Protein Structure Research Articles

A Novel Mutation of FOXC1 (P136L) in an Axenfeld-Rieger Syndrome Patient With a Systematized Delusion of Jealousy: A Case Report and Literature Review.

The main features of Axenfeld-Rieger Syndrome (ARS) are ocular, auditory, neurological, and morphological brain abnormalities. Mutations in forkhead box protein C1 (FOXC1) are among the responsible genes causing ARS, but neuropsychiatric features have rarely been reported. The case of an ARS patient (a 77-year-old man) with delusions of jealousy and impairment of working memory, in addition to the main clinical features, glaucoma and leukoencephalopathy, is presented. The mutation in the patient's genome was found with whole exome sequencing and in silico analysis using PolyPhen-2 and SIFT. Furthermore, AlphaFold2 and PyMOL were used to predict the protein structure based on the mutation. A novel mutation at the forkhead domain of FOXC1 gene (c.408C>A, p.Phe136Leu) was found and confirmed in the patient's family, and it was predicted to cause protein damage; the SIFT score was 0, meaning deleterious, and the PolyPhen2 result also indicated damaging (score: 0.997). The predicted protein structure based on the novel mutation was different from that of the native structure. In the literature review, 6 of 95 (6.3%) cases showed neuropsychiatric features. Of them, 5 of 6 (83.3%) mutations were located in the forkhead domain. A novel mutation was found in the FOXC1 gene (c.408C>A, p.Phe136Leu), which possibly induces delusions of jealousy and impairment of working memory, as well as features of ARS, by changing the protein structure. Mutations in that domain of the FOXC1 gene may be important not only for ocular abnormalities but also for brain function.

Exploring structural diversity across the protein universe with The Encyclopedia of Domains.

The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and functional contexts. Identifying domains can enable many functional and evolutionary analyses but has remained challenging because of the sheer scale of the data. Using deep learning methods, we have detected and classified every domain in the AFDB, producing The Encyclopedia of Domains. We detected nearly 365 million domains, over 100 million more than can be found by sequence methods, covering more than 1 million taxa. Reassuringly, 77% of the nonredundant domains are similar to known superfamilies, greatly expanding representation of their domain space. We uncovered more than 10,000 new structural interactions between superfamilies and thousands of new folds across the fold space continuum.

Insights into genomic sequence diversity of the SAG surface antigen superfamily in geographically diverse Eimeria tenella isolates

Eimeria tenella is among the protozoan parasites that cause the infectious disease coccidiosis in chickens, incurring huge economic losses to the global poultry industry. Surface antigens (EtSAGs) involved in host-parasite interaction are potential targets for control strategies. However, the occurrence of genetic diversity for EtSAGs in field populations is unknown, as is the risk of such diversity to the efficacy of EtSAG-based control approaches. Here, the extent of EtSAG genetic diversity and its implications on protein structure and function is assessed. Eighty-seven full-length EtSAG genomic sequences were identified from E. tenella genome assemblies of isolates sampled from continents including North America (United States), Europe (United Kingdom), Asia (Malaysia and Japan) and Africa (Nigeria). Limited diversity was observed in the EtSAG sequences. However, distinctive patterns of polymorphism were identified between EtSAG subfamilies, suggesting functional differences among these antigen families. Polymorphisms were sparsely distributed across isolates, with a small number of variants exclusive to specific geographical regions. These findings enhance our understanding of EtSAGs, particularly in elucidating functional differences among the antigens that could inform the development of more effective and long-lasting anticoccidial control strategies.

