I-TASSER Server Research Articles

Three-Dimensional Structure of Human Epididymis Protein 4 (HE4): A Protein Modelling of an Ovarian Cancer Biomarker Through In Silico Approach

The Human Epididymis Protein 4 (HE4) biomarker has been extensively investigated for its potential in diagnosing ovarian cancer (OC). For the application of diagnostic techniques and drug delivery, it is crucial to understand the protein tertiary structure. However, the Protein Data Bank (PDB) does not currently contain the three-dimensional (3D) structure of HE4. Therefore, an in silico analysis was conducted to model the HE4 protein using AlphaFold, I-TASSER, and Robetta servers, with the sequence retrieved from UniProt (ID: Q14508). These three servers employed deep learning algorithms, threading templates, and de novo methods, respectively. Subsequently, Molecular Dynamics (MD) simulation using the GROMACS software package improved each 3D structure model, resulting in optimized and refined structures: RF1, RF2, and RF3. PROCHECK and ERRAT programs were employed to assess the structure quality. The Ramachandran plots from PROCHECK indicated that 100% of residues were within the allowed regions for all servers except for I-TASSER. For the refined structures, RF1 and RF3, all residues were concentrated within the allowed regions. According to the ERRAT program, the RF1 model exhibited the highest overall quality factor of 97.701, followed by RF3 and AlphaFold models with scores of 94.643 and 93.750, respectively. After these validations, RF1 emerged as the most accurately predicted 3D structure of HE4 and has one tunnel identified by CAVER 3.0 tool that facilitates the transportation of small particles to the active site, supported by FTsite and PrankWeb binding site predictions. This model holds potential for various computational studies, including the development of OC diagnostic kits. It will enhance our comprehension of the interactions between the protein and other biomolecules.

3D STRUCTURE AND FUNCTION ANALYSIS OF RECOMBINANT ALDII PROTEIN FROM Uncultured Acidilobus sp. USING I-TASSER

The AldII protein is a new recombinant protein produced from a novel gene obtained via a metagenome approach. Previous studies showed that this protein is strong and has the same metal binding aspect as the class II Aldolase enzyme. Aldolase is a valuable enzyme used in pharmaceuticals, food processing, and biochemistry. Further investigation is required to comprehend the structure and function of the AldII protein due to its potential. Researchers will conduct sophisticated bioinformatic analysis on the 3D shape and function prediction of AldII using the I-TASSER webserver from Zhanglab. The AldII protein is a new recombinant protein produced from a novel gene obtained via a metagenome approach. Previous studies showed that this protein is strong and has the same metal binding aspect as the class II Aldolase enzyme. Aldolase is a valuable enzyme used in pharmaceuticals, food processing, and biochemistry. Further investigation is required to comprehend the structure and function of the AldII protein due to its potential. Researchers will conduct sophisticated bioinformatic analysis on the 3D shape and function prediction of AldII using the I-TASSER webserver from Zhanglab. The I-TASSER server is an online tool for the automated prediction of protein structure and annotation of functions based on structure. Analysis of the AldII protein using the I-TASSER webserver shows that this protein has a stable structure with the closest structural homology to deoxyribose-phosphate aldolase from Bacillus thuringiensis with PDB code 6btdA. Additionally, the biological structure analysis shows that this protein shares the biological function of the enzyme L-fuculose-1-phosphate aldolase, which is part of the class II Aldolase enzyme that plays a role in the catabolism of arabinose, L-Fuculose, and Rhamnose. The results align with prior research that states the AldII protein is a stable protein with a catalytic side that is homologous to the class II Aldolase enzyme.

Application of Cell Penetrating Peptides for Intracellular Delivery of Endostatin: A Computational Approach.

