WHAT IF Research Articles

Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita

In lower eukaryotes-like fish, innate immunity contributed by various pattern recognition receptor (PRR) plays an essential role in protection against diseases. Nucleotide-binding and oligomerization domain (NOD)-2 is a cytoplasmic PRR that recognizes MDP (muramyl dipeptide) of the Gram positive and Gram negative bacteria as ligand and activates signalling to induce innate immunity. Hypothesizing a similar NOD2 signalling pathway of higher eukaryotes, the peripheral blood leucocytes (PBLs) of rohu (Labeo rohita) was stimulated with MDP. The data of quantitative real-time PCR (qRT-PCR) revealed MDP-mediated inductive expression of NOD2 and its down-stream molecule RICK/RIP2 (receptor-interacting serine-threonine protein kinase-2). This observation suggested the existence of MDP-binding sites in rohu NOD2 (rNOD2). To investigate it, 3D model of ligand-binding leucine-rich repeat (LRR) region of rNOD2 (rNOD2-LRR) was constructed following ab initio and threading approaches in I-TASSER web server. Structural refinement of the model was performed by energy minimization, and MD (molecular dynamics) simulation was performed in GROMACS (Groningen Machine for Chemical Simulations). The refined model of rNOD2-LRR was validated through SAVES, ProSA, ProQ, WHAT IF and MolProbity servers, and molecular docking with MDP was carried out in GOLD 4.1. The result of docking identified LRR3-7 comprising Lys820, Phe821, Asn822, Arg847, Gly849, Trp877, Trp901 and Trp931 as MDP-binding critical amino acids in rNOD2. This is the first study in fish to provide an insight into the 3D structure of NOD2-LRR region and its important motifs that are expected to be engaged in MDP binding and innate immunity.

In silico predictive studies of mAHR congener binding using homology modelling and molecular docking

The aryl hydrocarbon receptor (AHR) is one of the principal xenobiotic, nuclear receptor that is responsible for the early events involved in the transcription of a complex set of genes comprising the CYP450 gene family. In the present computational study, homology modelling and molecular docking were carried out with the objective of predicting the relationship between the binding efficiency and the lipophilicity of different polychlorinated biphenyl (PCB) congeners and the AHR in silico. Homology model of the murine AHR was constructed by several automated servers and assessed by PROCHECK, ERRAT, VERIFY3D and WHAT IF. The resulting model of the AHR by MODWEB was used to carry out molecular docking of 36 PCB congeners using PatchDock server. The lipophilicity of the congeners was predicted using the XLOGP3 tool. The results suggest that the lipophilicity influences binding energy scores and is positively correlated with the same. Score and Log P were correlated with r = +0.506 at p = 0.01 level. In addition, the number of chlorine (Cl) atoms and Log P were highly correlated with r = +0.900 at p = 0.01 level. The number of Cl atoms and scores also showed a moderate positive correlation of r = +0.481 at p = 0.01 level. To the best of our knowledge, this is the first study employing PatchDock in the docking of AHR to the environmentally deleterious congeners and attempting to correlate structural features of the AHR with its biochemical properties with regards to PCBs. The result of this study are consistent with those of other computational studies reported in the previous literature that suggests that a combination of docking, scoring and ranking organic pollutants could be a possible predictive tool for investigating ligand-mediated toxicity, for their subsequent validation using wet lab-based studies.

Sequence analysis and homology modeling of peroxidase from Medicago sativa.

