively clustered in clade 2.3.4.4b. After 2020, the re-introduced clade 2.3.4.4b viruses replaced the clade 2.3.4.4h viruses detected in 2020. The N6 genes were divided into two clusters, distinguished by an 11 amino acid deletion in the stalk region, while the N8 genes clustered with clade 2.3.4.4 H5N8 viruses circulating among wild birds. Genomic analysis identified 10 transient genotypes. H5N6, which was more prevalently detected, was also clustered into more genotypes than H5N8. Specifically, H5N6 isolates contained genes derived from HPAI H5Nx viruses and low pathogenic avian influenza in China, while the H5N8 isolates contained genes derived from HPAI A(H5N8) 2.3.4.4b and A(H5N1) 2.3.2.1c. No positive selection on amino acid residues associated with mammalian adaptation was found. Our results suggest expanded genetic diversity of H5Nx viruses in China since 2021 with increasing challenges for pandemic preparedness.IMPORTANCESince 2016/2017, clade 2.3.4.4b H5Nx viruses have spread via migratory birds to all continents except Oceania. Here, we evaluated the impact of the re-introduction of clade of 2.3.4.4b on highly pathogenic avian influenza (HPAI) virus genetic diversity in China. Twenty-two H5N6 and H5N8 HPAI isolated from monthly surveillance in two poultry markets in Guangdong between 2020 and 2022 were characterized. Our findings showed that clade 2.3.4.4h, detected in 2020, was replaced by clade 2.3.4.4b in 2021-2022. H5N6 (n = 18) were clustered into more genotypes than H5N8 (n = 4), suggesting that H5N6 may possess better replication fitness in poultry. Conversely, the H5N8 genotypes are largely derived from the clade 2.3.4.4b wild bird isolates. As clade 2.3.4.4b continues to spread via migratory birds, it is anticipated that the genetic diversity of H5N6 viruses circulating in China may continue to expand in the coming years. Continuous efforts in surveillance, genetic analysis, and risk assessment are therefore crucial for pandemic preparedness.

Lineage-specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases.

Most eukaryotes possess two Rad51/RecA family DNA recombinases that are thought to have arisen from an ancient gene duplication event: Rad51, which is expressed in both mitosis and meiosis; and Dmc1, which is only expressed in meiosis. To explore the evolutionary relationship between these recombinases, here, we present high-resolution CryoEM structures of S. cerevisiae Rad51 filaments and S. cerevisiae Dmc1 filaments bound to ssDNA, which reveal a pair of stacked interfacial aromatic amino acid residues that are nearly universally conserved in Rad51 but are absent from Dmc1. We use a combination of bioinformatics, genetic analysis of natural sequence variation, and deep mutational analysis to probe the functionally tolerated sequence space for these stacked aromatic residues. Our findings demonstrate that the functional landscape of the interfacial aromatic residues within the Rad51 filament is highly constrained. In contrast, the amino acids at the equivalent positions within the Dmc1 filament exhibit a broad functional landscape. This work helps highlight the distinct evolutionary trajectories of these two eukaryotic recombinases, which may have contributed to their functional and mechanistic divergence.