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Objective: Congenital Cataract is a type of ophthalmic genetic disorder that appears at birth or in early childhood. Among 30 genes, CRYBB2 is one of the most common and a water-soluble protein of lens’s that code for the βB2- crystallin. This study aimed to investigate the novel silent mutation in CRYBB2 of exon six in the Pakistani families of Autosomal Dominant Congenital Cataracts (ADCC). Methods: It is a family-based study that presents three to five-generations of two Pakistani families. Data and blood samples from the families were collected from January to August 2019 from LRBT (Layton Rahmatullah Benevolent Trust) Hospital, Mansehra, Pakistan. We only included patients >15 years old. Before enrollment in the current study, each patient obtained a thorough optical examination. Samples were moved to the molecular lab using the collection and storage method. The phenol-chloroform technique was used to extract the DNA. The technique of Sanger sequencing was used to find any potential mutation in some of the selected families. Statistical and bioinformatics analysis were carried out. Results: By using bioinformatics tools, the novel silent mutation was identified. Heterozygous silent mutation of CRYBB2 of exon 6 (c. 495G>A) was detected by the alignment of sequences. Computational prediction program did not predict the silent mutation. Conclusion: This study investigated a novel important sequence variant in the beta-crystalline protein that causes autosomal dominant congenital cataract (ADCC) in Pakistani families. Thus, our study enlarges the CRYBB2 mutation spectrum and associated phenotypes to help clinical diagnosis of human genetic diseases. [ABSTRACT FROM AUTHOR]

Abstract Background Arsenic, a ubiquitous toxic metalloid, is a threat to the survival of all living organisms. Bioaccumulation of arsenic interferes with the normal physiological pathway. To overcome arsenic toxicity, organisms have developed arsenite methyltransferase enzyme, which methylates inorganic arsenite to organic arsenic MMA (III) in the presence of S-adenosylmethionine (SAM). Bacteria-derived arsM might be horizontally transported to different domains of life as arsM or as3mt (animal ortholog). A systematic study on the functional diversity of arsenite methyltransferase from various sources will be used in arsenic bioremediation. Results Several arsenite methyltransferase protein sequences of bacteria, fungi, fishes, birds, and mammals were retrieved from the UniProt database. In silico physicochemical studies confirmed the acidic, hydrophilic, and thermostable nature of these enzymes. Interkingdom relationships were revealed by performing phylogenetic analysis. Homology modeling was performed by SWISS-MODEL, and that was validated through SAVES-v.6.0. QMEAN values ranged from − 0.93 to − 1.30, ERRAT score (83–96), PROCHECK (88–92%), and other parameters suggested models are statistically significant. MOTIF and PrankWeb discovered several functional motifs and active pockets within the proteins respectively. The STRING database showed protein–protein interaction networks. Conclusion All of our in silico studies confirmed the fact that arsenite methyltransferase is a cytosolic stable enzyme with conserved sequences over a wide range of organisms. Thus, because of its stable and ubiquitous nature, arsenite methyltransferase could be employed in arsenic bioremediation.

The β-glucanase enzyme is an enzyme protein that can hydrolyze β-glucan, one of the main components of the fungal cell wall. This enzyme protein is produced by several bacteria, one of which is B. subtilis. The three-dimensional (3D) structure of proteins is necessary to understand their properties and functions of proteins. Enzyme proteins can be analyzed for their structure and function using in silico method. This study aims to detect the β-glucanase gene from B. subtilis W3.15 and analyze it using the in silico method. The methods in this research are homology modeling and molecular docking analyses. Modeling was carried out using the SWISS-MODEL server and docking analysis using the PLANTS 1.1 program. Modeling the β-glucanase enzyme is based on the template of the β-glucanase enzyme protein model with PDB code 3o5s. The results of sequence alignment and model visualization were quite good as indicated by the model having a Ramachandran Plot value in the favored area of 91.10 %, a MolProbity score of 0.95, and a QMEAN value of 0.90 ± 0.06. The β-glucanase enzyme model was then docked using the PLANTS1.1 program with native ligand B3P, 1,4-β-D-Glucan, D-glucose, β-D-Glucan from oats, and N-Acetyl glucosamine. The results of docking analysis showed that the β-glucan ligand (β-D-glucan from oats) used as a substrate in the cultivation of isolate B. subtilis W3.15 had a better binding energy prediction value compared to the B3P ligand, which is a natural ligand in the template proteins.