Plant peroxidases are one of the most extensively studied group of enzymes which find applications in the environment, health, pharmaceutical, chemical and biotechnological processes. Class III secretary peroxidase from alfalfa (Medicago sativa) has been characterized using bioinformatics approach Physiochemical properties and topology of alfalfa peroxidase were compared with that of soybean and horseradish peroxidase, two most popular commercially available peroxidase preparations. Lower value of instability index as predicted by ProtParam and presence of extra disulphide linkages as predicted by Cys_REC suggested alfalfa peroxidase to be more stable than either of the commercial preparations. Multiple Sequence Alignment (MSA) with other functionally similar proteins revealed the presence of highly conserved catalytic residues. Three dimensional model of alfalfa peroxidase was constructed based on the crystal structure of soybean peroxidase (PDB Id: 1FHF A) by homology modelling approach. The model was checked for stereo chemical quality by PROCHECH, VERIFY 3D, WHAT IF, ERRAT, 3D MATCH AND ProSA servers. The best model was selected, energy minimized and used to analyze structure function relationship with substrate hydrogen peroxide by Autodock 4.0. The enzyme substrate complex was viewed with Swiss PDB viewer and one residue ASP43 was found to stabilize the interaction by hydrogen bonds. The results of the study may be a guiding point for further investigations on alfalfa peroxidase.

In Silico Study and Validation of Phosphotransacetylase (PTA) as a Putative Drug Target for Staphylococcus aureus by Homology-Based Modelling and Virtual Screening

Staphylococcus aureus, a Gram-positive bacterium, can cause a range of illnesses from minor skin infections to life-threatening diseases, such as bacteraemia, endocarditis, meningitis, osteomyelitis, pneumonia, toxic shock syndrome and sepsis. Due to the emergence of antibiotic resistance strains, there is a need to develop of new class of antibiotics or drug for this pathogen. The phosphotransacetylase enzyme plays an important role in the acetate metabolism and found to be essential for the survival of the S. aureus. This enzyme was evaluated as a putative drug target for S. aureus by in silico analysis. The 3D structure of the phosphotransacetylase from S. aureus was modelled, using the 1TD9 chain 'A' from Bacillus subtilis as a template at the resolution of 2.75 Å. The generated model has been validated by PROCHECK, WHAT IF and SuperPose. The docking was performed by the Molegro virtual docker using the ZINC database generated ligand library. The ligand library was generated within the limitation of the Lipinski rule of five. Based on the dock-score, five molecules have been subjected to ADME/TOX analysis and subjected for pharmacophore model generation. The zinc IDs of the potential inhibitors are ZINC08442078, ZINC8442200, ZINC 8442087 and ZINC 8442184 and found to be pharmacologically active antagonist of phosphotransacetylase. The molecules were evaluated as no-carcinogenic and persistent molecule by START programme.

Water-Refined Solution Structure of the Human Grb7-SH2 Domain in Complex with the erbB2 Receptor Peptide pY1139

We report a refinement in implicit water of the previously published solution structure of the Grb7-SH2 domain bound to the erbB2 receptor peptide pY1139. Structure quality measures indicate substantial improvement, with residues in the most favored regions of the Ramachandran plot increasing by 14 % and with WHAT IF statistics (Vriend, G. J. Mol. Graph., 1990, 8(1), 52-56) falling closer to expected values for well-refined structures.

High-definition NMR structure of PED/PEA-15 death effector domain reveals details of key polar side chain interactions

Death effector domain (DED) proteins constitute a subfamily of the large death domain superfamily that is primarily involved in apoptosis pathways. DED structures have characteristic side chain–side chain interactions among polar residues on the protein surface, forming a network of hydrogen bonds and salt bridges. The polar interaction network is functionally important in promoting protein–protein interactions by maintaining optimal side chain orientations. We have refined the solution DED structure of the PED/PEA-15 protein, a representative member of DED subfamily, using traditional NMR restraints with the addition of residual dipolar coupling (RDC) restraints from two independent alignment media, and employed the explicit solvent refinement protocol. The newly refined DED structure of PED/PEA-15 possesses higher structural quality as indicated by WHAT IF Z-scores, with most significant improvement in the backbone conformation normality quality factor. This higher quality DED structure of PED/PEA-15 leads to the identification of a number of key polar side chain interactions, which are not typically observed in NMR protein structures. The elucidation of polar side chain interactions is a key step towards the understanding of protein–protein interactions involving the death domain superfamily. The NMR structures with extensive details of protein structural features are thereby termed high-definition (HD) NMR structures.

