NMR Structure Implications of Enhanced Efficacy of Obestatin Fragment Analogs

Obestatin is a more recently discovered hormone that is encoded by the ghrelin gene and produced in the stomach and gut. We report NMR analysis on synthetic Obestatin (OB23), a 23 residue peptide, along with three overlapping fragments of the same in methanol solvent as a first step towards structure activity relationship. Selective substitutions on the promising N-terminal and middle fragments of obestatin have been carried out in order to improve the efficacy and potency. In the N-terminal fragment two peptides were obtained by the replacement of Gly (8) with a-aminoisobutyric acid (Aib, U) and Phe (F5) with Cyclohexylalanine (Cha). In case of the middle fragment both Gly (3) and Gly (8) were replaced with Aib residues. The rationale being, these unusual amino acids could provide protection from immediate degradation and aid structure stabilization. Our previous studies showed that the N-terminal and the middle fragment were unstructured and hence this substitution would directly evaluate the effect of structure on the activity of these fragment analogs. Detailed NMR analysis clearly demonstrates formation of helical secondary structure in all the peptide analogues and provides justification for relative activities reported by our group previously (Nagaraj et al. 2009).

Mutations in Drosophila Myosin Rod Cause Defects in Myofibril Assembly

The roles of myosin during muscle contraction are well studied, but how different domains of this protein are involved in myofibril assembly in vivo is far less understood. The indirect flight muscles (IFMs) of Drosophila melanogaster provide a good model for understanding muscle development and function in vivo. We show that two missense mutations in the rod region of the myosin heavy-chain gene, Mhc, give rise to IFM defects and abnormal myofibrils. These defects likely result from thick filament abnormalities that manifest during early sarcomere development or later by hypercontraction. The thick filament defects are accompanied by marked reduction in accumulation of flightin, a myosin binding protein, and its phosphorylated forms, which are required to stabilise thick filaments. We investigated with purified rod fragments whether the mutations affect the coiled-coil structure, rod aggregate size or rod stability. No significant changes in these parameters were detected, except for rod thermodynamic stability in one mutation. Molecular dynamics simulations suggest that these mutations may produce localised rod instabilities. We conclude that the aberrant myofibrils are a result of thick filament defects, but that these in vivo effects cannot be detected in vitro using the biophysical techniques employed. The in vivo investigation of these mutant phenotypes in IFM development and function provides a useful platform for studying myosin rod and thick filament formation generically, with application to the aetiology of human myosin rod myopathies. (C) 2012 Elsevier Ltd. All rights reserved.

Simultaneous refolding and purification of recombinant proteins by macro-(affinity ligand) facilitated three-phase partitioning

A strategy called macro-(affinity ligand) facilitated three-phase partitioning (MLFTPP) is described for refolding of a diverse set of recombinant proteins starting from the solubilized inclusion bodies. It essentially consists of: (i) binding of the protein with a suitable smart polymer and (ii) precipitating the polymer-protein complex as an interfacial layer by mixing in a suitable amount of ammonium sulfate and t-butanol. Smart polymers are stimuli-responsive polymers that become insoluble on the application of a suitable stimulus (e.g., a change in the temperature, pH, or concentration of a chemical species such as Ca 2+ or K +). The MLFTPP process required approximately 10min, and the refolded proteins were found to be homogeneous on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The folded proteins were characterized by fluorescence emission spectroscopy, circular dichroism spectroscopy, biological activity, melting temperature, and surface hydrophobicity measurements by 8-anilino-1-naphthalenesulfonate fluorescence. Two refolded antibody fragments were also characterized by measuring K D by Biacore by using immobilized HIV-1 gp120. The data demonstrate that MLFTPP is a rapid and convenient procedure for refolding a variety of proteins from inclusion bodies at high concentration. Although establishing the generic nature of the approach would require wider trials by different groups, its success with the diverse kinds of proteins tried so far appears to be promising.

Model synthetic studies toward jiadifenin and majucin type seco-prezizaane natural products via a stereo- and enantioselective approach

A concise stereo- and enantioselective approach to seco-prezizaane sesquiterpenoids, leading to the acquisition of two bicyclic fragments, is delineated. (c) 2012 Elsevier Ltd. All rights reserved.

Silver nanoparticles modified nanocapsules for ultrasonically activated drug delivery

Novel ultrasound-sensitive nanocapsules were designed via layer-by-layer assembly (LbL) of polyelectrolytes for remote activated release of biomolecules/drug. Nanocapsules embedded with silver nanoparticles in the walls were synthesized by alternate assembly of poly(allylamine hydrochloride) (PAH) and dextran sulfate (DS) on silica template followed by nanoparticle synthesis and subsequent template removal thus yielding nanocapsules. The silver NPs were synthesized in situ within the capsule walls under controlled conditions. The nanocapsules were found to be well dispersed and the silver NPs were evenly distributed within the shell. FITC-dextran permeated easily into the capsules containing silver NP's due to the pores generated during the formation of NP's. When the loaded nanocapsules were sonicated, the presence of the silver NPs in the shell structure led to rupturing of the shell into smaller fragments thus releasing the FITC-dextran. Such nanocapsules have the potential to be used as drug delivery vehicles and offer the scope for further development in the areas of modern medicine, material science, and biochemistry. (C) 2012 Elsevier B.V. All rights reserved.