Chitosan oligosaccharide efficiently inhibits Cronobacter sakazakii biofilm by interacting with out membrane protein A for regulating CpxRA-mediated cellulose production pathway

Chitosan oligosaccharide (COS) can efficiently inhibit Cronobacter sakazakii (C. sakazakii) biofilm independent on antibacterial activity. However, the mechanism is still unclear. In this study, the role of out membrane protein A (OmpA) and its downstream CpxRA-mediated cellulose production pathway in COS's inhibition on C. sakazakii biofilm were explored. The spectroscopic results were shown that COS could interact with OmpA, and this changed OmpA's second structure and spatial conformation as well as cell membrane permeability and COS uptake. C. sakazakii ΔOmpA strain had a lower cell membrane permeability and COS uptake rate. The interaction between OmpA and COS could further initiate CpxRA system. The regulon cpxP expression level was therefore up-regulated. The deletion of the response regulator cpxR gene reduced inhibitory effect of COS on biofilm. CpxRA system inhibited expression of csgD and adrA, which coded diguanylate cyclase to generate cyclic diguanosine monophosphate (c-di-GMP). The expression of bcsAB was then down-regulated by c-di-GMP, and the cellulose production as well as biofilm were reduced. The addition of exogenous c-di-GMP could mitigate the inhibition of COS on C. sakazakii biofilm. These results not only help to elucidate biofilm inhibition mechanism of COS, but also provided a basis for developing anti-biofilm agents targeted OmpA.

Multi-Omic characterization of the effects of Ocrelizumab in patients with relapsing-remitting multiple sclerosis

The study examined changes in the plasma proteome, metabolome, and lipidome of N = 14 patients with relapsing-remitting multiple sclerosis (RRMS) initiating treatment with ocrelizumab, assayed at baseline, 6 months, and 12 months. Analyses of >4000 circulating biomarkers identified depletion of B-cell associated proteins as the early effect observed following ocrelizumab (OCR) initiation, accompanied by the reduction in plasma abundance of cytokines and cytotoxic proteins, markers of neuronaxonal damage, and biologically active lipids including ceramides and lysophospholipids, at 6 months. B-cell depletion was accompanied by decreases in B-cell receptor and cytokine signaling but a pronounced increase in circulating plasma B-cell activating factor (BAFF). This was followed by an upregulation of a number of signaling and metabolic pathways at 12 months. Patients with higher baseline brain MRI lesion load demonstrated both higher levels of cytotoxic and structural proteins in plasma at baseline and more pronounced biomarker change trajectories over time. Digital cytometry identified a putative increase in myeloid cells and a pro-inflammatory subset of T-cells. Therapeutic effects of ocrelizumab extend beyond CD20-mediated B-cell lysis and implicate metabolic reprogramming, juxtaposing the early normalization of immune activation, cytokine signaling and metabolite and lipid turnover in periphery with changes in the dynamics of immune cell activation or composition. We identify BAFF increase following CD20 depletion as a tentative compensatory mechanism that contributes to the reconstitution of targeted B-cells, necessitating further research.

Exploring the Targets of Dengue Virus and Designs of Potential Inhibitors.

Dengue, a mosquito-borne viral disease spread by the dengue virus (DENV), has become one of the most alarming health issues in the global scenario in recent days. The risk of infection by DENV is mostly high in tropical and subtropical areas of the world. The mortality rate of patients affected with DENV is ever-increasing, mainly due to a lack of anti-dengue viral-specific synthetic drug components. Repurposing synthetic drugs has been an effective tool in combating several pathogens, including DENV. However, only the Dengvaxia vaccine has been developed so far to fight against the deadly disease despite the grave situation, mainly because of the limitations of understanding the actual pathogenicity of the disease. To address this particular issue and explore the actual disease pathobiology, several potential targets, like three structural proteins and seven non-structural (NS) proteins, along with their inhibitors of synthetic and natural origin, have been screened using docking simulation. Exploration of these targets, along with their inhibitors, has been extensively studied in culmination with molecular docking-based screening to potentiate the treatment. These screened inhibitors could possibly be helpful for the designing of new congeneric potential compounds to combat dengue fever and its complications.