The ‘WHAT OF’ and the ‘WHAT IF’ of Agential Realism – In Search of the Gendered Subject

The article explores Karen Barad’s theoretical framework, agential realism, to seek out theoretical perspectives that can be used as analytical approaches to empirical data. By selecting two pieces of data we aim to illustrate the analytical possibilities offered by this approach. The first piece of data stipulates an opening of ‘WHAT OF’ of the activities in a world of computer games: WHAT OF the myriad of real and virtual voices, sentiments and actions and their interconnections and meaning for gendered subjectification? The second piece is guided by ‘WHAT IF’ thinking: WHAT would we be able to see IF we brought insights from quantum physics, i.e. spacetimemattering, to the conception of thinking subjects. The examples show that agential realism offers a theoretical framework that allows access to a much wider set of enacting forces to be considered in the analysis. By reading agential realism diffractively with two different empirical examples and two different research ambitions, our attention is drawn to specificities of what the engagements may enact consequently.

Structural Dynamics of Bacterial Translation Initiation Factor IF2

Bacterial translation initiation factor IF2 promotes ribosomal subunit association, recruitment, and binding of fMet-tRNA to the ribosomal P-site and initiation dipeptide formation. Here, we present the solution structures of GDP-bound and apo-IF2-G2 of Bacillus stearothermophilus and provide evidence that this isolated domain binds the 50 S ribosomal subunit and hydrolyzes GTP. Differences between the free and GDP-bound structures of IF2-G2 suggest that domain reorganization within the G2-G3-C1 regions underlies the different structural requirements of IF2 during the initiation process. However, these structural signals are unlikely forwarded from IF2-G2 to the C-terminal fMet-tRNA binding domain (IF2-C2) because the connected IF2-C1 and IF2-C2 modules show completely independent mobility, indicating that the bacterial interdomain connector lacks the rigidity that was found in the archaeal IF2 homolog aIF5B.

Virtual screening and evaluation of Ketol-Acid Reducto-Isomerase (KARI) as a putative drug target for Aspergillosis

Aspergillus is a leading causative agent for fungal morbidity and mortality in immuno-compromised patients. To identify a putative target to design or identify new antifungal drug, against Aspergillus is required. In our previous work, we have analyzed the various biochemical pathways, and we found Ketol Acid Reducto-Isomerase (KARI) an enzyme involves in the amino acid biosynthesis, could be a better target. This enzyme was found to be unique by comparing to host proteome through BLASTp analysis. A homology based model of KARI was generated by Swiss model server. The generated model had been validated by PROCHECK and WHAT IF programs. The Zinc library was generated within the limitation of the Lipinski rule of five, for docking study. Based on the dock-score six molecules have been studied for ADME/TOX analysis and subjected for pharmacophore model generation. The Zinc ID of the potential inhibitors is ZINC00720614, ZINC01068126, ZINC0923, ZINC02090678, ZINC00663057 and ZINC02284065 and found to be pharmacologically active agonist and antagonist of KARI. This study is an attempt to Insilco evaluation of the KARI as a drug target and the screened inhibitors could help in the development of the better drug against Aspergillus.

P5-23-07: Treatment Strategy of Locally Advanced Breast Cancer in Sub Group (T3N1M0, T4bN1M0) in Developing Countries.