Background: Arsenic, a ubiquitous toxic metalloid, is a threat to the survival of all living organisms. Bioaccumulation of arsenic interferes with the normal physiological pathway. To overcome arsenic toxicity, organisms have developed arsenite methyltransferase enzyme, which methylates inorganic arsenite to organic arsenic MMA (III) in the presence of S-adenosylmethionine (SAM). Bacteria-derived arsM might be horizontally transported to different domains of life as arsM or as3mt (animal ortholog). A systematic study on the functional diversity of arsenite methyltransferase from various sources will be used in arsenic bioremediation. Results: Several arsenite methyltransferase protein sequences of bacteria, fungi, fishes, birds, and mammals were retrieved from the UniProt database. In silico physicochemical studies confirmed the acidic, hydrophilic, and thermostable nature of these enzymes. Interkingdom relationships were revealed by performing phylogenetic analysis. Homology modeling was performed by SWISS-MODEL, and that was validated through SAVES-v.6.0. QMEAN values ranged from − 0.93 to − 1.30, ERRAT score (83–96), PROCHECK (88–92%), and other parameters suggested models are statistically significant. MOTIF and PrankWeb discovered several functional motifs and active pockets within the proteins respectively. The STRING database showed protein–protein interaction networks. Conclusion: All of our in silico studies confirmed the fact that arsenite methyltransferase is a cytosolic stable enzyme with conserved sequences over a wide range of organisms. Thus, because of its stable and ubiquitous nature, arsenite methyltransferase could be employed in arsenic bioremediation. [ABSTRACT FROM AUTHOR]

Objective: The major purpose of the present study was to predict the structure of Radical s-adenosyl-L-methionine Domain 2 (RSAD2), the most targeted protein of the Zika virus using comparative modeling, to validate the models that were generated and molecular dynamics (MD) simulations were performed. Methods: The secondary structure of RSAD2 was estimated using the Garnier-Osguthorpe-Robson, Self-Optimized Prediction method with Alignment, and Position-Specific Iterative-Blast based secondary structure prediction algorithms. The best of them were preferred based on their DOPE score, then three-dimensional structure identification using SWISS-MODEL and the Protein Homology/Analogy Recognition Engine (Phyre2) server. SAVES 6.0 was used to validate the models, and the preferred model was then energetically stabilized. The model with least energy minimization was used for MD simulations using iMODS. Results: The model predicted using SWISS-MODEL was determined as the best among the predicted models. In the Ramachandran plot, there were 238 residues (90.8%) in favored regions, 23 residues (8.8%) in allowed regions, and 1 residue (0.4%) in generously allowed regions. Energy minimization was calculated using Swiss PDB viewer, reporting the SWISS-MODEL with the lowest energy (E = −18439.475 KJ/mol) and it represented a stable structure conformation at three-dimensional level when analyzed by MD simulations. Conclusion: A large amount of sequence and structural data is now available, for tertiary protein structure prediction, hence implying a computational approach in all the aspects becomes an opportunistic strategy. The best three-dimensional structure of RSAD2 was built and was confirmed with energy minimization, secondary structure validation and torsional angles stabilization. This modeled protein is predicted to play a role in the development of drugs against Zika virus infection. [ABSTRACT FROM AUTHOR]

There are some bacteria and protozoan that is a major public health problem. The protein which is responsible for disease as a suitable target for drug discovery for cholera, tuberculosis, kala azar and malaria. General conclusions and knowledge about ligand binding modes and protein flexibility are decisive for the drug design process, particularly in the structure-based part of it. In general, if two ligands are structurally similar, then the binding mode as defined by the relative orientation in the protein is conserved. That is, a majority of the ligand pairs occupy the same space in the binding sites. For understanding the various organisms' protein ligand structure similarity with respect to all similar ligand of protein and comparative structural conformation study between bacteria and protozoan using structure model structure alignment and draw the ligand structure respectively by SWISS-MODEL, chimera software and chem-sketch. [ABSTRACT FROM AUTHOR]

Antibodies are essential to life, and knowing their structures can facilitate the understanding of antibody–antigen recognition mechanisms. Precise antibody structure prediction has been a core challenge for a prolonged period, especially the accuracy of H3 loop prediction. Despite recent progress, existing methods cannot achieve atomic accuracy, especially when the homologous structures required for these methods are not available. Recently, RoseTTAFold, a deep learning-based algorithm, has shown remarkable breakthroughs in predicting the 3D structures of proteins. To assess the antibody modeling ability of RoseTTAFold, we first retrieved the sequences of 30 antibodies as the test set and used RoseTTAFold to model their 3D structures. We then compared the models constructed by RoseTTAFold with those of SWISS-MODEL in a different way, in which we stratified Global Model Quality Estimate (GMQE) into three different ranges. The results indicated that RoseTTAFold could achieve results similar to SWISS-MODEL in modeling most CDR loops, especially the templates with a GMQE score under 0.8. In addition, we also compared the structures modeled by RoseTTAFold, SWISS-MODEL and ABodyBuilder. In brief, RoseTTAFold could accurately predict 3D structures of antibodies, but its accuracy was not as good as the other two methods. However, RoseTTAFold exhibited better accuracy for modeling H3 loop than ABodyBuilder and was comparable to SWISS-MODEL. Finally, we discussed the limitations and potential improvements of the current RoseTTAFold, which may help to further the accuracy of RoseTTAFold's antibody modeling. [ABSTRACT FROM AUTHOR]