Enhancing soy protein isolate flexibility through non-covalent ferulic acid modification: implications for interfacial characteristics and protein-based emulsion performance

This study aims to enhance the flexibility of soy protein isolate (SPI) to improve its functional properties, focusing on the investigated the effects of ferulic acid (FA) on the structure, interfacial behaviour and emulsification performance of SPI. Our study showed that FA induces SPI structures to depolymerization and unfolding primarily through hydrogen bonding and hydrophobic interactions, thereby increasing the flexible structures (random coils and β-turns) of protein. These changes enhanced the interfacial functional properties of SPI, with 150 μmol/g of FA-modified SPI exhibiting the best molecular flexibility, and its emulsification and emulsification stability were improved by 21.26% and 39.86%, respectively, compared to unmodified SPI. In addition, non-covalently modified FA significantly improved emulsions stability. Emulsions stabilized by SPI-FA150 complexes exhibited better storage, heat, and freeze-thaw stability than SPI, with a significant reduction in oxidation products. This relationship between flexibility and function reveals the importance of structural modification in enhancing protein functionality. These discoveries shed new light on flexible protein processing technologies and the application of FA in protein functional modification.

Exploring Free Energy Landscapes for Protein Partitioning into Membrane Domains in All-Atom and Coarse-Grained Simulations.

It is known that membrane environment can impact the structure and function of integral membrane proteins. As such, elucidation of the thermodynamic driving forces governing protein partitioning between membrane domains of varying lipid composition is a fundamental topic in membrane biophysics. Molecular dynamics simulations provide valuable tools for quantitatively characterizing the free energy landscapes governing protein partitioning at the molecular level. In this study, we propose an efficient simulation methodology for the calculation of free energies for the partitioning of transmembrane proteins between liquid-disorder (Ld) and liquid-ordered (Lo) domains in all-atom (AA) phase-separated lipid bilayers. The computed potential of mean force defining the equilibrium partition coefficients is compared for AA and coarse-grained systems. Energy decomposition is used to identify differences in the underlying thermodynamics. Our findings highlight the importance of employing AA models to accurately estimate relevant free energy changes during protein translation between membrane domains.

Construction and evaluation of transdermal delivery system of terbinafine-loaded plant exosomes for the treatment of cutaneous fungal infections

Local transdermal of antifungal agents is a problem that limits the effectiveness of clinical treatment of dermatomycosis. In this study, cucumber-derived plant extracellular vesicles (PEV) were extracted and loaded with the antifungal drug terbinafine (TBF) to form TBF-PEV, which was applied locally to the site of skin fungal infection to improve the transdermal transport capacity of TBF and the antifungal effect in vitro and in vivo. Chemical enhancer and physical enhancer methods were replaced by low immunogenicity and non-irritating PEV. TBF-PEV caused obvious curling and wrinkling in the skin, induced changes in the distribution of skin lipids, and changed the structure and content of skin lipids and proteins, thereby increasing the transdermal efficiency of TBF. The local drug concentration was increased, and the antifungal effect was improved in vitro and in vivo. It was first found that PEV inhibited the growth of Candida albicans with high efflux pump expression. In general, this paper has certain significance in local transdermal treatment of fungal skin infections and reversal of fungal resistance.

Effect of limited hydrolysis on the structure and gel properties of soybean isolate proteins: A comparative study of papain or/and trypsin

Plant protein's gelation is crucial in various food applications, and hydrolysis may enhance their gelation properties. In this study, we prepared soybean protein isolate hydrolysates (SPIH) using trypsin and/or papain, and found significant improvement in the solubility and gelling properties. These proteases broken down the peptide bonds and caused the exposure of hydrophobic groups as well as the unfolding of protein. Low molecular weight (<35 kDa) SPIHs were generated by the two-step enzymatic hydrolysis, showing significant improvements in storage modulus (G′), loss modulus (G″), viscosity, strength, and water-holding capacity (WHC). Among, PT-10 exhibited the highest WHC (61.72 ± 0.36 %), gel strength (4.67 ± 0.12 g), and network cross-linking density (0.33 ± 0.01 mol/m3), while its solubility was also significantly increased up to 254 %. According to the results of gel molecular force interactions, disulfide bonds, hydrophobic interactions and hydrogen bonds involved in the gel network formation. These findings reveal that the appropriate hydrolysis modification may improve SPI gel's properties and expand its application in gel foods.