Endostatin is an antiangiogenic compound with anticancer activity. The poor stability and low half-life of endostatin are the main barriers to the clinical use of this protein. Cell-penetrating peptides (CPPs) are extensively applied as carrier in the delivery of drugs and different therapeutic agents. Therefore, they can be proper candidates to improve endostatin delivery to the target cells. In this study, we aim to computationally predict appropriate CPPs for the delivery of endostatin. Potential appropriate CPPs for protein delivery were selected based on the literature. The main parameters for detection of best CPP-endostatin fusions, including stability, hydrophobicity, antigenicity, and subcellular localization, were predicted using ProtParam, VaxiJen, and DeepLoc-1.0 servers, respectively. The 3D structures of the best CPP-Endostatin fusions were modeled by the I-TASSER server. The predicted models were validated using PROCHECK, ERRAT, Verify3D and ProSA-Web servers. The best models were visualized by the PyMol molecular graphics system. Considering the principal parameters in the selection of best CPPs for endostatin delivery, endostatin fusions with four CPPs, including Cyt c-ss-MAP, TP-biot1, MPGα, and DPV1047, high stability and hydrophobicity, no antigenicity and extracellular localization were predicted as the best potential fusions for endostatin delivery. Four CPPs, including Cyt c-ss-MAP, TP-biot1, MPGα, and DPV1047, were predicted as the best potential candidates to improve endostatin delivery. Application of these CPPs may overcome the limitation of endostatin therapeutic applications, including poor stability and low half-life. Subsequent experimental studies will contribute to verifying these computational results.

Identification and in-silico characterization of RPN10 gene as a candidate for genome editing to develop little leaf disease resistance in brinjal

Brinjal is an economically important nutrition-rich fruit vegetable. Among the various biotic stresses, the little leaf of brinjal caused by phytoplasma is a severe threat to its production. The disease occurrence has tremendously increased in the recent past causing almost 100% yield losses in severe conditions. Due to the non-availability of a strong resistance source in brinjal genotypes, its management is a challenging task. In the present study, 26S proteasome non-ATPase regulatory subunit 4 homolog or RPN10 gene which is the target of SAP05 effector of phytoplasma is identified in phytoplasma resistant Kashi Uttam variety of brinjal. The RPN10 gene in brinjal was amplified and sequenced. Evolutionary analysis showed that the RPN10 gene is highly conserved in plant species which are natural hosts for phytoplasma. A comparison of motifs and domains in RPN10 protein of Arabidopsis and brinjal revealed 100% similarity. 3-dimensional protein structures were generated using I-TASSER server and structural comparison also showed perfect similarity between RPN10 protein in brinjal and Arabidopsis. The results in the study propose RPN10 protein in brinjal as the potential candidate gene target for genome editing to develop resistance against little leaf disease in brinjal.

Beyond traditional medications: exploring novel and potential inhibitors of trypanothione reductase (LmTr) of Leishmania parasites

The trypanothione reductase enzyme, which neutralizes the reactive oxygen species produced inside the macrophages to kill the parasites, is one of the evasion strategies Leishmania uses to survive inside the cells. The vitality of the parasite depends on Leishmania major trypanothione reductase (LmTr), a NADPH-dependent flavoprotein oxidoreductase essential for thiol metabolism. Since this enzyme is distinct and lacking in humans, we focused on it in our study to screen for new inhibitors to combat leishmaniasis. Using the I-TASSER server, a three-dimensional model of LmTr was generated. The Autodock vina program was used in high-throughput virtual screening of the ZINC database. The top seven molecules were ranked according to their binding affinity. The compounds with the highest binding affinities and the right number of hydrogen bonds were chosen. These compounds may be effective at inhibiting the target enzyme’s (LmTr) activity, making them new leishmaniasis treatments. These compounds may serve as a useful starting point for a hit-to-lead approach in the quest for new anti-Leishmania drugs that are more efficient and less cytotoxic. The average node degree is 5.09, the average local clustering coefficient is 0.868, and the PPI enrichment p-value is 8.9e-06, indicating that it is sufficiently connected to regulate the network. TRYR (LmTr protein) also interacts physically with ten additional proteins in the pathogenesis network. The findings of the study indicated that successfully suppressing the LmTr protein in vitro and in vivo may finally result in regulating the L. major pathogenesis. Communicated by Ramaswamy H. Sarma

Targeting the Major Capsid Protein of Rock Bream Iridovirus by Trapa Natans Phytochemical Compounds; a Molecular Docking Approach