The study provides simple protocol for identifying unknown genes (DNA and RNA) and proteins present in the plants. The exact mechanism of nanoparticle synthesis from plant extracts is still unclear. Although functionalization of nanoparticle has been achieved by binding biomolecules and stabilizing through exchange of ligands and electrostatic interactions. This study will help in case of difficulty in extraction of proteins and DNA from nanoparticles due to less sample collection or degradation of active biomolecules. Plant extracts holds various biomolecules and can be used to presume the basic formulae of plant proteins by using software. The presence of DNA traces on silver nanoparticles confirmed and DNA sequence was extracted from NCBI gene bank. Homology modeling is an alternative method to predict 3D structure of proteins in the absence of experimental results. DNA gel electrophoresis and quantification of biomolecules and 3D protein structures have built from known sequences of conforming family members of protein using SWISS-MODEL. A major advantage of automated homology modeling is creating protein models that are easy to design the structure. Protein sequencing is continuously evolving nowadays. Experts are improving SWISS-MODEL to enhance the efficient transition. The study will help in easy and rapid identification of genes and proteins present on the surface of biological nanoparticles. Structural analysis of protein (proteomics) helps to identify novel functions that could facilitate designing of efficient biosensors.

Siderophores are produced by bacteria, fungi and plants to facilitate uptake of iron, they are low-molecular-weight chelation agents and protect from stress responses. Pyoverdines act as fluorescent siderophores, plays an important role under iron-limiting conditions. During the stress condition a change in the broth culture was observed where it turned green from yellow, indicating some kind of pigment release. According to some reports the pigment release happens due to the presence of Siderophore in microorganisms. This colour change can also be considered as microbial sensor for color change detection. The bacterial sample was tested for the chromium (VI) and Nickel (II) resistant capacity, presence of siderophore, DNA and protein content. The chromium (VI) and nickel (II) resistant isolates were identified as Bacillus cereus (BF2). The siderophore was detected using qualitative and quantitative assays. Using various bioinformatics softwares the siderophore produced by Bacillus cereus (Rock 3-28) was compared with the isolated culture because both of their molecular weight varied from the range of 48kDa-65kDa. National Center For Biotechnology Information (NCBI), Basic Local Alignment Search Tool (BLAST), Clustal Omega, Expert Protein Analysis System (ExPASy), Self-Optimized Prediction Method with Alignment (SOPMA) and SWISS-MODEL tools were used to study the pyoverdine protein which coded for the enzyme L-ornithine N5-oxygenase. The FASTA sequences of the query sequence were compared with other species using BLAST. The sequences of protein were used for structural and functional analysis and for phylogenetic tree construction. [ABSTRACT FROM AUTHOR]

Pyruvate dehydrogenase complex deficiency is a major cause of primary lactic acidemia resulting in high morbidity and mortality, with limited therapeutic options. PDHA1 mutations are responsible for >82% of cases. The E1 component of PDC is a symmetric dimer of heterodimers (αβ/α′β′) encoded by PDHA1 and PDHB. We measured solvent accessibility surface area (SASA), utilized nearest‐neighbor analysis, incorporated sequence changes using mutagenesis tool in PyMOL, and performed molecular modeling with SWISS‐MODEL, to investigate the impact of residues with disease‐causing missense variants (DMVs) on E1 structure and function. We reviewed 166 and 13 genetically resolved cases due to PDHA1 and PDHB, respectively, from variant databases. We expanded on 102 E1α and 13 E1β nonduplicate DMVs. DMVs of E1α Arg112‐Arg224 stretch (exons 5‐7) and of E1α Arg residues constituted 40% and 39% of cases, respectively, with invariant Arg349 accounting for 22% of arginine replacements. SASA analysis showed that 86% and 84% of residues with nonduplicate DMVs of E1α and E1β, respectively, are solvent inaccessible ("buried"). Furthermore, 30% of E1α buried residues with DMVs are deleterious through perturbation of subunit‐subunit interface contact (SSIC), with 73% located in the Arg112‐Arg224 stretch. E1α Arg349 represented 74% of buried E1α Arg residues involved in SSIC. Structural perturbations resulting from residue replacements in some matched neighboring pairs of amino acids on different subunits involved in SSIC at 2.9‐4.0 Å interatomic distance apart, exhibit similar clinical phenotype. Collectively, this work provides insight for future target‐based advanced molecular modeling studies, with implications for development of novel therapeutics for specific recurrent DMVs of E1α. [ABSTRACT FROM AUTHOR]

