Surface Protein Research Articles

Supported ionic liquids to purify microbial L-Asparaginase

L-Asparaginase (ASNase) is a versatile enzyme that converts L-asparagine into ammonia and aspartic acid. This enzyme has applications in the food industry and health sector. However, high purity ASNase is required, resulting in high production costs. Therefore, in this work, two supported ionic liquids (SILs), specifically silica modified with dimethylbutylpropylammonium chloride ([Si][N3114]Cl) or triethylpropylammonium chloride ([Si][N3222]Cl), were investigated as alternative adsorption materials to purify ASNase. Different conditions were evaluated to improve enzyme purity, including total protein content in the cell extract, contact time, and SIL/cell extract ratio (w/v). Under optimal conditions using [Si][N3114]Cl, a maximum ASNase purification of 6.1-fold is achieved in a single step, resulting from the preferential attachment of other proteins on [Si][N3114]Cl SIL. According to the results, hydrophobic interactions rule the selective adsorption of protein impurities from the cell extract by the SIL, thereby increasing the ASNase purification levels. This approach offers a significant advantage, not requiring the desorption and elution of the target enzyme, while envisioning the application of SILs in a flow-through elution approach. The protonation state of protein surface was calculated by computational analysis, revealing that positively charged amino acids such as arginine and lysine block the effective binding of the enzyme to the SILs. Overall, if properly designed, SILs are promising alternative supports for the downstream processing of ASNase from cell extracts.

The Hepatitis B Virus PreS1/HBsAg Ratio Is a Predictive Marker for the Occurrence of Hepatocellular Carcinoma

The preS1 region of the large hepatitis B virus (HBV) surface protein is a crucial component in HBV infection; however, its impact on the development of hepatocellular carcinoma (HCC) remains unknown. This study investigated the relationship between serum preS1 levels and hepatocarcinogenesis in patients with chronic hepatitis B (CHB). The preS1 levels were measured in 531 patients with CHB without a history of HCC. Among the patients, 293 HBV carriers who had never received nucleotide/nucleoside analog (NA) therapy had their preS1 levels measured at their first visit (non-NA group), and 238 patients who had received NA therapy had their preS1 levels measured at the start of NA administration (NA group). The two groups had no significant differences in hepatitis B surface antigen (HBsAg) levels; however, the NA group’s preS1/HBsAg ratio was significantly higher. The preS1/HBsAg ratio was significantly different between patients with CHB not meeting the NA treatment criteria and patients with chronic hepatitis and cirrhosis who were eligible for NA treatment. The predictors of HCC development were analyzed, and the preS1/HBsAg ratio was identified in both groups. The preS1/HBsAg ratio could predict hepatocarcinogenesis in patients with CHB with or without NA administration.

Trimethylamine N-oxide (TMAO) doubly locks the hydrophobic core and surfaces of protein against desiccation stress.

Interactions between proteins and osmolytes are ubiquitous within cells, assisting in response to environmental stresses. However, our understanding of protein-osmolyte interactions underlying desiccation tolerance is limited. Here, we employ solid-state NMR (ssNMR) to derive information about protein conformation and site-specific interactions between the model protein, SH3, and the osmolyte trimethylamine N-oxide (TMAO). The data show that SH3-TMAO interactions maintain key structured regions during desiccation and facilitate reversion to the protein's native state once desiccation stress is even slightly relieved. We identify 10 types of residues at 28 sites involved in the SH3-TMAO interactions. These sites comprise hydrophobic, positively charged, and aromatic amino acids located in SH3's hydrophobic core and surface clusters. TMAO locks both the hydrophobic core and surface clusters through its zwitterionic and trimethyl ends. This double locking is responsible for desiccation tolerance and differs from ideas based on exclusion, vitrification, and water replacement. ssNMR is a powerful tool for deepening our understanding of extremely weak protein-osmolyte interactions and providing insight into the evolutionary mechanism of environmental tolerance.