Surface-induced self-assembly of peptides turns superhydrophobic surface of electrospun fibrous into superhydrophilic one

Current surface modification strategies for electrospun materials always require covalent conjugation technology, which is relatively inefficient and might damage the bioactivity and structure of peptides and proteins. Here we introduce the use of surface-induced self-assembly technology to modify electrospun materials, which is a simple but efficient noncovalent-based process. Results show that the peptide NapFFGRGD forms burr-like structures on the surface of PCL fibers, reducing the water contact angle of the fibers. Adjusting the peptide sequence and salt concentration affects the self-assembly and surface properties of modified PCL fibers. Additionally, we demonstrate the potential application of this surface modification technique for enhancing cellular responses in tissue engineering applications. The research provides valuable insights into the surface modification of PCL fibers and offers a new method for improving the biological compatibility of materials in tissue engineering.

Effects of mono- and dual-frequency ultrasounds on structure and physicochemical properties of faba bean proteins

Faba bean proteins are currently viewed as promising animal protein alternatives. However, certain functional properties e.g. relatively low solubility compared to whey protein isolates, can limit the application of faba bean protein isolates (FPIs) in certain food products. Therefore, it may be desirable to use modification approaches such as the application of ultrasound to alter such limiting physicochemical properties. In this study, Faba Bean Protein Isolates (FPI) were treated by ultrasound with different frequencies (20 kHz, 40 kHz and 20 + 40 kHz) prior to hydration (1 %) at different pH levels (3, 7, and 9). Then the structure and physicochemical properties (i.e. particle size, ζ-potential, surface hydrophobicity, thermal behavior, and solubility) of control and untreated FPIs were investigated. Ultrasound treatment had no obvious effect on the molecular weight of FPIs, whereas it changed the secondary structure of FPIs from a more ordered structure to a more disordered structure. The applied treatment resulted in an increase in surface hydrophobicity across all treatment levels and pHs. It also decreased the particle size of FPI at pH 3, while it increased the particle size at pH 7 and 9, compared to the untreated FPI. In addition, the solubility and thermal properties of FPI were modified through the ultrasound treatment. The higher solubility of FPI could improve its potential to be used as a functional ingredient for many food applications. Ultrasound treatment at 20 kHz and 20 + 40 kHz had more effects on the physiochemical properties of FPI compared to that at 40 kHz. Overall, ultrasound treatment with different frequencies (20 kHz, 40 kHz, and 20 + 40 kHz) modified the structure and physiochemical properties of FPI to different degrees and may be beneficial for the development of FPI for certain food applications.

The anti-fouling activity of solvothermally synthesized Nb2O5-coated Fe ship strip on optimal interactions at the targeted interfaces of barnacle attachments -An Insilico study

Abstract Fouling is a major issue occurring in water-going vessels, such as ships that cause increased surface roughness and drag resistance. The fouling organisms produce extracellular polymeric substances (EPS), which negatively impact water-going vessels. The settlement-inducing protein complex (SIPC) is a contact pheromone that promotes the gregarious settling of barnacle larvae (cyprids). The SIPC can be found in both adult barnacle cuticles and cyprids as transient adhesive secretions (footprints). The presence of SIPC in the footprints plays a critical role during the initial adhesion, which facilitates further settlement. The adsorption of of SIPC on Iron/Fe ship strip(FSS) surface was often found to be irreversible even after physical treatements. For the antifouling studies, Nb2O5 coated FSS were constructed and simulated to analyze the interaction of barnacles Aacp20K protein. For simulation studies, the homology model of barnacles Aacp20K protein is fabricated using the SWISS automated comparative modeling platform. The result of homology model showed a good 3D secondary structure of Aacp20K protein, especially 7q1y template protein. Adsorption location analysis results illustrate that the surface of the FSS coated with Nb2O5 film disfavour the binding of SIPC inhibiting the binding of barnacle cuticles and cyprids. For validating the simulation results, Nb2O5 nanostructure film was synthesized using a solvothermal process and characterized using XRD,SEM and EDS. Furthermore, the wetting behaviour was studied experimentally. The simulations and experimental results indicate Nb2O5-coated FSS as potent anti-fouling surfaces.

