A tracked approach for automated NMR assignments in proteins (TATAPRO)

A novel automated approach for the sequence specific NMR assignments of ¹H^N, ¹³C, ¹³C, ¹³C/¹H and ¹⁵N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate ¹H^N and ¹⁵N chemical shifts with those of ¹³C, ¹³C and ¹³C/¹H. The information derived from such correlations is used to create a `master_list' consisting of all possible sets of ¹H^N _i, ¹⁵N_i, ¹³C _i, ¹³C _i, ¹³C_i/¹H _i, ¹³C _i–1, ¹³C _i–1 and ¹³C_i–1/ ¹H _i–1 chemical shifts. On the basis of an extensive statistical analysis of ¹³C and ¹³C chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master_list and also to translate the protein primary sequence into an array called pps_array. The program then uses the master_list to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so, each assigned residue is tracked in an array called assig_array, with the two-digit code assigned earlier. The assig_array is then mapped onto the pps_array for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18–42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the master_list created for the test proteins.     

Luminescence properties of green‐emitting Ca2MgSi2O7:Eu2+ phosphor by a solid‐state reaction method

A europium (Eu)‐doped di‐calcium magnesium di‐silicate phosphor, Ca₂MgSi₂O₇:Eu²⁺, was prepared using a solid‐state reaction method. The phase structure, particle size, surface morphology, elemental analysis, different stretching mode and luminescence properties were analyzed by X‐ray diffraction (XRD), transmission electron microscopy (TEM), field emission scanning electron microscopy (FESEM) with energy dispersive X‐ray spectroscopy (EDX), Fourier transform infrared (FTIR) spectroscopy, photoluminescence (PL) and mechanoluminescence (ML). The phase structure of Ca₂MgSi₂O₇:Eu²⁺ was an akermanite‐type structure, which belongs to the tetragonal crystallography with space group P4?2₁m; this structure is a member of the melilite group and forms a layered compound. The surface of the prepared phosphor was not found to be uniform and particle distribution was in the nanometer range. EDX and FTIR confirm the components of Eu²⁺‐doped Ca₂MgSi₂O₇ phosphor. Under UV excitation, the main emission peak appeared at 530 nm, belonging to the broad emission ascribed to the 4f⁶5d¹→4f⁷ transition of Eu²⁺. The ML intensity of the prepared phosphor increased linearly with increasing impact velocity. A CIE color chromaticity diagram and ML spectrum confirmed that the prepared Ca₂MgSi₂O₇:Eu²⁺ phosphor would emit green color and the ML spectrum was similar to that of PL, which indicated that ML is emitted from the same center of Eu²⁺ ions. Copyright © 2015 John Wiley & Sons, Ltd.     

Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity

Allergic reactions can be considered as maladaptive IgE immune responses towards environmental antigens. Intriguingly, these mechanisms are observed to be very similar to those implicated in the acquisition of an important degree of immunity against metazoan parasites (helminths and arthropods) in mammalian hosts. Based on the hypothesis that IgE-mediated immune responses evolved in mammals to provide extra protection against metazoan parasites rather than to cause allergy, we predict that the environmental allergens will share key properties with the metazoan parasite antigens that are specifically targeted by IgE in infected human populations. We seek to test this prediction by examining if significant similarity exists between molecular features of allergens and helminth proteins that induce an IgE response in the human host. By employing various computational approaches, 2712 unique protein molecules that are known IgE antigens were searched against a dataset of proteins from helminths and parasitic arthropods, resulting in a comprehensive list of 2445 parasite proteins that show significant similarity through sequence and structure with allergenic proteins. Nearly half of these parasite proteins from 31 species fall within the 10 most abundant allergenic protein domain families (EF-hand, Tropomyosin, CAP, Profilin, Lipocalin, Trypsin-like serine protease, Cupin, BetV1, Expansin and Prolamin). We identified epitopic-like regions in 206 parasite proteins and present the first example of a plant protein (BetV1) that is the commonest allergen in pollen in a worm, and confirming it as the target of IgE in schistosomiasis infected humans. The identification of significant similarity, inclusive of the epitopic regions, between allergens and helminth proteins against which IgE is an observed marker of protective immunity explains the ‘off-target’ effects of the IgE-mediated immune system in allergy. All these findings can impact the discovery and design of molecules used in immunotherapy of allergic conditions.     