TCR-like bispecific antibodies toward eliminating infected hepatocytes in HBV mouse models

Therapeutics for eradicating hepatitis B virus (HBV) infection are still limited and current nucleos(t)ide analogs (NAs) and interferon are effective in controlling viral replication and improving liver health, but they cannot completely eradicate the hepatitis B virus and only a very small number of patients are cured of it. The TCR-like antibodies recognising viral peptides presented on human leukocyte antigens (HLA) provide possible tools for targeting and eliminating HBV-infected hepatocytes. Here, we generated three TCR-like antibodies targeting three different HLA-A2.1-presented peptides derived from HBV core and surface proteins. Bispecific antibodies (BsAbs) were developed by fusing variable fragments of these TCR-like mAbs with an anti-CD3ϵ antibody. Our data demonstrate that the BsAbs could act as T cell engagers, effectively redirecting and activating T cells to target HBV-infected hepatocytes in vitro and in vivo. In HBV-persistent mice expressing human HLA-A2.1, two infusions of BsAbs induced marked and sustained suppression in serum HBsAg levels and also reduced the numbers of HBV-positive hepatocytes. These findings highlighted the therapeutic potential of TCR-like BsAbs as a new strategy to cure hepatitis B.

A novel recombinant Theileria annulata surface protein as an antigen in indirect enzyme-linked immunosorbent assay for the serological diagnosis of tropical theileriosis

Background and Aim: Theileria annulata infection in cattle causes major economic losses in livestock production in many Central Asian countries, including the southern region of Kazakhstan. This study aimed to obtain a recombinant T. annulata surface protein (TaSP) and to investigate its possible use as an antigen in an indirect enzyme-linked immunosorbent assay (ELISA) for the serological diagnosis of bovine theileriosis. Materials and Methods: Recombinant TaSP was obtained by cloning a polymorphic region of the TaSP gene, expressing it in Escherichia coli strain BL21, and purifying it by metal chelating chromatography. An indirect ELISA using recombinant TaSP as an antigen was developed and evaluated for the detection of T. annulata-specific antibodies in plasma samples from 69 cows polymerase chain reaction (PCR)-positive or PCR-negative for T. annulata and/or Theileria orientalis from southern Kazakhstan. Results: The obtained recombinant protein had a molecular weight of 32 kDa, and mass spectrometry analysis of the purified protein identified it as a fragment of the surface protein of T. annulata. Initial testing of 69 field plasma samples from cattle showed that the results of indirect ELISA using TaSP as an antigen agreed substantially with those of T. annulata PCR (κ: 0.78). The relative sensitivity and specificity of indirect ELISA were 88.7% and 100%, respectively, using PCR as a reference. There was no evidence of cross-reaction with T. orientalis. Conclusion: Initial results using recombinant TaSP as an antigen in indirect ELISA are promising and support the widespread use of this assay for routine diagnosis and T. annulata seroprevalence studies in cattle in Kazakhstan and possibly neighboring countries. Keywords: cattle, indirect enzyme-linked immunosorbent assay, Kazakhstan, recombinant T. annulata surface protein, Theileria annulata.

Modification of soybean lipophilic protein based on pH-shifting and high-pressure homogenization: Focus on structure, physicochemical properties and delivery vehicle

High-pressure homogenization and pH-shifting can be used to modify soybean lipophilic protein (SLP), and to enhance its ability to deliver vitamin B12. The structural changes of SLP were analyzed by multispectral techniques and the results showed that secondary and tertiary structures of SLP were altered by modification. The modification unfolded the SLP structure, released more free hydrogen ions, and increased positive charge density on the protein surface. Also, the solubility of modified SLP increased by maximum of 34.75 %. Furthermore, molecular docking showed that complexes were formed between SLP and vitamin B12 mainly through hydrogen bonding and hydrophobic interactions, and the encapsulation rate of modified SLP was maximally increased by 2.3 %. In vitro digestion showed that modified SLP enhanced stability and bioaccessibility of vitamin B12. This study provides theoretical basis for modification of SLP and effective delivery of bioactive substances.