Glucose 6-phosphate dehydrogenase is one of many enzymes found in Lactic Acid Bacteria (LAB). Leuconostoc mesenteroides strain K7 has been isolated from Kelengkeng (Dimocarpus longan) fruit. Kelengkeng fruit can generate LAB in previous research. The type of microbial isolate in form of the acidophilic microbe with pH 2.0 till 5.0 and it has macroscopic and microscopic characteristics is LAB and able to generate antimicrobial activity. The amplification results of the PCR technique showed glucose 6-phosphate dehydrogenase gene from L. mesenteroides strain K7 of 1112 pb as glucose-6-phosphate dehydrogenase (L. suionicum) with a similarity percentage of 99.41%. The modeling structure with SWISS-MODEL server was obtained of 486 amino acids with MSA analysis result of target protein sequence was LTGGGDKANDDAVEDDANNSATDAS FLADGTNSATMPSKA. It means that the sample variance is very significant and protein database to glucose-6-phosphate-1-dehydrogenase. The 3D modeling predictions of sequence identification results from target protein isolate and template (1h9a.1.A) have a similarity of 91.55% by glucose 6-phosphate dehydrogenase. [ABSTRACT FROM AUTHOR]

Glucose 6-phosphate dehydrogenase is one of many enzymes found in Lactic Acid Bacteria (LAB). Leuconostoc mesenteroides strain K7 has been isolated from Kelengkeng (Dimocarpus longan) fruit. Kelengkeng fruit can generate LAB in previous research. The type of microbial isolate in form of the acidophilic microbe with pH 2.0 till 5.0 and it has macroscopic and microscopic characteristics is LAB and able to generate antimicrobial activity. The amplification results of the PCR technique showed glucose 6-phosphate dehydrogenase gene from L. mesenteroides strain K7 of 1112 pb as glucose-6-phosphate dehydrogenase (L. suionicum) with a similarity percentage of 99.41%. The modeling structure with SWISS-MODEL server was obtained of 486 amino acids with MSA analysis result of target protein sequence was LTGGGDKANDDAVEDDANNSATDAS FLADGTNSATMPSKA. It means that the sample variance is very significant and protein database to glucose-6-phosphate-1-dehydrogenase. The 3D modeling predictions of sequence identification results from target protein isolate and template (1h9a.1.A) have a similarity of 91.55% by glucose 6-phosphate dehydrogenase. [ABSTRACT FROM AUTHOR]

Background: The coronavirus spike glycoprotein is a trimeric structural surface protein that facilitates the viral adhesion through attaching receptors on the human cell surface. This study aims to analyze and compare the genomic and phylogenetic properties of these spike glycoprotiens from China, Iran, and Tunisia. Methods: This is a descriptive cross-sectional comparative study for the different properties of S glycoprotein from 12 SARS-CoV-2 specimens from GenBank. Clustal Omega was used to study model sequences alignment, residual conservation, phylogeny, and identity matrix. SWISS-MODEL developed and validated the 3D models for three protein sequences with the highest model quality. The different physicochemical characteristics of different models were assessed by ExPASy proteomics. Results: The Chinese and the Iranian sequences share 100% identity, although they have a different amino acids number, and 25-29.27% identity to the Tunisian sequences. The 12 models are monophyletic, with varying stages of evolutionary divergence. There are six fully, three highly, and five lowly conserved residues across the sequences. The resulting three highly reliable 3D models were of different global qualities, being the lowest for the Tunisian, and the highest for the Iranian models. All the models are highly hydrophilic. The Tunisian models were unstable in comparison to the relatively stable other models with different physicochemical characteristics. Conclusion: The models had different N-terminal residues and side group's polarity and charge. The S glycoprotiens are neither identical nor unique in neither model structure nor the physicochemical profiles in different parts of the world. The Tunisian models are drastically biodiversity from the Chinese and Iranian models. [ABSTRACT FROM AUTHOR]

Honey bee venom (HBV) is composed of an intricate mixture of polypeptides, enzymes, amines, lipids, and amino acids. The principal enzyme present in HBV is Phospholipase A2 (PLA2). The present investigation includes retrieval of amino acid sequence information, sequence analysis and physicochemical characterization of PLA2 protein sequences of three honey bee species viz., Apis mellifera, Apis dorsata, and Apis cerana using computational tools retrieved from NCBI (National Centre for Biotechnology Information) protein sequence database. The physicochemical parameters viz., amino acid composition, molecular weight, isoelectric point, aliphatic index, hydropathicity were determined. The result of the primary structure analysis suggests that most of the PLA2 is hydrophobic due to the presence of high non-polar residues content. The isoelectric point predicted ranged from 7.05 to 8.65. The aliphatic index computed by Expasy's Protparam infers that most of the PLA2 is stable at a wide range of temperatures (51.64–85.17). The secondary structure analysis by SOPMA showed that PLA2 contains more random-coils and alpha-helices than beta-sheets. SMART values revealed an expected range of 0.00000146–12. SVM prot analysis of proteins predicted that these proteins may act as drug targets for inflammatory response lipid-binding proteins, hydrolases, transferases and metal binding. Multiple Sequence alignment by MUSCLE tool revealed significantly conserved (Leucine) and semi-conserved regions (Proline, Alanine). Genebee service software was used to predict the RNA structure. The 3 D structure analysis of PLA2 was done by using SWISS-MODEL. [ABSTRACT FROM AUTHOR]