Probing ADAMTS13 Substrate Specificity using Phage Display

Von Willebrand factor (VWF) is a large, multimeric protein that regulates hemostasis by tethering platelets to the subendothelial matrix at sites of vascular damage. The procoagulant activity of plasma VWF correlates with the length of VWF multimers, which is proteolytically controlled by the metalloprotease ADAMTS13. To probe ADAMTS13 substrate specificity, we created phage display libraries containing randomly mutated residues of a minimal ADAMTS13 substrate fragment of VWF, termed VWF73. The libraries were screened for phage particles displaying VWF73 mutant peptides that were resistant to proteolysis by ADAMTS13. These peptides exhibited the greatest mutation frequency near the ADAMTS13 scissile residues. Kinetic assays using mutant and wild-type substrates demonstrated excellent agreement between rates of cleavage for mutant phage particles and the corresponding mutant peptides. Cleavage resistance of selected mutations was tested in vivo using hydrodynamic injection of corresponding full-length expression plasmids into VWF-deficient mice. These studies confirmed the resistance to cleavage resulting from select amino acid substitutions and uncovered evidence of alternate cleavage sites and recognition by other proteases in the circulation of ADAMTS13 deficient mice. Taken together, these studies demonstrate the key role of specific amino acids residues including P3-P2’ and P11’, for substrate specificity and emphasize the importance in flowing blood of other ADAMTS13–VWF exosite interactions outside of VWF73.     

Evaluation of Hs-CRP Levels and Interleukin 18 (-137G/C) Promoter Polymorphism in Risk Prediction of Coronary Artery Disease in First Degree Relatives

Background

Coronary Artery Disease (CAD) is clearly a multifactorial disease that develops from childhood and ultimately leads to death. Several reports revealed having a First Degree Relatives (FDRS) with premature CAD is a significant autonomous risk factor for CAD development. C - reactive protein (CRP) is a member of the pentraxin family and is the most widely studied proinflammatory biomarker. IL-18 is a pleiotrophic and proinflammatory cytokine which is produced mainly by macrophages and plays an important role in the inflammatory cascade.

Methods and Results

Hs-CRP levels were estimated by ELISA and Genotyping of IL-18 gene variant located on promoter -137 (G/C) by Allele specific PCR in blood samples of 300 CAD patients and 300 controls and 100 FDRS. Promoter Binding sites and Protein interacting partners were identified by Alibaba 2.1 and Genemania online tools respectively. Hs-CRP levels were significantly high in CAD patients followed by FDRS when compared to controls. In IL-18 -137 (G/C) polymorphism homozygous GG is significantly associated with occurrence of CAD and Hs-CRP levels were significantly higher in GG genotype subjects when compared to GC and CC. IL-18 was found to be interacting with 100 protein interactants.

Conclusion

Our results indicate that Hs-CRP levels and IL-18-137(G/C) polymorphism may help to identify risk of future events of CAD in asymptomatic healthy FDRS.     

Stocking density‐dependent growth and survival of Asian sun catfish,Horabagrus brachysoma (Gunther 1861) larvae

The aim of the experiment was to evaluate the growth and survival of Horabagrus brachysoma larvae at different stocking densities (3, 7, 13, 20, 27 and 33 larvae L^?1) during their hatchery phase. Total length and wet weight of the larvae consistently decreased (P < 0.05) at the end of 14 and 28 days of rearing as the density increased. The specific growth rate was significantly (P < 0.05) highest at three larvae L^?1 compared to the other five densities. The percent weight gain and survival of larvae was also highest at lowest density. The observation corroborates that catfish larvae can be reared at low densities in stagnant water conditions. Considering the value of larval growth, survival and overall weight gain, the stocking density of seven larvae L^?1 has been identified as the maximum for larval rearing of H.  brachysoma under hatchery conditions.     