A clinically used anti-human papilloma virus agent (3-hydroxyphthalic anhydride-modified bovine β-lactoglobulin) has a potential for topical application to prevent sexual transmission of monkeypox virus.

A global outbreak of monkeypox (mpox) caused by the mpox virus (MPXV) has posed a serious threat to public health worldwide, thus calling for the urgent development of antivirals and vaccines to curb its further spread. In this study, we screened 41 anhydride-modified proteins and found that 3-hydroxyphthalic anhydride-modified β-lactoglobulin (3HP-β-LG), a clinically used anti-HPV agent, was highly effective in inhibiting infection of vaccinia virus Tiantan strain (VACV-VTT) and MPXV. Mechanistic studies demonstrated that 3HP-β-LG bound to the virus, not the host cell, by targeting the early stage of virus entry, possibly through the interaction between the amino acids with negatively charges in 3HP-β-LG and the key amino acids with positive charges in the target region of A29L, a key surface protein of MPXV. A synergistic effect was observed when 3HP-β-LG was combined with tecovirimat, a small-molecule antiviral drug approved by the United States Food and Drug Administration and the European Medicine Agency for the treatment of smallpox and mpox. Because of its clinically proven safety and stability, 3HP-β-LG shows promise for further development as a prophylactic agent to prevent the sexual transmission of MPXV.

Preparation Method and Quality Evaluation of Novel Frozen Human Platelets

To optimize the technical parameters related to the preparation of novel frozen human platelets and formulate corresponding protocol for its preparation. Novel frozen human platelets were prepared with O-type bagged platelet-rich plasma (PRP), the key technical parameters (DMSO addition, incubation time, centrifugation conditions, etc.) of the preparation process were optimized, and the quality of the frozen platelets was evaluated by routine blood tests, apoptosis rate, platelet activation rate and surface protein expression level. In the preparation protocol of novel frozen human platelets, the operation of centrifugation to remove supernatant was adjusted to before the procedure of platelets freezing, and the effect of centrifugation on platelets was minimal when the centrifugation condition was 800×g for 8 min. In addition, platelets incubated with DMSO for 30 min before centrifugation exhibited better quality after freezing and thawing. The indexes of novel frozen human platelets prepared with this protocol remained stable after long-term cryopreservation. The preparation technique of novel frozen human platelets was established and the protocol was formulated. It was also confirmed that the quality of frozen platelets could be improved by incubating platelets with DMSO for 30 min and then centrifuging them at 800×g for 8 min in the preparation of novel frozen human platelets.

Endothelial protein disulfide isomerase A1 enhances membrane stiffness and platelet-endothelium interaction in hyperglycemia via SLC3A2 and LAMC1

BackgroundDiabetes carries an increased risk of cardiovascular disease and thromboembolic events. Upon endothelial dysfunction, platelets bind to endothelial cells to precipitate thrombus formation; however, it is unclear which surface proteins regulate platelet-endothelium interaction. We and others have shown that peri/epicellular protein disulfide isomerase A1 (pecPDI) influences the adhesion and migration of vascular cells. ObjectivesWe investigated whether pecPDI regulates adhesion-related molecules on the surface of endothelial cells and platelets that influence the binding of these cells in hyperglycemia. MethodsImmunofluorescence was used to assess platelet-endothelium interaction in vitro, cytoskeleton reorganization, and focal adhesions. Hydrogen peroxide production was assessed via Amplex Red assays (ThermoFisher Scientific). Cell biophysics was assessed using atomic force microscopy. Secreted proteins of interest were identified through proteomics (secretomics), and targets were knocked down using small interfering RNA. Protein disulfide isomerase A1 (PDI) contribution was assessed using whole-cell PDI or pecPDI inhibitors or small interfering RNA. ResultsPlatelets of healthy donors adhered more onto hyperglycemic human umbilical vein endothelial cells (HUVECs). Endothelial, but not platelet, pecPDI regulated this effect. Hyperglycemic HUVECs showed marked cytoskeleton reorganization, increased H2O2 production, and elongated focal adhesions. Indeed, hyperglycemic HUVECs were stiffer compared with normoglycemic cells. PDI and pecPDI inhibition reversed the abovementioned processes in hyperglycemic cells. A secretomics analysis revealed 8 proteins secreted in a PDI-dependent manner by hyperglycemic cells. Among these, we showed that genetic deletion of LAMC1 and SLC3A2 decreased platelet-endothelium interaction and did not potentiate the effects of PDI inhibitors. ConclusionEndothelial pecPDI regulates platelet-endothelium interaction in hyperglycemia through adhesion-related proteins and alterations in endothelial membrane biophysics.