Asian rock bream aquaculture is challenged by iridovirus, a pathogen with no effective vaccines or antiviral agents. The present study aimed to identify natural antiviral compounds from Trapa natans, an aquatic plant, with potential to target the activities of major capsid protein in rock bream iridovirus (RBIVmcp). The investigation commenced by constructing a novel 3D homology structure for RBIVmcp using I-TASSER server, followed by refinement and validation through galaxy refiner, ModRefiner, PDBSum, ProSA, and ERRAT servers. Active binding regions of refined protein structures were employed for molecular docking simulations using PyRx and AutoDock Vina tools. Leveraging IMPPAT and PubChem servers, a total of 13 phytochemical compounds from Trapa natans were identified in silico and subjected to docking analysis against RBIVmcp. Among them, Ellagic acid, Galactoarabinan, and Thiamine exhibited the most favorable docking scores of -5.1 kcal/mol, -6.4 kcal/mol, and -5.9 kcal/mol, respectively. Assessment of compounds' toxicity and ADME properties by Swiss-ADME and ProTox-II servers indicated their non-hepatotoxic, non-carcinogenic, non-immunotoxic, and non-mutagenic nature within environments. These findings suggest aforementioned compounds might act as promising antiviral agents against RBIV by interacting with its major capsid protein. However, in vitro and in vivo studies are essential to validate their efficacy.

Immunoinformatics analysis of Brucella melitensis to approach a suitable vaccine against brucellosis

BackgroundBrucellosis caused by B. melitensis is one of the most important common diseases between humans and livestock. Currently, live attenuated vaccines are used for this disease, which causes many problems, and unfortunately, there is no effective vaccine for human brucellosis. The aim of our research was to design a recombinant vaccine containing potential immunogenic epitopes against B. melitensis. MethodsIn this study, using immunoinformatics approaches, 3 antigens Omp31, Omp25, and Omp28 were identified and the amino acid sequence of the selected antigens was determined in NCBI. Signal peptides were predicted by SignaIP-5.0 server. To predict B-cell epitopes from ABCpred and Bcepred servers, to predict MHC-I epitopes from RANKPEP and SYFPEITHI servers, to predict MHC-II epitopes from RANKPEP and MHCPred servers, and to predict CTL epitopes were used from the CTLPred server. Potentially immunogenic final epitopes were joined by flexible linkers. Finally, allergenicity (AllerTOP 2.0 server), antigenicity (Vaxijen server), physicochemical properties (ProtParam server), solubility (Protein-sol server), secondary (PSIPRED and GRO4 servers) and tertiary structure (I-TASSER server), refinement (GalaxyWEB server), validation (ProSA-web, Molprobity, and ERRAT servers), and optimization of the codon sequence (JCat server) of the structure of the multi-epitope vaccine were analyzed. ResultsThe analysis of immunoinformatics tools showed that the designed vaccine has high quality, acceptable physicochemical properties, and can induce humoral and cellular immune responses against B. melitensis bacteria. In addition, the high expression level of recombinant antigens in the E. coli host was observed through in silico simulation. ConclusionAccording to the results in silico, the designed vaccine can be a suitable candidate to fight brucellosis and in vitro and in vivo studies are needed to evaluate the research of this study.

Restraint of VP1 Protein of Foot and Mouth Disease Virus using Specific Antiviral Peptides: an in Silico Investigation.

Foot and mouth diseases are among the important threats in the animal husbandry industry which lead to huge economic losses. In this regard, the current project aimed to inhibit the VP1 protein of foot and mouth disease viruses using specific peptides. For this purpose, a wide range of potential antiviral peptides were collected from the database. Physicochemical properties, hydrophobicity/hydrophilicity, and solubility properties of potential antiviral peptides were investigated using reliable servers. Afterward, the tertiary structures of the selected peptides along with the VP1 protein were modeled by the I-TASSER server. Moreover, interactions between VP1 protein and selected antiviral peptides were investigated using the ClusPro 2.0 server. Finally, the outputs of molecular docking were assessed by LigPlot+ and visualized by PyMol software. The results revealed that Dermaseptin-3, Ginkbilobin, Circulin-F, Maximin1, Cycloviolin-A, Cycloviolin-D, Circulin-C, Cycloviolin-C, and Antihypertensive protein BDS-1 peptides with a hydrophobicity value of > 30 were soluble with positive instability index and positive net charge. Moreover, the results of the molecular docking process demonstrated that Dermaseptin-3 and Ginkbilobin peptides could strongly inhibit the VP1 protein using 10 hydrogen bonds. Therefore, these two peptides, which had the most hydrogen bonds, were introduced as the best anti-foot and mouth disease virus peptides to apply.