Coconut palm (Cocos nucifera L.) is rich in protein and consumed worldwide, coconut protein as a plant protein contains many nutrients and is beneficial for human health, but its allergic components also need to be considered. Therefore, further research on coconut protein is of great significance. In this study, nine proteins were identified through matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). Three proteins, namely, (1) 63 kDa globulin-like protein [Elaeis guineensis], (2) 63 kDa globulin-like protein [Phoenix dactylifera], and (3) glutelin type-A 3-like [E. guineensis] were initially found in coconut proteins. To further purify and identify the coconut protein, we used dialysate membrane and high-performance liquid chromatography-Ultraviole (HPLC-UV) to concentrate and separate the extracted protein. Two types of 63 kDa globulins were further purified and identified, namely, P. dactylifera and E. guineensis proteins with 564 and 398 amino acids, respectively, were identified. SWISS-MODEL was used to predict the tertiary structure of the 63 kDa globulins and showed that the structures of the coconut proteins were mostly similar to those of vicilin. This work provided a feasible and simple separation approach for the isolation and purification of coconut protein, and predicts the structure of newly identified protein. [ABSTRACT FROM AUTHOR]

The present investigation focused on a series of antioxidant flavonoids previously claimed for its various physiological and biochemical functions including antipsychotic actions. Eleven flavonoid compounds were screened for their binding affinity with serotonin transporter (SERT) by molecular docking using AUTODOCK Tools-1.5.6 & 4.2. The new SERT protein was designed and validated through homology modeling by using the SWISS-Model server. Binding interaction of Tamarixetin and Ombuin flavonoids exhibited appreciable conformation among other flavonoids with SERT protein which could be comparable with fluoxetine and serotonin. This study also helps to predict the delayed action of natural ligands towards SERT protein resulting in the finding of distinguishing binding energy. These results and pose interaction, suggest that natural antioxidant flavonoids could potentially act due to its action against the SERT system as like as selective serotonin reuptake inhibitors (SSRI). [ABSTRACT FROM AUTHOR]

Information about three-dimensional structure of protein is important to clearly understand its character and function in molecular level. Protein structure determination through laboratory testing needs highly cost of steps and instrument. Three dimensional structure of protein can be scientifically predicted using several in silico methods. The structure of allergen protein was predicted using SWISS-MODEL as homology method in this research. The result showed that structure prediction of allergen protein B7TWE7 (UniProt ID) from Fagus sylfatica (beechnut) have three-dimensional structure with identity value 72% and e-value = 3,4x10-58. This study used the 1e09A (PDB ID) of Prunus avinus (cherry) as a template.Keywords: allergen, homology method, protein structure, swiss-model ABSTRAKInformasi struktur tiga dimensi protein penting untuk memahami sifat dan fungsi protein ditingkat molekular secara detil. Penentuan struktur protein dengan cara pengujian di laboratorium memerlukan tahapan dan instrumentasi dengan biaya tinggi. Struktur tiga dimensi protein dapat diprediksi secara ilmiah dengan menggunakan beberapa metode secara in silico. Metode yang digunakan pada penelitian ini adalah metode homologi menggunakan program SWISS-MODEL. Protein yang akan diprediksi struktur tiga dimensinya adalah protein alergen pangan. Hasil penelitian menunjukkan bahwa prediksi struktur protein alergen B7TWE7 (UniProt ID) dari Fagus sylfatica (beechnut) dengan metode homologi menggunakan program SWISS-MODEL menghasilkan model struktur tiga dimensi protein dengan nilai identity 72% dan e-value = 3,4x10-58. Template protein yang digunakan adalah 1e09A (PDB ID) dari Prunus avinus (cherry).Kata kunci: alergen, metode homologi, struktur protein, swiss-model

Ganoderma lucidum is a basidiomycete fungus that produces ligninase for the modification of lignin. Lignin peroxidase (LiP) is a glycoprotein that acts on the recalcitrant cell wall component lignin. In the present study, the phylogenetic analysis of Ganoderma lucidum GD88 with the partial coding sequence (cds) of other LiP isoforms was performed using MEGA6. After determination of the open reading frame, the +3 frame nucleotide sequence was converted to protein using the EMBOSS Transseq and the secondary structure was predicted using the Chou and Fasman Secondary Structure Prediction server (CFSSP). Protein modeling was also performed by SWISS-MODEL. The obtained result shows that the lipH partial cds of Ganoderma lucidum GD88 is homologous to the lipD gene of Phanerochaete chrysosporium. The secondary structure prediction result revealed that the percent content of the helix (67) is higher than the percent contents of sheet (53.4) and turns (13.6). According to the generated model, LiP H protein is a homodimer with chains A and B. The heme acts as a ligand and plays a major role in structure stabilization.