Comparison of EV characterization by commercial high-sensitivity flow cytometers and a custom single-molecule flow cytometer.

High-sensitivity flow cytometers have been developed for multi-parameter characterization of single extracellular vesicles (EVs), but performance varies among instruments and calibration methods. Here we compare the characterization of identical (split) EV samples derived from human colorectal cancer (DiFi) cells by three high-sensitivity flow cytometers, two commercial instruments, CytoFLEX/CellStream, and a custom single-molecule flow cytometer (SMFC). DiFi EVs were stained with the membrane dye di-8-ANEPPS and with PE-conjugated anti-EGFR or anti-tetraspanin (CD9/CD63/CD81) antibodies for estimation of EV size and surface protein copy numbers. The limits of detection (LODs) for immunofluorescence and vesicle size based on calibration using cross-calibrated, hard-dyed beads were ∼10 PE/∼80nm EV diameter for CytoFLEX and ∼10 PEs/∼67nm for CellStream. For the SMFC, the LOD for immunofluorescence was 1 PE and ≤ 35nm for size. The population of EVs detected by each system (di-8-ANEPPS+/PE+ particles) differed widely depending on the LOD of the system; for example, CellStream/CytoFLEX detected only 5.7% and 1.5% of the tetraspanin-labelled EVs detected by SMFC, respectively, and median EV diameter and antibody copy numbers were much larger for CellStream/CytoFLEX than for SMFC as measured and validated using super-resolution/single-molecule TIRF microscopy. To obtain a dataset representing a common EV population analysed by all three platforms, we filtered out SMFC and CellStream measurements for EVs below the CytoFLEX LODs as determined by bead calibration (10 PE/80nm). The inter-platform agreement using this filtered dataset was significantly better than for the unfiltered dataset, but even better concordance between results was obtained by applying higher cutoffs (21 PE/120nm) determined by threshold analysis using the SMFC data. The results demonstrate the impact of specifying LODs to define the EV population analysed on inter-instrument reproducibility in EV flow cytometry studies, and the utility of threshold analysis of SMFC data for providing semi-quantitative LOD values for other flow cytometers.

Septins promote macrophage pyroptosis by regulating gasdermin D cleavage and ninjurin-1-mediated plasma membrane rupture

The septin cytoskeleton is primarily known for roles in cell division and host defense against bacterial infection. Despite recent insights, the full breadth of roles for septins in host defense is poorly understood. In macrophages, Shigella induces pyroptosis, a pro-inflammatory form of cell death dependent upon gasdermin D (GSDMD) pores at the plasma membrane and cell surface protein ninjurin-1 (NINJ1) for membrane rupture. Here, we discover that septins promote macrophage pyroptosis induced by lipopolysaccharide (LPS)/nigericin and Shigella infection, but do not affect cytokine expression or release. We observe that septin filaments assemble at the plasma membrane, and cleavage of GSDMD is impaired in septin-depleted cells. We found that septins regulate mitochondrial dynamics and the expression of NINJ1. Using a Shigella-zebrafish infection model, we show that septin-mediated pyroptosis is an invivo mechanism of infection control. The discovery of septins as a mediator of pyroptosis may inspire innovative anti-bacterial and anti-inflammatory treatments.