Penetrance of missense mutation of OR2AT4 and OR9G1/9 gene polymorphism increases risk factor in azoospermic patients

Objectives: In human, olfactory receptor (ORs) gene polymorphism regulate testicular development and physiological functions during spermatogenesis. However, the etiopathology of OR gene in male infertility is still restricted that required further studies. Basic mechanism involves the identification of peripheral signals based on specific chemoreceptors site that are expressed on the surface of mature spermatozoa inside the female reproductive tract. These receptors belong to G-protein couple receptors (GPCR) of superfamily and the roles of ORs gene linked to sperm chemotaxis through chemokinesis. In the present study, we have studied the role of Olfactory receptor family 2 subfamilies AT member 4 (OR2AT4) and Olfactory receptor family 9 subfamily G member 1/9 (OR9G1/9) genes polymorphism in clinically diagnosed azoospermic patients. Materials and Methods: Systematically, GTG banded karyotypes were developed using short term lymphocyte cultures, fluorescence in situ hybridization using SRY probe and PCR based microdeletion of Y-chromosome was characterized using STS marker (SY255). Whole exome sequencing (WES) based analysis was performed in azoospermic patients to identify the involvement of de-novo mutation in OR2AT4 and OR9G1/OR9G9 genes mutation followed by bioinformatics tools used for the analysis to identify changes in respective amino acids. Results: OR2AT4 showing missense mutation after substitution of nucleotide (G→A) followed by lack of change in amino acid (Gln→Gln), but in OR9G1/G9 gene showing changes of substitution of nucleotide thymidine into adenine (T→A), whereas valine is replaced by glutamine (Val→ Glu), similarly thymidine is substituted by cysteine (T→C), after decode phenylalanine is replaced by leucine (Phe→Leu). Further, 3D protein helical structure was developed with the help of bioinformatics on the basis of amino acids coded protein and compare with mutated amino acid or truncated protein residues with the help of iTASSER server. Conclusion: Present study demonstrate the role of OR2AT4 and OR9G1/9 gene polymorphism elucidates the functional role of protamine in ectopic receptors followed by increasing “risk” of developing male infertility that leads the clinical condition defined as non-obstructive azoospermia.

Structural analysis of open reading frames of bovine immunodeficiency virus proteins

The goal of this study was determining the structural organization peculiarities of the ORF2 and ORF3 proteins of the bovine immunodeficiency virus (BIV). Five ORFs were determined for two BIV isolates with complete genome using the ATGpr software, which permits effective prediction of translation initiation codons with nucleotide accuracy. Phyre2 software was used to predict, analyze the secondary structure and function of proteins. PONDR-FIT software was used to search for protein fragments in a disordered or natively unfolded state. Analysis of the amino acid composition of ORF2 and ORF3 proteins of BIVisolates regarding the presence of nonpolar, polar, aromatic, and hydrophobic amino acid residues was carried out using PSIPRED software. Models of the 3D-structure of proteins were obtained by I-TASSER server. 14% of α helices, 17% of β strands and 43% of disordered structure are predicted for the ORF3 protein. 37% of α helices, 0% of β strands, and 41% of disordered structure were determined for Gag polyprotein, which is translated from ORF2. The distribution of charged amino acid residues characterizes the surface properties of proteins. Their number reaches 23.9% for ORF2 protein. The amount of Arg is 5.2%, Lys — 8.0%, Glu — 7.3%, Asp — 3.4%. The total number of charged amino acid residues of ORF3 is 23.3%. The number of Arg is 12.6%, Lys — 4.9%, Glu — 1.9%, Asp — 3.9%. Only two ORFs of five ones coincide in nucleotide length (and, therefore, in length of corresponding proteins) for the two BIV isolates. The ORF3 protein belongs to the intrinsically disordered proteins that cannot be stably folded into a unique three-dimensional structure under physiological conditions, and the Gag polyprotein, which is translated from ORF2, belongs to the class of fully structured proteins. The secondary structure of both proteins shows the presence of α-helices