Fabrication and characterization of acidic high internal phase emulsion gels stabilized solely by wheat gluten for plant-based mayonnaise

Plant-based diets are currently gaining more popularity as a means of reducing the environmental footprint and promoting human health. Herein, plant protein-based acidic high internal phase emulsion gels (HIPE gels) were fabricated via a facile one-pot approach using wheat gluten (WG) solely. Pre-dissolving WG in edible vinegar-water solution was contributed to the fabrication of stable emulsion gels. Factors that affect the structure and performance of plant proteins as HIPE gels stabilizers were investigated. The results indicated that the stable HIPE gels could be formed with a vinegar concentration between 5 % and 20 % and a WG concentration of 1.0 %–7.5 % only. Microscopy images reveal that a collaboration of the soluble protein molecules adsorption and protein aggregate Pickering stabilization at oil-water interface, which was turned to form stable HIPE gels. In addition, the resulted HIPE gels exhibited shear thinning behavior, viscoelastic features, and good thixotropic recovery, which provide a similar perceived texture and sensory property for formulating egg-free mayonnaise. These findings provide a useful approach to construct HIPE-based softs from low-cost wheat gluten for preparing plant-based mayonnaise.

High-resolution cryo-EM analysis of a Streptococcus pyogenes M-protein/human plasminogen complex.

The importance of human plasminogen (hPg)/plasmin (hPm)/cell receptor complexes in invasiveness of cells has been amply established. The objective of this investigation was to determine a high-resolution structure of a major Group A Streptococcus (GAS) bacterial receptor (PAM) for hPg/hPm when bound on a cell surface to its major ligand, hPg. As a model cell surface with endogenous PAM, we employed engineered PAM-expressing lentivirus (LV) particles. We show that the ectodomain of a PAM-type M-Protein (M-Prt), in complex with hPg, is folded through distinct intra- and inter-domain interactions to a more compact form on the cell surface, thus establishing a new paradigm for membrane-bound M-Prt/ligand structures. These studies provide a framework for addressing the need for treatments of GAS disease by providing a molecular platform to solve structures of virulence-determining membrane proteins.

Effect of polyphenol-hydrocolloids interaction on protein oxidation, structure and water distribution properties of thermally processed meat

Effect of polyphenol-hydrocolloids interaction on protein oxidation, structure and water distribution properties of thermally processed meat

GACT-PPIS: Prediction of protein-protein interaction sites based on graph structure and transformer network

The prediction of protein-protein interaction sites (PPIS) is currently crucial for regulating many biological activities in cells and developing drugs for various diseases. Deep learning-based methods have been proposed for predicting PPIS, significantly reducing the manpower and time costs associated with traditional experimental methods such as yeast two-hybrid, mass spectrometry, and affinity purification. However, the predictive accuracy of these deep learning methods has not yet reached the expected level. Therefore, we introduce a model called GACT-PPIS.The design of the GACT-PPIS algorithm aims to utilize combined information from protein sequences and structures as input to predict protein-protein interaction sites. The core of GACT-PPIS utilizes an Enhanced Graph Attention Network (EGAT) with initial residual and identity mappings, along with a deep Transformer network as the basic units, supplemented by Graph Convolutional Networks (GCN), effectively aggregating information from neighboring nodes for each node. After multiple network layers, the information of the entire protein is also fused into the nodes, and the Transformer network further enhances the model's performance.Experimental results show that GACT-PPIS outperforms the most representative models in terms of Recall, F1-measure, MCC, AUROC, and AUPRC on the benchmark test set (Test-60). Additionally, on other independent test sets (UBTest-31-6), GACT-PPIS leads in terms of Accuracy, Precision, Recall, F1-measure, MCC, AUROC, and AUPRC compared to the most representative models. It is worth noting that GACT-PPIS demonstrates excellent generalization and versatility across different test sets, showcasing good performance on multiple test sets for the same trained GACT-PPIS model.