Detection of Wolbachia in field‐collected Aedes aegypti mosquitoes from Jeddah, Saudi Arabia

AbstractRecent reports have disclosed the occurrence of Wolbachia in Aedes aegypti. Our study detected Wolbachia infection in Ae. aegypti by screening wild adult mosquitoes using two Wolbachia‐specific molecular markers. Overall, 444 adult Ae. aegypti mosquitoes were collected from April 2022 to October 2022 in Jeddah, Saudi Arabia. Each individual sample was processed and screened for the presence of Wolbachia using selected markers, the Wolbachia‐specific 16S rDNA and the Wolbachia surface protein gene (wsp), under optimized polymerase chain reaction (PCR) conditions, and sequenced. In total, 39 (8.78%) and 48 (10.81%) individual mosquito samples were determined to be infected with Wolbachia using the wsp and 16S rDNA markers, respectively. By utilizing two Wolbachia‐specific molecular markers, our study demonstrated the presence of Wolbachia from individual Ae. aegypti samples. Our results showed a low rate of Wolbachia infection and inferred that the detected strain belongs to supergroup B.

Development and characterization of a portable electrochemical aptasensor for IsdA protein and Staphylococcus aureus detection.

Staphylococcus aureus (S. aureus) is recognized as one of the most common causes of gastroenteritis worldwide. This pathogen is a major foodborne pathogen that can cause many different types of various infections, from minor skin infections to lethal blood infectious diseases. Iron-regulated surface determinant protein A (IsdA) is an important protein on the S. aureus surface. It is responsible for iron scavenging via interaction with hemoglobin, haptoglobin, and hemoglobin-haptoglobin complexes. This study develops a portable aptasensor for IsdA and S. aureus detection using aptamer-modified gold nanoparticles (AuNPs) integrated into screen-printed carbon electrodes (SPCEs). The electrode system was made of three parts, including a carbon counter electrode, an AuNPs/carbon working electrode, and a silver reference electrode. The aptamer by Au-S bonding was conjugated on the electrode surface to create the aptasensor platform. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were utilized to investigate the binding interactions between the aptasensor and the IsdA protein. CV studies showed a linear correlation between varying S. aureus concentrations within the range of 101 to 106CFU/mL, resulting in a limit of detection (LOD) of 0.2CFU/mL. The results demonstrated strong reproducibility, selectivity, and sensitivity of the aptasensor for enhanced detection of IsdA, along with about 93% performance stability after 30days. The capability of the aptasensor to directly detect S. aureus via the IsdA surface protein binding was further investigated in a food matrix. Overall, the aptasensor device showed the potential for rapid detection of S. aureus, serving as a robust approach to developing real-time aptasensors to identify an extensive range of targets of foodborne pathogens and beyond.

CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea.

Sorting signals are crucial for the anchoring of proteins to the cell surface in archaea and bacteria. These proteins often feature distinct motifs at their C-terminus, cleaved by sortase or sortase-like enzymes. Gram-positive bacteria exhibit the LPXTGX consensus motif, cleaved by sortases, while Gram-negative bacteria employ exosortases recognizing motifs like PEP. Archaea utilize exosortase homologs known as archaeosortases for signal anchoring. Traditionally identification of such C-terminal sorting signals was performed with profile Hidden Markov Models (pHMMs). The Cell-Wall PREDiction (CW-PRED) method introduced for the first time a custom-made class HMM for proteins in Gram-positive bacteria that contain a cell wall sorting signal which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues. Here we present a new and updated version of CW-PRED for predicting C-terminal sorting signals in Archaea, Gram-positive, and Gram-negative bacteria. We used a large training set and several model enhancements that improve motif identification in order to achieve better discrimination between C-terminal signals and other proteins. Cross-validation demonstrates CW-PRED's superiority in sensitivity and specificity compared to other methods. Application of the method in reference proteomes reveals a large number of potential surface proteins not previously identified. The method is available for academic use at http://195.251.108.230/apps.compgen.org/CW-PRED/ and as standalone software.