Stabilization of Mn(II) and Mn(III) in mononuclear complexes derived from tridentate ligands with N2O donors: Synthesis, crystal structure, superoxide dismutase activity and DNA interaction studies

A new family of tridentate ligands PhimpH (2-((2-phenyl-2-(pyridin-2-yl)hydazono)methyl)phenol), N-PhimpH (2-((2-phenyl-2-(pyridin-2-yl)hydrazono)methyl)napthalen-1-ol), Me-PhimpH (2-(1-(2-phenyl-2-(pyridine-2-yl)hydrazono)ethyl)phenol) have been synthesized and characterized. The ligands PhimpH and N-PhimpH after deprotonation react with manganese(II) and manganese(III) starting materials affording [Mn(Phimp)₂] (1), [Mn(Phimp)₂](ClO₄) (2), [Mn(N-Phimp)₂] (3), [Mn(N-Phimp)₂](ClO₄) (4). Complexes [Mn(Phimp)₂] (1) and [Mn(N-Phimp)₂] (3) convert to [Mn(Phimp)₂]⁺ (cation of 2) and [Mn(N-Phimp)₂]⁺ (cation of 4) respectively upon oxidation. Ligand Me-PhimpH stabilized only manganese(III) centre resulting [Mn(Me-Phimp)₂](ClO₄) (5). The molecular structures of [Mn(Phimp)₂], 1 and [Mn(Phimp)₂](ClO₄), 2 were determined by single crystal X-ray diffraction. X-ray crystal structures of 1 and 2 have revealed the presence of distorted octahedral MnN₄O₂ coordination sphere having meridionally spanning ligands. Electrochemical studies for the complexes showed Mn(II)/Mn(III), (E_1/2 = 0.14-0.40 V) and Mn(III)/Mn(IV), (E_1/2 = 0.80-1.06 V) couples vs. Ag/AgCl. The redox properties were exploited to examine superoxide dismutase (SOD) activity using Mn(II)/Mn(III) couple. The complexes 1, 2, 4 and 5 have been revealed to catalyze effectively the dismutation of superoxide () in xanthine-xanthine oxidase-nitro blue tetrazolium assay and IC₅₀ values were found to be 0.29, 0.39, 1.12 and 0.76 μM respectively. DNA interaction studies with complex 2 showed binding of DNA in a non-intercalative pathway. Complexes 1, 2 and 4 exhibited nuclease activity in presence of H₂O₂ and inhibition of activity was noted in presence of KI.     

Development and Characterization of Enteric-Coated Immediate-Release Pellets of Aceclofenac by Extrusion/Spheronization Technique Using κ-Carrageenan as a Pelletizing Agent

In the present study, an attempt was made to prepare immediate-release enteric-coated pellets of aceclofenac, a poorly soluble nonsteroidal anti-inflammatory drug that has a gastrointestinal intolerance as its serious side effect. Formulation of enteric-coated pellets with improved solubility of aceclofenac could address both of these problems. To achieve these goals, pellets were prepared by extrusion–spheronization method using pelletizing agents that can contribute to the faster disintegration and thereby improve the solubility of the drug. Different disintegrants like β-cyclodextrin, kollidon CL, Ac-Di-Sol, and sodium starch glycolate were tried in order to further improve disintegration time. The pellets were characterized for drug content, particle size distribution, flow properties, infrared spectroscopy, surface morphology, disintegration rate, and dissolution profile. The formulations, which showed best disintegration and dissolution profiles, were coated with Eudragit L100-55, an enteric-coated polymer which does not dissolve at gastric pH but dissolves at intestinal pH, releasing the drug immediately in the dissolution medium. The optimized enteric-coated formulation containing 20% κ-carrageenan, lactose, and sodium starch glycolate as a disintegrant did inhibit the release of the drug for 2 h in 0.1 N HCl, whereas 87% of the drug was released within 45 min. The improvement was substantial when it was compared with solubility of pure drug under the same conditions. Thus, dissolution profiles suggested that combination of κ-carrageenan and sodium starch glycolate resulted into fast-disintegrating, immediate-release pellets, overcoming the bioavailability problem of the poorly soluble drug, aceclofenac, and enteric coating of these pellets avoids the exposure of aceclofenac to ulcer-prone areas of the gastrointestinal tract.