Abstract With the recent advances in modern day chemotherapy and hormonal therapy for locally advanced breast cancer [stage III, T3 N1 and T4bN1], most of the oncologist around the globe now prefer to give neoadjuvent chemotherapy and, or hormonal therapy followed by surgery in the treatment of these cases. Randomized research have also shown that this strategy provides ‘pathological complete resolution’ as compared to surgery and then adjuvant chemotherapy in terms of decreasing in size of tumar, decrease in vascularity of tumor mass and micrometastasis. Some author believes that this improve the overall survival duration of patients. This protocol is widely accepted but …. BUT WHAT IF YOU LOSE YOUR PATIENT ON FOLLOWUP … Especially in the developing countries of south east asian region and African continent, where there is poor socioeconomic status and lack of education among common people. The patient gets frustrated after first few doses of neoadjuvent therapy, due to side effects of chemotherapy and don't consider chemotherapy as a treatment compare to surgery. Thus the patient loses faith in treatment strategy itself and go untraceable after one or two sessions of the therapy. The government of developing countries lack resources in terms of manpower and money for satisfactory completion of treatment making the above condition even worse. In our study we followed 230 patients of locally advanced breast cancer in subgroup of stage III [T3 N1, T4bN1] and divided them into two plans on random basis. In first plan we approached with the surgical management followed by adjuvant chemotherapy & counseled the patients for completion of chemotherapy. This plan was shown to 115 patients, out of which 100 patients provided good acceptance & completed the course of chemotherapy. There were 15 patients who remained untraceable after surgery. On the other hand in the 2 group the patients were counseled for neoadjuvent chemotherapy and then surgery in next stage. In this group 115 patients were introduced, out of which 60 patients were lost on follow up after 2–3 sessions. The majority of patients complained about the side effects of chemotherapy and financial reasons and did not come back. Rest of the patients completed the whole course. With no doubt about the result of the treatment, the second group has equivocal survival advantages in terms of morbidity and mortality, but we lost more than half of the patients of second group before completion of treatment. Primarily the acceptance of surgical treatment is more in developing countries, as it is quite more feasible for government and even economical for common people. Thus we prefer the strategy of surgery followed by adjuvant chemo/hormonal therapy in locally advanced breast cancer [stage III T3N1, T4bN1] especially in developing countries like India. THE MOTTO OF THIS STRATEGY IS TO PROVIDE BENEFIT OF COMPLETE TREATMENT TO THE PATIENT THAN TO LOSE THE PATIENT COMPLETELY BEFORE TREATMENT. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-23-07.

Synthesis of anomeric 1,5-anhydrosugars as conformationally locked selective α-mannosidase inhibitors

Anomeric 1,5-anhydrosugar 2 was synthesized from d-glucose derived N-Cbz protected aminodiol 8. The key step involves, acid catalyzed hydrolysis of 1,2-acetonide group in 8 to get hemiacetal that concomitantly undergoes formation of the pyranose ring by attack of C-3 hydroxyethyl group on anomeric C-1, leading to the formation of dioxabicyclo[3.2.1]octane skeleton which on hydrogenolyis gave 2. The glycosidase inhibitory activities of hydroxy- and amino-substituted anomeric 1,5-anhydrosugars 1 and 2, respectively, showed selective inhibition of α-mannosidase. These results were substantiated by molecular docking studies using WHAT IF software and AUTODOCK 4.0 program.

3D modeling and molecular dynamics simulation of an immune-regulatory cytokine, interleukin-10, from the Indian major carp, Catla catla

Interleukin-10 (IL-10) is a pleiotropic immune-regulatory cytokine that is expressed in various species of fish and higher vertebrates, and is activated during infection. In spite of its important role, IL-10 has not been well characterized either functionally or structurally in fish. To analyze its properties and function, we constructed a 3D model of IL-10 in the Indian major carp, the catla (Catla catla), which is a highly preferred fish species and the most commercially important one in the Indian subcontinent. The catla IL-10 model was constructed by comparative modeling using human IL-10 (2ILK) as the template, and a 5 ns molecular dynamics (MD) simulation was carried out to characterize its structural and dynamical features, which was validated by the SAVES, WHAT IF and MolProbity servers. Analysis using the VAST server revealed a comparatively low level of homology between catla and human IL-10 amino acids at the N-terminal (22.7%) compared to the C-terminal (38.29%). Six conserved domains (A-F) were predicted in catla that threaded well with human IL-10, but their putative interaction sites varied significantly. The amino acid residues in helices A and F differed in length between catla and human IL-10, which may lead to the differences in the IL-10/IL-10R complexes of these two species. The existence of two highly conserved amino acid residues (Cys5 and Cys10) in fish IL-10 but not in higher vertebrate (including human) IL-10 was analyzed in this 3D model. CastP, cons-PPISP and InterProSurf server identified several binding pockets with various probe radii, but Cys5 and Cys10 did not form any significant bonds relating to structural stabilization or protein-protein interactions.