α-Bungarotoxin labelling of AMPA receptor-associated TARPs in living neurons

In mammalian central neurons AMPARs are clustered at glutamatergic synapses where they mediate fast excitatory transmission. In addition to four pore-forming subunits (GluA1-4), AMPARs contain auxiliary transmembrane AMPAR regulatory proteins (γ2, γ3, γ4, γ5, γ7 or γ8) whose incorporation can vary between neuron types, brain regions, and stages of development. As well as modulating the functional properties of AMPARs, these auxiliary subunits play a central role in AMPAR trafficking. Directly visualizing TARPs could therefore provide a valuable insight into mechanisms underlying these processes. Although antibodies are routinely used for the detection of surface proteins, our experience suggests anti-TARP antibodies are too bulky to access their target, possibly due to close interactions between the extracellular domains of TARP and AMPAR subunits. We therefore assessed the utility of a small monovalent probe – fluorescent α-bungarotoxin (α-Btx) – for TARP labelling in living neurons. We inserted the bungarotoxin binding site (BBS) within the extracellular domain of TARPs to enable their detection in cells exposed to fluorescent α-Btx. Focusing on the prototypical TARP γ2, we demonstrate that the small size of fluorescent α-Btx allows it to bind to the BBS-tagged TARP when associated with AMPARs. Importantly, labelled γ2 enhances AMPAR function in the same way as unmodified γ2. In living neurons, fluorescent α-Btx-labelled γ2 associates with AMPAR clusters at synapses. As a proof-of-principle, we employed our method to compare the surface trafficking of γ2 and γ7 in cerebellar stellate neurons. Our approach provides a simple way to visualize TARPs within AMPARs in living cells.

Bulky glycocalyx drives cancer invasiveness by modulating substrate-specific adhesion.

The majority of the eukaryotic cell surface is decorated with a layer of membrane-attached polysaccharides and glycoproteins collectively referred to as the glycocalyx. While the formation of a bulky glycocalyx has been associated with the cancer progression, the mechanisms by which the glycocalyx regulates cancer invasiveness are incompletely understood. We address this question by first documenting subtype-specific expression of the major glycocalyx glycoprotein Mucin-1 (MUC1) in breast cancer patient samples and breast cancer cell lines. Strikingly, glycocalyx disruption led to inhibition of 2D motility, loss of 3D invasion, and reduction of clonal scattering in breast cancer cells at the population level. Tracking of 2D cell motility and 3D invasiveness of MUC1-based sorted subpopulations revealed the fastest motility and invasiveness in intermediate MUC1-expressing cells, with glycocalyx disruption abolishing these effects. While differential sensitivity in 2D motility is attributed to a nonmonotonic dependence of focal adhesion size on MUC1 levels, higher MUC1 levels enhance 3D invasiveness via increased traction generation. In contrast to inducing cell rounding on collagen-coated substrates, high MUC1 level promotes cell adhesion and confers resistance to shear flow on substrates coated with the endothelial surface protein E-selectin. Collectively, our findings illustrate how MUC1 drives cancer invasiveness by differentially regulating cell-substrate adhesion in a substrate-dependent manner.

Imputing abundance of over 2500 surface proteins from single-cell transcriptomes with context-agnostic zero-shot deep ensembles.

Cell surface proteins serve as primary drug targets and cell identity markers. The emergence of techniques like CITE-seq has enabled simultaneous quantification of surface protein abundance and transcript expression for multimodal data analysis within individual cells. The published data have been utilized to train machine learning models for predicting surface protein abundance based solely from transcript expression. However, the small scale of proteins predicted and the poor generalization ability for these computational approaches across diverse contexts, such as different tissues or disease states, impede their widespread adoption. Here we propose SPIDER (surface protein prediction using deep ensembles from single-cell RNA-seq), a context-agnostic zero-shot deep ensemble model, which enables the large-scale prediction of cell surface protein abundance and generalizes better to various contexts. Comprehensive benchmarking shows that SPIDER outperforms other state-of-the-art methods. Using the predicted surface abundance of >2500 proteins from single-cell transcriptomes, we demonstrate the broad applications of SPIDER including cell type annotation, biomarker/target identification, and cell-cell interaction analysis in hepatocellular carcinoma and colorectal cancer.