Characterization of bovine immunodeficiency virus genes and proteins

The goal of the study was determining the effect of natural selection on the bovine immunodeficiency virus (BIV) through the identification of polymorphisms by comparing a number of genes, open reading frames and proteins and analyzing the effect of nonsynonymous substitutions in the Vif protein of BIV isolates on the Vif conformational parameters. The selection pressure on the genes was estimated by Tajima test, as well as the determination of the ratio of nonsynonymous substitutions (Ka) to synonymous (Ks) Ka/Ks. Ka and Ks coefficients, their ratio (Ka/Ks) were calculated on the basis of alignments of amino acid and nucleotide sequences of the vif gene of BIV isolates. The nonsynonymous (dN) to synonymous (dS) substitution rate ratio per nucleotide site dN/dS was calculated to estimate the effect of selection on the vif gene by SLAC method on Datamonkey server. The number of hydrogen bonds, α-helices, β-sheets, β-turns for the protein tertiary structures of proteins was determined by I-TASSER server. Genes, open reading frames (ORFs) and the U3 regulatory region of BIV genome which are under the influence of selection have been identified. Gag, pol, s, vif genes, ORF W and ORF Y are under the negative (purifying) selection pressure. Env gene and the U3 regulatory region are under positive selection. Shannon entropy analysis (peaks that are specific to the positions of amino acid residues), interpreted as polymorphisms, revealed 16, 8, and 4 nonsynonymous substitutions for Pol, Gag, and Vif BIV proteins, respectively. Significant changes in the number of hydrogen bonds, α-helices, β-layers, β-turns were determined by the analysis of the effect of four nonsynonymous substitutions in the Vif protein on the conformational parameters of Vif of two BIV isolates. The multidirectional effect of selection on BIV genes is shown

Immunoinformatics design of B-cell multi-epitope peptide for the diagnosis of Methicillin Resistant Staphylococcus aureus (MRSA) infection

Background: Methicillin (oxacillin)-resistant Staphylococcus aureus (MRSA) remains a significant clinical and epidemiological pathogen in hospital settings and in the community world-wide. The resistance to methicillin in Staphylococcus aureus is mediated by the mecA gene, which encodes penicillin-binding protein 2a (PBP2A). Rapid patient screening for MRSA is essential for infection control procedures in order to possibly enhance the outcomes of infected patients. In this study, we utilized PBP2A to predict and create a novel synthetic protein with multiple immunodominant B cell epitopes for rapid diagnosis of MRSA using an in-silico approach. Methods: Seven putative PBP2A peptides were used to analyze the protein’s primary, secondary, and tertiary structures (BepiPred). The B cell construct was then evaluated using I-TASSER server, and physicochemical properties, and homology modeling of the 3 D structure of the protein were obtained. Results: In silico analyses revealed regions with high immunogenicity. Altogether, 19 consented epitopes were selected for the in-silico succession; three consented epitopes from ALJ10988.1, three from ORN56903.1, three from AFJ06714.1, one from AEO00772.1, three from WP_000721309.1, three from WP_057521704.1, and three from WP_063851348.1. The constructs have an average length of 503 amino acids, molecular weight of 55,151.78, instability index of 41.44, theoretical PI of 9.28 and a C score −1.50. In addition, the parameters that were examined indicated the newly multi-epitope construct could potentially serve as a theoretical framework for the development of a MRSA diagnostic kit. Conclusions: Overall, we have developed an antigen-based multi-epitope peptide for the rapid and accurate diagnosis of MRSA infection through an in-silico approach, acceptable in terms of antigenicity, physicochemical properties, structural stability and strong immunogenicity.

Molecular investigation of TSHR gene in Bangladeshi congenital hypothyroid patients.