In silico Homology Modeling of Prophenoloxidase activating factor Serine Proteinase Gene from the Haemocytes of Fenneropenaeus indicus

In invertebrates, immune system consist of encapsulation, phagocytosis, and nodule formation while humoral responses includes clotting, synthesis of antimicrobial peptides, and activation of the Prophenoloxidase (proPO) system. Serine proteinases (SPs) constitute one of the largest families of proteolytic enzymes involved in the activation of Prophenoloxidase. The major feature of serine proteinase is interlinked by three pairs of conserved disulfide bridges. Although the exact function of the clip domain presently remains unclear, there are certain speculations about its function. The present study reports the three-dimensional structures of novel immune related gene serine proteinase predicted by in silico homology modelling studies. Physico-chemical characterization interprets properties such as pI, EC, AI, GRAVY and instability index and provides valuable data about this clip domain serine proteinase. Prediction of motifs, patterns, disulfide bridges and secondary structure were performed for functional characterization of the serine proteinases. Three dimensional structures for these proteins were not available as yet at PDB. Therefore, a homology model for this serine proteinase protein was developed. The modelling of the three dimensional structure of the proteins showed that models generated by Modeller9V8 were more acceptable in comparison to that by Swiss Model. The models were validated using protein structure checking tools PROCHECK and WHAT IF. The structures will provide a good foundation for functional analysis of experimentally derived crystal structures. The better results of the in silico modelling study are presented, and may help lead to the discovery of new synthetic immune related peptides or derivatives of serine proteinases that could be useful to understand the mechanism of serine proteinase involvement in the Prophenoloxidase activating system of crustaceans. The crystal structure prediction of the immune related proteins serine proteinase of shrimps will help to explore the other life sciences Pharmacokinetics and toxicology, Drug designing and chemo informatics etc.

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces

BackgroundMany newly detected point mutations are located in protein-coding regions of the human genome. Knowledge of their effects on the protein's 3D structure provides insight into the protein's mechanism, can aid the design of further experiments, and eventually can lead to the development of new medicines and diagnostic tools.ResultsIn this article we describe HOPE, a fully automatic program that analyzes the structural and functional effects of point mutations. HOPE collects information from a wide range of information sources including calculations on the 3D coordinates of the protein by using WHAT IF Web services, sequence annotations from the UniProt database, and predictions by DAS services. Homology models are built with YASARA. Data is stored in a database and used in a decision scheme to identify the effects of a mutation on the protein's 3D structure and function. HOPE builds a report with text, figures, and animations that is easy to use and understandable for (bio)medical researchers.ConclusionsWe tested HOPE by comparing its output to the results of manually performed projects. In all straightforward cases HOPE performed similar to a trained bioinformatician. The use of 3D structures helps optimize the results in terms of reliability and details. HOPE's results are easy to understand and are presented in a way that is attractive for researchers without an extensive bioinformatics background.

WIWS: a protein structure bioinformatics Web service collection.