Pharmacological Activities of Zingiber officinale Roscoe: Inhibition of HSA Protein Glycation, Structure Stability and Function Restoration

Pharmacological Activities of Zingiber officinale Roscoe: Inhibition of HSA Protein Glycation, Structure Stability and Function Restoration

Structural basis for the effects of Ser387 phosphorylation of MgcRacGAP on its GTPase-activating activities for CDC42 and RHOA

MgcRacGAP is a GTPase-activating protein (GAP) for the Rho family GTPases. During cytokinesis, MgcRacGAP localizes to the midbody, where it activates the GTPase activity of Rho family GTPases to facilitate cytokinesis. In the midbody, Aurora B phosphorylates Ser387 within the GAP domain of human MgcRacGAP, a modification that is suggested to influence GTPase preference. However, there are conflicting reports, with some studies indicating that Ser387 phosphorylation does not alter the GTPase preference of MgcRacGAP. This controversy highlights the need for a deeper understanding of the molecular interactions involved, which can be clarified through structural analyses. In the present study, we determined the crystal structures of the wild-type MgcRacGAP GAP domain complexed with CDC42•GDP•AlF4− and the S378D phosphomimetic mutant GAP domain fused with RHOA•GDP•AlF4−. Additionally, crystal structures of the GAP domains were determined for the S387D and S387A mutants. Our analysis revealed that neither GTPase binding nor S387D mutation affected the overall structure of the GAP domain. However, comparison of the CDC42•MgcRacGAP (wild-type) complex with the RHOA-MgcRacGAP(S378D) fusion protein structure indicated that the S387D mutation caused positional shifts in both CDC42 and RHOA relative to MgcRacGAP. These shifts reduced interactions with CDC42 more severely than those with RHOA. In fact, the S387D mutation decreased the GTPase-activating activity of MgcRacGAP toward CDC42, while its impact on RHOA was only moderate. This difference in the rate of activity reduction may play an important role in GTPase preference.

Perspectives Toward an Integrative Structural Biology Pipeline With Atomic Force Microscopy TopographicImages.

After the recent double revolutions in structural biology, which include the use of direct detectors for cryo-electron microscopy resulting in a significant improvement in the expected resolution of large macromolecule structures, and the advent of AlphaFold which allows for near-accurate prediction of any protein structures, the field of structural biology is now pursuing more ambitious targets, including several MDa assemblies. But complex target systems cannot be tackled using a single biophysical technique. The field of integrative structural biology has emerged as a global solution. The aim is to integrate data from multiple complementary techniques to produce a final three-dimensional model that cannot be obtained from any single technique. The absence of atomic force microscopy data from integrative structural biology platforms is not necessarily due to its nm resolution, as opposed to Å resolution for x-ray crystallography, nuclear magnetic resonance, or electron microscopy. Rather a significant issue was that the AFM topographic data lacked interpretability. Fortunately, with the introduction of the AFM-Assembly pipeline and other similar tools, it is now possible to integrate AFM topographic data into integrative modeling platforms. The advantages of single molecule techniques, such as AFM, include the ability to confirm experimentally any assembled molecular models or to produce alternative conformations that mimic the inherent flexibility of large proteins or complexes. The review begins with a brief overview of the historical developments of AFM data in structural biology, followed by an examination of the strengths and limitations of AFM imaging, which have hindered its integration into modern modeling platforms. This review discusses the correction and improvement of AFM topographic images, as well as the principles behind the AFM-Assembly pipeline. It also presents and discusses a series of challenges that need to be addressed in order to improve the incorporation of AFM data into integrative modeling platform.