The disorder of thyroid gland development or thyroid dysgenesis accounts for 80-85% of congenital hypothyroidism (CH) cases. Mutations in the TSHR gene are mostly associated with thyroid dysgenesis, and prevent or disrupt normal development of the gland. There is limited data available on the genetic spectrum of congenital hypothyroid children in Bangladesh. Thus, an understanding of the molecular aetiology of thyroid dysgenesis is a prerequisite. The aim of the study was to investigate the effect of mutations in the TSHR gene on the small molecule thyrogenic drug-binding site of the protein. We identified two nonsynonymous mutations (p.Ser508Leu, p.Glu727Asp) in the exon 10 of the TSHR gene in 21 patients with dysgenesis by sequencing-based analysis. Later, the TSHR368-764 protein was modeled by the I-TASSER server for wild-type and mutant structures. The model proteins were targeted by thyrogenic drugs, MS437 and MS438 to perceive the effect of mutations. The damaging effect in drug-protein complexes of mutants was explored by molecular docking and molecular dynamics simulations. The binding affinity of wild-type protein was much higher than the mutant cases for both of the drug ligands (MS437 and MS438). Molecular dynamics simulates the dynamic behavior of wild-type and mutant complexes. MS437-TSHR368-764MT2 and MS438-TSHR368-764MT1 showed stable conformations in biological environments. Finally, Principle Component Analysis revealed structural and energy profile discrepancies. TSHR368-764MT1 exhibited much more variations than TSHR368-764WT and TSHR368-764MT2, emphasizing a more damaging pattern in TSHR368-764MT1. This genetic study might be helpful to explore the mutational impact on drug binding sites of TSHR protein which is important for future drug design and selection for the treatment of congenital hypothyroid children with dysgenesis.

In silico Validation of Pseudomonas aeruginosa Exotoxin A Domain I Interaction with the Novel Human scFv Antibody.

Pseudomonas(P.) aeruginosa is one of the leading causes of nosocomial infections. The pathogenicity of P. aeruginosa is related to its inherent antimicrobial resistance and the diverse virulence factors of this bacterium. Owing to the specific role of exotoxin A in P. aeruginosa pathogenesis, it is known as a promising therapeutic candidate to develop antibodies as an alternative to antibiotics. The present study aimed to validate the interaction between a single-chain fragment variable (scFv) antibody identified from an scFv phage library against domain I exotoxin A by bioinformatic tools. For this, several bioinformatics tools, including Ligplot, Swiss PDB viewer (SPDBV), PyMOL, I-TASSER, Gromacs, and ClusPro servers were used to evaluate the interaction of scFv antibody with P. aeruginosa exotoxin A. The I-TASSER server was utilized to predict the function and structure of proteins. The interaction of two proteins was analyzed using ClusPro tools. The best docking results were further analyzed with Ligplot, Swiss PDB viewer, and PyMOL. Consequently, molecular dynamics simulation was utilized to predict the stability of the secondary structure of the antibody and the binding energy of the scFv antibody to the domain I of exotoxin A. As a result, we demonstrated that data from computational biology could provide protein-protein interaction information between scFv antibody/domain I exotoxin A and offers new insights into antibody development and therapeutic expansion. In summary, a recombinant human scFv capable of neutralizing P. aeruginosa exotoxin is recommended as a promising treatment for infections caused by P. aeruginosa.

Gold nanoparticle assisted colorimetric biosensors for rapid polyethylene terephthalate (PET) sensing for sustainable environment to monitor microplastics

The extremely widespread and ubiquitous nature of plastics, estimated to boost its global production by 26 billion tons till 2050. The large chunks of plastic waste that decomposed down to micro- or nano plastics (MNPs) leads to various ill effects on biological entities. The conventional PET detection methods lack rapid detection of microplastics due to variances in microplastic features, long-drawn-out sample pre-processing procedures and complex instrumentation. Therefore, an instantaneous colorimetric evaluation of microplastic will ensures the simplicity of conducting assays on field. Several nanoparticle-based biosensors that detects proteins, nucleic acids, metabolites operate on either cluster or disperse state of nanoparticle. However, gold nanoparticle (AuNPs) emerges an ideal scaffold for sensory element in lateral flow biosensors due to their simple surface functionalization, unique optoelectronic properties and varied colour spectrum depending on morphologies and aggregation state. In this paper an effort has been made in the form of a hypothesis using in silico tools as a basis to detect polyethylene terephthalate (PET) – most abundant type of microplastic using gold nanoparticle based lateral flow biosensor. We retrieved sequences of PET-binding synthetic peptides and modelled their 3-D structure using I-Tasser server. The best protein model for each peptide sequences are docked with PET monomers – BHET, MHET and other PET polymeric ligands, to evaluate their binding affinities. The synthetic peptide SP 1 (WPAWKTHPILRM) docked with BHET and (MHET)4 exhibits 1.5-fold increases in binding affinity as compared to reference PET anchor peptide Dermaseptin SI (DSI). The GROMACS molecular dynamics simulation studies of synthetic peptide SP 1 - BHET & - (MHET)4 complexes for 50 ns further confirmed the stable binding. RMSF, RMSD, hydrogen bonds, Rg and SASA analysis provides useful structural insights of the SP 1 complexes as compared to reference DSI. Furthermore, SP 1 functionalized AuNP-based colorimetric device was described in detail for detection of PET.