The correlation between tuberous sclerosis complex 1 (TSC1) gene polymorphism and epilepsy was studied. In total, 38 patients with epilepsy treated in People's Hospital of Rizhao from May 2015 to June 2016 were selected as study subjects, as the observation group, 38 healthy people in the same period were selected as the control group. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to study the polymorphism of TSC1 gene in the above study subjects. The mRNA expression of TSC1 gene in the observation group and the control group was measured by fluorescence quantitative PCR, the expression of TSC1 protein in the control and observation group was measured by western blotting and ELISA. The polymorphisms of TSC1 gene in control group and observation group were analyzed by PCR-RFLP. There were three genotypes of TCS1 gene locus 142 in healthy population: CC (79.3%), CA (13.9%) and AA (6.8%), there were also three genotypes at locus 142 in the observation group: CC (21.3%), CA (26.4%) and AA (52.3%), there was significant difference in the genotypes at locus 142 between healthy population and the patients with epilepsy (P<0.05). It was observed by fluorescence quantitative PCR that there was no significant difference in the mRNA expression of TSC1 gene between the control group and the observation group (P>0.05). The expression of TSC1 gene was detected by western blot method. Western blotting showed no significant difference in TSC1 protein expression between the two groups (P>0.05). However, by determining the activity of TSC1 protein in the observation group and the control group by ELISA, it was found that TSC1 activity in healthy human body (8.95±2.41 U/ml) was much lower than that in the patients with epilepsy (29.27±4.06 U/ml), the difference was statistically significant (P<0.05). It was found that locus 142 may be located at the active center of TSC1 enzyme by homology modeling of SWISS-MODEL, the mutation of locus 142 could lead to the change of TSC1 activity. The polymorphism of locus 142 in TSC1 gene is correlated with epilepsy, that is, the increase of CA and AA content in locus 142 leads to the occurrence of epilepsy. [ABSTRACT FROM AUTHOR]

Beta-amylase (β-amylase, EC 3.2.1.2) is an enzyme that catalyses hydrolysis of glucosidic bonds in polysaccharides. In this study, we analyzed protein sequence of predicted beta-amylase 7-like protein in Brachypodium distachyon. pI (isoelectric point) value was found as 5.23 in acidic character, while the instability index (II) was found as 50.28 with accepted unstable protein. The prediction of subcellular localization was revealed that the protein may reside in chloroplast by using CELLO v.2.5. The 3D structure of protein was performed using comparative homology modeling with SWISS-MODEL. The accuracy of the predicted 3D structure was checked using Ramachandran plot analysis showed that 95.4% in favored region. The results of our study contribute to understanding of β-amylase protein structure in grass species and will be scientific base for 3D modeling of beta-amylase proteins in further studies.

In eukaryotes, serine proteases are cellular localized hydrolases reported to regulate essential biological reactions. Improved industrial applications of proteins are aided by prediction and analysis of their 3-dimensional structures (3D). A serine protease was identified from CTG-clade yeast Meyerozyma guilliermondii strain SO and its 3D structure as well as its catalytic attributes have not been fully understood yet, thus we seek to report on the catalytic mechanism of M. guilliermondii strain SO Mg PRB1 using substrate PMSF via in silico docking as well as its stability by way of disulfide bonds formation. Herein, bioinformatics tools and techniques were used to predict, validate and analyze the possible changes of CUG ambiguity (if any) in strain SO using template PDB ID: 3F7O. Structural assessments confirmed the classic catalytic triad Asp305, His337, and Ser499. Superimposition of Mg PRB1 and template 3F7O structures revealed the unlinked cysteine residues between Cys341, Cys440, Cys471 and Cys506 of MgPRB1 compared to template 3F7O with two disulfide bonds formation, which confers structural stability. In conclusion, serine protease structure from strain SO was successfully predicted and studies towards understanding at the molecular level may be undertaken for its potential applications in the degradation of peptide bonds. [Display omitted] • Serine protease (PRB1) was identified in our previous study from a novel yeast expression host, M. guilliermondii strain SO. • The 3D structure of M. guilliermondii strain SO serine protease (Mg PRB1) was modelled using the SWISS-MODEL web-server. • InterPro (https://www.ebi.ac.uk/interpro/result/InterProScan/) was used to annotate functional analysis of Mg PRB1 sequence. • Validation of the predicted protein structure of Mg PRB1 was carried out using ERRAT, Verify3D and PROCHECK. • AutoDock Vina was used to carry out the protein – ligand interaction. [ABSTRACT FROM AUTHOR]