The WHAT IF molecular-modelling and drug design program is widely distributed in the world of protein structure bioinformatics. Although originally designed as an interactive application, its highly modular design and inbuilt control language have recently enabled its deployment as a collection of programmatically accessible web services. We report here a collection of WHAT IF-based protein structure bioinformatics web services: these relate to structure quality, the use of symmetry in crystal structures, structure correction and optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely accessible web services are based on the industry standard WS-I profile and the EMBRACE technical guidelines, and are available via both REST and SOAP paradigms. The web services run on a dedicated computational cluster; their function and availability is monitored daily.

WHAT IF ELEPHANT SHREWS REALLY WERE RELATED TO ELEPHANTS?

Most of us have seen movies where, with the single beam of a gunlike device, a mad scientist in a white lab coat shrinks large-bodied animals to the size of an ant. Were elephants and elephant shrews victims of such a fantastic fate? From the time of their first description in 1800, elephant shrews (Macroscelidea) were considered related to shrews and other insectivores along with tenrecs (Tenrecidae) and golden moles (Chrysochloridae), whereas elephants (Proboscidea) were originally placed more or less close to ungulates such as hippos and rhinos (the now obsolete Pachydermata). Since then, paleontologists have unearthed numerous fossil relatives that have shed new light on the study of both taxa. Thanks to these fossil discoveries, and to the progress of comparative anatomy and phylogenetic methods, the relationships of both elephants and elephant shrews were eventually reconsidered (Fig. 1A). For instance, elephants were securely placed close to sirenians (dugongs and manatees) and hyracoids (dassies) in Paenungulata, whereas elephant shrews showed affinities with Glires (rabbits and rodents). These morphological analyses also recognized Cetacea (whales and dolphins) as the sister taxon of artiodactyls (cows, pigs, etc.) and that carnivorans shared a common ancestor with pangolins (Pholidota). On the verge of the new millennium, more than 250 years after Linnaeus's foundation of taxonomy, 18 living orders of placental mammals were recognized, but several of their proposed relationships were …

Infected foot ulcers in male and female diabetic patients: a clinico-bioinformative study

BackgroundThe study aimed at (i) characterizing the mode of transmission of blaCTX-M and blaTEM-1 among extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli strains isolated from infected diabetic foot ulcers, and (ii) identifying the risk factors for "sex-associated multidrug resistant Gram-negative bacterial (MDRGNB)-infection status" of the ulcers.MethodsSeventy-seven diabetic patients having clinically infected foot ulcers were studied in a consecutive series. The E. coli strains isolated from the ulcers were screened for blaCTX-M, blaTEM-1, armA, rmtA and rmtB during the 2-year study-period. PCR amplified blaCTX-M genes were cloned and sequenced. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was used for the analysis of genetic relatedness of the ESBL-producers. Risk factors for "sex-associated MDRGNB-infection status" of ulcers were assessed. Modeling was performed using Swiss-Model-Server and verified by Procheck and verify3D programmes. Discovery Studio2.0 (Accelrys) was used to prepare Ramachandran plots. Z-scores were calculated using 'WHAT IF'-package. Docking of cefotaxime with modeled CTX-M-15 enzyme was performed using Hex5.1.ResultsAmong 51 E. coli isolates, 14 (27.5%) ESBL-producers were identified. Only 7 Class1 integrons, 2 blaCTX-M-15, and 1 blaTEM-1 were detected. Ceftazidime and cefotaxime resistance markers were present on the plasmidic DNA of both the blaCTX-M-15 positive strains and were transmissible through conjugation. The residues Asn132, Glu166, Pro167, Val172, Lys234 and Thr235 of CTX-M-15 were found to make important contacts with cefotaxime in the docked-complex. Multivariate analysis proved 'Glycemic control at discharge' as the single independent risk factor.ConclusionsMale diabetic patients with MDRGNB-infected foot ulcers have poor glycemic control and hence they might have higher mortality rates compared to their female counterparts. Plasmid-mediated conjugal transfer, albeit at a low frequency might be the possible mechanism of transfer of blaCTX-M-15 resistance marker in the present setting. Since the docking results proved that the amino acid residues Asn132, Glu166, Pro167, Val172, Lys234 and Thr235 of CTX-M-15 (enzyme) make important contacts with cefotaxime (drug) in the 'enzyme-drug complex', researchers are expected to duly utilize this information for designing more potent and versatile CTX-M-inhibitors.