A Novel Liquid Biopsy Method Based on Specific Combinations of Vesicular Markers Allows Us to Discriminate Prostate Cancer from Hyperplasia.

Prostate cancer is the second most common cancer in males worldwide, and its incidence is rising. Early detection is crucial for improving the outcomes, but the current screening methods have limitations. While prostate-specific antigen (PSA) testing is the most widely used screening tool, it has poor specificity, leading to a high rate of false positives and unnecessary biopsies. The existing biopsy techniques are invasive and are associated with complications. The liquid biopsy methods that analyze the biomarkers in blood or other bodily fluids offer a non-invasive and more accurate alternative for detecting and characterizing prostate tumors. Here, we present a novel liquid biopsy method for prostate cancer based on the identification of specific proteins in the extracellular vesicles isolated from the blood of patients with prostate cancer. We observed that a specific combination of sEV proteins is a sensitive indicator of prostate cancer. Indeed, we found that the number of clusters expressed by specific combinations of either intra-vesicular (STAT3 and CyclinD1) or surface proteins (ERBB3, ALK, and CD81) allowed us to significantly discriminate the patients with prostate cancer from the individuals with hyperplasia. This new liquid biopsy method has the potential to improve prostate cancer screening by providing a non-invasive and more accurate diagnostic tool.

Immunodominant Protein of Kyasanur Forest Disease Virus: A retrospective study

Kyasanur forest disease is a febrile illness with hemorrhages caused by the Kyasanur Forest disease virus (KFDV) of the Flaviviridae family. KFD was first documented as an illness among forest dwellers in Kyasanur Forest (Shimoga) in Karnataka in the year 1957. Currently, KFD infections are not treated with effective, licensed therapies and existing treatment approaches are mostly limited to treating symptoms and providing supportive care. In the biology of KFDV, the major envelope glycoprotein E, a surface protein in Flavivirus plays an essential role. E protein contains structural elements that contribute to penetration, viral attachment and fusion, host range, cell tropism, hemagglutination, as well as virus virulency and diminution in the course of natural infection or immunization. The in silico studies were carried out on the proteins of KFD to determine the immunodominant characteristics and showed that E (envelope) protein can be considered as the most immunodominant among the polyproteins. In summary, E protein was revealed to be non-allergenic, more antigenic and immunogenic when compared to other proteins and plays a crucial role in pathogenesis and immune evasion, which mediates virus entry into the host cell, controls immunogenicity and plays a key role in phenotypic and immunogenic characteristics. A detailed study on E protein would open new horizons that can lead to better therapeutic agents and promising vaccine candidates and to save mankind.

Computer‐Aided Protein Surface Modification Strategy to Improve the Thermostability of α‐Amylase

AbstractStability under high‐temperature environments is crucial for amylase to function in starch‐based industries. This study develops a method of modifying protein surfaces by combining computer‐aided tools including FoldX, PoPMuSiC, Discovery Studio, and I‐Mutant 2.0 with conserved sequence analysis. A truncated α‐amylase ∆AmyPTG from Parageobacillus thermoglucosidasius DSMZ 2542 is rationally designed through this method to improve its thermostability. Seven single‐site variants are constructed and five of them displayed enhanced thermostability. Next, three double‐site variants are constructed with one particularly successful double‐site variant N31RT213R, exhibiting a 4.3‐fold longer half‐life at 80 °C. Notably, the specific activity of N31RT213R reaches 10 567.16 U mg−1, higher than ∆AmyPTG (6645.43 U mg−1). When applied to the corn starch liquefaction reaction, the mutant N31RT213R gets a higher yield of product concentration of about 255.70 µg mL−1, compared to 190.72 µg mL−1 for ∆AmyPTG. Intramolecular forces analysis and surface electrostatic charges analysis are conducted to determine possible causes for the improvement. Also, molecular dynamics simulation is used to analyze the flexibility shifts of the entire protein. This innovative rational engineering approach has proven to be a successful strategy for the selection of hot spots for protein thermostability evolution and has the potential to be applied to other enzymes.