Objective: The major purpose of the present study was to predict the structure of Radical s-adenosyl-L-methionine Domain 2 (RSAD2), the most targeted protein of the Zika virus using comparative modeling, to validate the models that were generated and molecular dynamics (MD) simulations were performed., Methods: The secondary structure of RSAD2 was estimated using the Garnier-Osguthorpe-Robson, Self-Optimized Prediction method with Alignment, and Position-Specific Iterative-Blast based secondary structure prediction algorithms. The best of them were preferred based on their DOPE score, then three-dimensional structure identification using SWISS-MODEL and the Protein Homology/Analogy Recognition Engine (Phyre2) server. SAVES 6.0 was used to validate the models, and the preferred model was then energetically stabilized. The model with least energy minimization was used for MD simulations using iMODS., Results: The model predicted using SWISS-MODEL was determined as the best among the predicted models. In the Ramachandran plot, there were 238 residues (90.8%) in favored regions, 23 residues (8.8%) in allowed regions, and 1 residue (0.4%) in generously allowed regions. Energy minimization was calculated using Swiss PDB viewer, reporting the SWISS-MODEL with the lowest energy (E = -18439.475 KJ/mol) and it represented a stable structure conformation at three-dimensional level when analyzed by MD simulations., Conclusion: A large amount of sequence and structural data is now available, for tertiary protein structure prediction, hence implying a computational approach in all the aspects becomes an opportunistic strategy. The best three-dimensional structure of RSAD2 was built and was confirmed with energy minimization, secondary structure validation and torsional angles stabilization. This modeled protein is predicted to play a role in the development of drugs against Zika virus infection., (Copyright: © International Journal of Health Sciences.)

Ganoderma lucidum is a basidiomycete fungus that produces ligninase for the modification of lignin. Lignin peroxidase (LiP) is a glycoprotein that acts on the recalcitrant cell wall component lignin. In the present study, the phylogenetic analysis of Ganoderma lucidum GD88 with the partial coding sequence (cds) of other LiP isoforms was performed using MEGA6. After determination of the open reading frame, the +3 frame nucleotide sequence was converted to protein using the EMBOSS Transseq and the secondary structure was predicted using the Chou and Fasman Secondary Structure Prediction server (CFSSP). Protein modeling was also performed by SWISS-MODEL. The obtained result shows that the lipH partial cds of Ganoderma lucidum GD88 is homologous to the lipD gene of Phanerochaete chrysosporium. The secondary structure prediction result revealed that the percent content of the helix (67) is higher than the percent contents of sheet (53.4) and turns (13.6). According to the generated model, LiP H protein is a homodimer with chains A and B. The heme acts as a ligand and plays a major role in structure stabilization. [ABSTRACT FROM AUTHOR]

KLF proteins are highly conserved among mammals from human to mouse, with many KLFs also having homologs in Gallus gallus (Chicken), Danio rerio (Zebra fish), and Xenopus laevis (Frog). On the basis of functional characteristics, KLF proteins can be divided into three distinct groups. KLFs in group 1 (KLFs 3, 8, and 12) serve as transcriptional repressors through their interaction with the carboxy-terminal binding protein (CtBP). Family members in group 2 (KLFs 1, 2, 4, 5, 6, and 7) function predominantly as transcriptional activators. KLFs in group 3 (KLFs 9, 10, 11, 13, 14, and 16) have repressor activity through their interaction with the common transcriptional corepressor Sin3A. The encoded protein is thought to play an important role in the regulation of epithelial to mesenchymal transition, a process which occurs normally during development but also during metastasis. A homology modelling method was used for the prediction of the structure and other various physico-chemical properties of protein were obtained using ProtParam. 3D structure was constructed for the target protein using I- TASSER and SWISS-MODEL. The comparison between the structures generated from above mentioned tools indicates greater acceptability of the structure generated from I- TASSER and validation of structure was performed by using Ramachandran plot. The present study gave an outlook on KLF8 protein and further research to be carried out in preventing the cancer in human. [ABSTRACT FROM AUTHOR]

Beta-amylase (β-amylase, EC 3.2.1.2) is an enzyme that catalyses hydrolysis of glucosidic bonds in polysaccharides. In this study, we analyzed protein sequence of predicted beta-amylase 7-like protein in Brachypodium distachyon. pI (isoelectric point) value was found as 5.23 in acidic character, while the instability index (II) was found as 50.28 with accepted unstable protein. The prediction of subcellular localization was revealed that the protein may reside in chloroplast by using CELLO v.2.5. The 3D structure of protein was performed using comparative homology modeling with SWISS-MODEL. The accuracy of the predicted 3D structure was checked using Ramachandran plot analysis showed that 95.4% in favored region. The results of our study contribute to understanding of β-amylase protein structure in grass species and will be scientific base for 3D modeling of beta-amylase proteins in further studies. [ABSTRACT FROM AUTHOR]