Synthesis, computational study and glycosidase inhibitory activity of polyhydroxylated conidine alkaloids—a bicyclic iminosugar

New bicyclic conidine iminosugars 1d and 1e were synthesized from D-glucose. Thus, D-glucose was converted to sugar beta-amino acids 3a and 3b in good yields. Individual treatment of 3a/3b with the Mukaiyama reagent afforded sugar beta-lactams 4a/4b that on reduction with LiAlH(4)/AlCl(3) gave azetidines 5a/5b with a sugar appendage. Reductive aminocyclization of sugar azetidines 5a/5b afforded the corresponding conidine iminosugars 1d/1e. Based on the (1)H NMR and DFT calculation studies the conformation of 1d was assigned as half chair A2 and that of 1e as a boat B2. The glycosidase inhibitory activities of 1d and 1e such as alpha-mannosidase, alpha-glucosidase and alpha-galactosidase were studied. The alpha-amylase activity was compared with acarbose. Compound 1d was found to be a moderate inhibitor of glycosidases while 1e was noticed to be a good inhibitor of alpha-mannosidase and a moderate inhibitor of other glycosidases. These results were substantiated by molecular docking studies using WHAT IF software and the AUTODOCK 3.0 program.

Prediction of 3D Structure of Paralytic Insecticidal Toxin (ITX-1) of Tegenaria agrestis (Hobo Spider)

Paralytic insecticidal toxin (ITX-1) (Tegenaria agrestis) involved multiple antigenic components to direct and empower the immune system to protect the host from infection. Spider peptide toxins with nanomolar affinities for their receptors are promising pharmacological tools for understanding the physiological role of ion channels and as leads for the development of novel therapeutic agents and strategies for ion channel-related diseases. A 3-dimensional model (3D) was developed for the Paralytic insecticidal toxin of the (ITX-1) of Tegenaria agrestis (Hobo spider). A homology modeling method was used for the prediction of the structure. For the modeling, a template protein was obtained by mGenTHERADER, namely the high-resolution X-ray crystallography structure of a FERREDOXIN (1FCA) of Clostridium acidurici. By comparing the template protein a rough model was constructed for the target protein using MODELLER, a program for comparative modelling. The model was validated using protein structure checking tools such as PROCHECK and WHAT IF for reliability. The information thus discussed provides insight to the molecular understanding of Paralytic insecticidal toxin (Tegenaria agrestis). The predicted 3-D model may be further used in characterizing the protein in wet laboratory.

In silico Analysis and Homology Modelling of Antioxidant Proteins of Spinach

Spinach is an important dietary vegetable often associated with bene fi cial health effects. In this paper, a bioinformatics and molecular modeling approach was adopted to explore properties and structure of spinach antioxidant proteins. The antioxidant proteins selected for this study are ascorbate peroxidase (APX), dehydro ascorbate reductase (DHAR), phospholipid hydroperoxide glutathione peroxidase-like protein (PHGPX) and 2-Cys peroxiredoxin BAS1 (2-CPs). Physico-chemical characterization interprets properties such as pI, EC, AI, GRAVY and instability index and provides data about these proteins and their properties. Prediction of motifs, patterns, disul fi de bridges and secondary structure were performed for functional characterization. Three dimensional structures for these proteins were not available as yet at PDB. Therefore, homology models for these antioxidant proteins were developed. The modelling of the three dimensional structure of these proteins shows that models generated by Modeller were more acceptable in comparison to that by Geno3D and Swiss Model. The models were validated using protein structure checking tools PROCHECK and WHAT IF. These structures will provide a good foundation for functional analysis of experimentally derived crystal structures.