In silico and In vitro Assessment of Antibacterial Activity, LPS Binding Affinity, and Toxicity of the GKY25 Peptide.

Extensively and multi-drug resistant isolates of bacteria (MDR, XDR) have caused significant health problems and are responsible for high morbidity and mortality as well. In this critical condition, the discovery, design, or development of new antibiotics is of great concern. According to this necessity, antimicrobial peptides (AMPs) suggested as promising agents. Accordingly, this study aims to evaluate the GKY25 peptide to develop its future antibacterial applications as well as confirmation of LPS neutralization. Predictions of 3D structure and helical wheel projection analysis of the peptide were performed by ITASSER and Heliquest servers. Binding affinity and antibacterial activity were performed using molecular docking and CAMPR4, respectively, followed by experimental binding assay as well as in vitro antibacterial assay. GKY25 was predicted as an alpha-helical peptide, and its helicity showed probable projection of hydrophobic and positively-charged amino acid residues. Docking studies showed binding affinity of GKY25 peptide to gram-positive and outer and inner gram-negative bacterial membranes as -5.7, -6.8, and -4 kcal/mole, respectively. CAMPR4 analysis predicted the peptide as an AMP. Experimental binding assay showed that the peptide binds LPS immediately and their interaction was observed at 274 nm. Gathering all in silico and in vitro data together, GKY25 is a good drug lead that could be examined further using clinical isolates of gram-negative bacteria in vitro.

Restraint of VP1 Protein of Foot and Mouth Disease Virus using Specific Antiviral Peptides: an in Silico Investigation

Foot and mouth diseases are among the important threats in the animal husbandry industry which lead to huge economic losses. In this regard, the current project aimed to inhibit the VP1 protein of foot and mouth disease viruses using specific peptides. For this purpose, a wide range of potential antiviral peptides were collected from the database. Physicochemical properties, hydrophobicity/hydrophilicity, and solubility properties of potential antiviral peptides were investigated using reliable servers. Afterward, the tertiary structures of the selected peptides along with the VP1 protein were modeled by the I-TASSER server. Moreover, interactions between VP1 protein and selected antiviral peptides were investigated using the ClusPro 2.0 server. Finally, the outputs of molecular docking were assessed by LigPlot+ and visualized by PyMol software. The results revealed that Dermaseptin-3, Ginkbilobin, Circulin-F, Maximin1, Cycloviolin-A, Cycloviolin-D, Circulin-C, Cycloviolin-C, and Antihypertensive protein BDS-1 peptides with a hydrophobicity value of > 30 were soluble with positive instability index and positive net charge. Moreover, the results of the molecular docking process demonstrated that Dermaseptin-3 and Ginkbilobin peptides could strongly inhibit the VP1 protein using 10 hydrogen bonds. Therefore, these two peptides, which had the most hydrogen bonds, were introduced as the best anti-foot and mouth disease virus peptides to apply.