Two structurally novel classes of small helix-rich Fatty acid and retinoid binding (FAR) proteins are produced by parasitic nematodes. The plant and animal hosts of these parasitic nematodes have no counterparts of these proteins. FAR proteins play an active role in nematode development and survival when in contact with host tissue. Thus FAR proteins represent potential targets for new synthetic drug designing. A 3-dimensional model (3D) was designed for the Fatty acid and retinoid binding protein (178 aa) from the filarial nematode Acanthocheilonema viteae. A predicted model was constructed for the target protein using SWISS-MODEL. The constructed model was validated using protein structure checking tools for reliability. The prediction of 3D structure of a protein is a prerequisite and is also required for identifying the conformational epitopes which are essential for synthetic drug designing vaccines. Altogether, these data makes FAR protein a potentially valuable target for drug and vaccine development against filarial nematodes. [ABSTRACT FROM AUTHOR]

By constructing the genomic library, a β-glucosidase gene, with a length of 2,382 bp, encoding 793 amino acids, designated bgla, is cloned from a marine bacterium Aeromonas sp. HC11e-3. The enzyme is expressed successfully in the recombinant host Escherichia coli BL21 (DE3) and purified using glutathione affinity purification system. It shows the optimal activity at pH 6, 55 °C and hydrolyzes aryl-glucoside specially. Ca, Mn, Zn, Ba, Pb, Sr can activate the enzyme activity, whereas SDS, EDTA, DTT show slight inhibition to the enzyme activity. Homologous comparing shows that the enzyme belongs to glycosyl hydrolase family 3, exhibiting 46 % identity with a fully characterized glucosidase from Thermotoga neapolitana DSM 4359. Such results provide useful references for investigating other glucosidases in the glycosyl family 3 as well as developing glucosidases using in suitable industrial area. [ABSTRACT FROM AUTHOR]

A reliable model of tobacco acetohydroxy acid synthase (AHAS) was obtained by homology modeling based on a yeast AHAS X-ray structure using the Swiss-Model server. Conserved residues at the dimer interface were identified, of which the functional roles of four residues, namely H142, E143, M489, and M542, were determined by site-directed mutagenesis. Eight mutants were successfully generated and purified, five of which (H142T, M489V, M542C, M542I, and M542V) were found to be inactive under various assay conditions. The H142K mutant was moderately altered in all kinetic parameters to a similar extent. In addition, the mutant was more thermo-labile than wild type enzyme. The E143A mutant increased the Km value more than 20-fold while other parameters were not significantly changed. All mutations carried out on residue M542 inactivated the enzyme. Though showing a single band on SDS–PAGE, the M542C mutant lost its native tertiary structure and was aggregated. Except M542C, each of the other mutants showed a secondary structure similar to that of wild type enzyme. Although all the inactive mutants were able to bind FAD, the mutants M489V and M542C showed a very low affinity for FAD. None of the active mutants constructed was strongly resistant to three tested herbicides. Taken together, the results suggest that the residues of H142, E143, M489, and M542 are essential for catalytic activity. Furthermore, it seems that H142 residue is involved in stabilizing the dimer interaction, while E143 residue may be involved in binding with substrate pyruvate. The data from the site-directed mutagenesis imply that the constructed homology model of tobacco AHAS is realistic. [Copyright &y& Elsevier]

Manuel Peitsch is Global Head of Informatics and Knowledge Management at the Novartis Institutes for BioMedical Research, a position he has held since he joined Novartis in 2001. He is a world-renowned leader in bioinformatics, with more than 90 publications and several patents and awards. His pioneering research impacted bioinformatics by introducing high-throughput automated protein modeling and web-based bioinformatics. Manuel''s findings and developments in this area have had important implications for the use of protein structures in biology. Most of his career has been focused on cell death research (complement, T cells and apoptosis), bioinformatics and scientific computing in life sciences.Prior to Novartis, Manuel held positions at the National Cancer Institute FCRF in Frederick, MA, and at the Institute of Biochemistry at the University of Lausanne. In 1994, he was head of Bioinformatics at GlaxoWellcome''s Geneva Biomedical Research Institute. In 1997 and 1998 he co-founded three bioinformatics organizations: Geneva Bioinformatics (GeneBio), the Swiss Institute of Bioinformatics and GlaxoWellcome Experimental Research, where he was Director for Scientific Computing. In 2000 he headed Informatics & Knowledge Management at GlaxoSmithKline Research & Development.Since 2002, Manuel has been Professor for Bioinformatics at the University of Basel. He is also a member of the Foundation Council of the Swiss Institute of Bioinformatics. [Copyright &y& Elsevier]