Breast Cancer in Mauritania: Mutations in Exon 4 of the <I>TP53</I> Gene

Cancer is one of the leading causes of death worldwide, with approximately 10 million cancer-related deaths reported in 2020. Approximately 70% of these deaths occurred in developing countries. In 2020, 2.3 million women were diagnosed with breast cancer and 685,000 deaths due to breast cancer were reported worldwide. Cancer is characterized by the presence of most triggers in the genome. Mutations in genes, either passed from one generation to the next or acquired throughout life, can cause breast cancer. Tumor suppressor genes encode proteins that negatively regulate cell proliferation and repress certain oncogenes. One of these genes, the <I>TP53</I> gene, has multiple biological functions. Understanding the mechanism of action of p53 in breast carcinogenesis has been an important challenge in cancer research. This study aimed to investigate the involvement of alterations in exon 4 of the <I>TP53</I> gene in Mauritanian patients with breast cancer. The study was conducted using 45 tumor tissue sequences and 35 control sequences. The nature and position of the mutations were determined using Mutation Surveyor V5.1.2 The pathogenicity of the mutations was determined using Polyphen2, SIFT, and Mutation Tester, and their three-dimensional structure was determined using the I-Tasser server. DnaSP version 5.10, MEGA version 7.014, and Arlequin version 3.1 were used to highlight the variability of exon 4 of the <I>TP53</I> gene. Our results revealed the presence of a single-nucleotide variant at position (c.139 C>T), which causes an amino acid change from proline to serine at codon 47 in the coding region of exon 4 of the <I>TP53</I> gene. Of note, this variant has already been listed in the database (rs1800371). In addition, five novel mutations were found in the cancer tissue sequences alone, with statistically significant scores. Analyses of genetic variability indicated a relatively high polymorphism in tumor tissue sequences compared with control sequences. This variability may contribute to the involvement of exon 4 mutations in the occurrence of breast cancer in our population, and serves as the first data on <I>TP53</I> exon 4 alterations in Mauritania.

Molecular modeling, simulation and docking of Rv1250 protein from Mycobacterium tuberculosis.

Computational prediction and protein structure modeling have come to the aid of various biological problems in determining the structure of proteins. These technologies have revolutionized the biological world of research, allowing scientists and researchers to gain insights into their biological questions and design experimental research much more efficiently. Pathogenic Mycobacterium spp. is known to stay alive within the macrophages of its host. Mycobacterium tuberculosis is an acid-fast bacterium that is the most common cause of tuberculosis and is considered to be the main cause of resistance of tuberculosis as a leading health issue. The genome of Mycobacterium tuberculosis contains more than 4,000 genes, of which the majority are of unknown function. An attempt has been made to computationally model and dock one of its proteins, Rv1250 (MTV006.22), which is considered as an apparent drug-transporter, integral membrane protein, and member of major facilitator superfamily (MFS). The most widely used techniques, i.e., homology modeling, molecular docking, and molecular dynamics (MD) simulation in the field of structural bioinformatics, have been used in the present work to study the behavior of Rv1250 protein from M. tuberculosis. The structure of unknown TB protein, i.e., Rv1250 was retrived using homology modeling with the help of I-TASSER server. Further, one of the sites responsible for infection was identified and docking was done by using the specific Isoniazid ligand which is an inhibitor of this protein. Finally, the stability of protein model and analysis of stable and static interaction between protein and ligand molecular dynamic simulation was performed at 100ns The designing of novel Rv1250 enzyme inhibitors is likely achievable with the use of proposed predicted model, which could be helpful in preventing the pathogenesis caused by M. tuberculosis. Finally, the MD simulation was done to evaluate the stability of the ligand for the specific protein.

Isolation and Characterization of Dehydrin Gene from Egyptian Gray Mangrove in Nabq Protectorate

ABSTRACT: Dehydrins have a key role in protecting plants, especially in the grey mangrove tree Avicennia marina (Forssk.) Vierh. from salt stress. Understanding the mangrove plants at the molecular level will be necessary for developing such highly salt-tolerant crops. The full-length cDNA of the DHN gene sequence AmDHN was isolated from Avicennia marina and contained a 588bp open reading frame (ORF) encoding a 195 amino acid protein with a molecular weight of about 19.746k Da. As well as, multiple alignment sequences and phylogenetic relationships were analyzed for sequences using MEGA7 software revealing that AmDHN has a high identity with other DHNs plants and suggesting that AmDHN belongs to group II (LEA) proteins. Using bioinformatics analysis tools, we have investigated characterize and gene expression to better understand the structure and function analysis prediction of the AmDHN protein. AmDHN protein contains motifs (SYK2), Sn, Yn segment, and at least one copy of a lysine-rich conserved sequence known as K-segment (consensus EKKGIME/DKIKEKLPG) near the C terminal, the 3D predicted the structure protein sequence of the secondary structure, the top 5 final models using by I-TASSER server and several parameters computed by the software were obtained. Our results indicate that the AmDHN gene plays an essential role in salt stress remediation in the Avicennia marina. They could be used for further studies to understand the molecular mechanisms of salinity tolerance in plants and can be potentially utilized in transforming other plants to improve tolerance to salinity stress.