Ballistic Studies on TiB2-Ti Functionally Graded Armor Ceramics

The objective of this paper is to discuss the results of the ballistic testing of spark plasma sintered TiB2-Ti based functionally graded materials (FGMs) with an aim to assess their performance in defeating small-calibre armor piercing projectiles. We studied the efficacy of FGM design and compared its ballistic properties with those of TiB2-based composites as well as other competing ceramic armors. The ballistic properties are critically analyzed in terms of depth of penetration, ballistic efficiency, fractographs of fractured surfaces as well as quantification of the shattered ceramic fragments. It was found that all the investigated ceramic compositions exhibit ballistic efficiency (eta) of 5.1 -5.9. We also found that by increasing the thickness of FGM from 5 mm to 7.8 mm, the ballistic property of the composite degraded. Also, the strength of the ceramic compositions studied is sufficient to completely fracture the nose of the pointed projectile used. Analysis of the ceramic fragments (2 mu m-10 mm) showed that harder the ceramic, coarser were the fragments formed. On comparing the results with available armor systems, it has been concluded that TiB2 based composites can show better ballistic properties, except B4C. SEM analysis of the fragments obtained after testing with FGM showed formation of cleavage steps as well as presence of intergranular cracks, indicating that the FGM fractured by mixed mode of failure. It can be concluded that the FGM developed has lower ballistic properties compared to its monolith TiB2-20 wt.% Ti.

Packing in molten globules and native states

Close packing of hydrophobic residues in the protein interior is an important determinant of protein stability. Cavities introduced by large to small substitutions are known to destabilize proteins. Conversely, native states of proteins and protein fragments can be stabilized by filling in existing cavities. Molten globules (MGs) were initially used to describe a state of protein which has well-defined secondary structure but little or no tertiary packing. Subsequent studies have shown that MGs do have some degree of native-like topology and specific packing. Wet molten globules (WMGs) with hydrated cores and considerably decreased packing relative to the native state have been studied extensively. Recently there has been renewed interest in identification and characterization of dry molten globules (DMGs). These are slightly expanded forms of the native state which show increased conformational flexibility, native-like main-chain hydrogen bonding and dry interiors. The generality of occurrence of DMGs during protein unfolding and the extent and nature of packing in DMGs remain to be elucidated. Packing interactions in native proteins and MGs can be probed through mutations. Next generation sequencing technologies make it possible to determine relative populations of mutants in a large pool. When this is coupled to phenotypic screens or cell-surface display, it becomes possible to rapidly examine large panels of single-site or multi-site mutants. From such studies, residue specific contributions to protein stability and function can be estimated in a highly parallelized fashion. This complements conventional biophysical methods for characterization of packing in native states and molten globules.

Design of an Escherichia coli expressed HIV-1 gp120 fragment Immunogen that binds to b12 and induces broad and potent neutralizing antibodies

b12, one of the few broadly neutralizing antibodies against HIV-1, binds to the CD4 binding site (CD4bs) on the gp120 subunit of HIV-1 Env. Two small fragments of HIV-1 gp120, b121a and b122a, which display about 70% of the b12 epitope and include solubility-enhancing mutations, were designed. Bacterially expressed b121a/b122a were partially folded and could bind b12 but not the CD4bs-directed non-neutralizing antibody b6. Sera from rabbits primed with b121a or b122a protein fragments and boosted with full-length gp120 showed broad neutralizing activity in a TZM-bl assay against a 16-virus panel that included nine Tier 2 and 3 viruses as well as in a five-virus panel previously designed to screen for broad neutralization. Using a mean IC50 cut-off of 50, sera from control rabbits immunized with gp120 alone neutralized only one virus of the 14 non-Tier 1 viruses tested (7%), whereas sera from b121a- and b122a-immunized rabbits neutralized seven (50%) and twelve (86%) viruses, respectively. Serum depletion studies confirmed that neutralization was gp120-directed and that sera from animals immunized with gp120 contained lower amounts of CD4bs-directed antibodies than corresponding sera from animals immunized with b121a/b122a. Competition binding assays with b12 also showed that b121a/2a sera contained significantly higher amounts of antibodies directed toward the CD4 binding site than the gp120 sera. The data demonstrate that it is possible to elicit broadly neutralizing sera against HIV-1 in small animals.

Processing of DNA double-stranded breaks and intermediates of recombination and repair by saccharomyces cerevisiae Mre11 and its stimulation by Rad50, Xrs2, and Sae2 proteins

Saccharomyces cerevisiae RAD50, MRE11, and XRS2 genes are essential for telomere length maintenance, cell cycle checkpoint signaling, meiotic recombination, and DNA double-stranded break (DSB) repair via nonhomologous end joining and homologous recombination. The DSB repair pathways that draw upon Mre11-Rad50-Xrs2 subunits are complex, so their mechanistic features remain poorly understood. Moreover, the molecular basis of DSB end resection in yeast mre11-nuclease deficient mutants and Mre11 nuclease-independent activation of ATM in mammals remains unknown and adds a new dimension to many unanswered questions about the mechanism of DSB repair. Here, we demonstrate that S. cerevisiae Mre11 (ScMre11) exhibits higher binding affinity for single-over double-stranded DNA and intermediates of recombination and repair and catalyzes robust unwinding of substrates possessing a 3' single-stranded DNA overhang but not of 5' overhangs or blunt-ended DNA fragments. Additional evidence disclosed that ScMre11 nuclease activity is dispensable for its DNA binding and unwinding activity, thus uncovering the molecular basis underlying DSB end processing in mre11 nuclease deficient mutants. Significantly, Rad50, Xrs2, and Sae2 potentiate the DNA unwinding activity of Mre11, thus underscoring functional interaction among the components of DSB end repair machinery. Our results also show that ScMre11 by itself binds to DSB ends, then promotes end bridging of duplex DNA, and directly interacts with Sae2. We discuss the implications of these results in the context of an alternative mechanism for DSB end processing and the generation of single-stranded DNA for DNA repair and homologous recombination.

Rapid mass spectrometric determination of disulfide connectivity in peptides and proteins

Disulfide crosslinks are ubiquitous in natural peptides and proteins, providing rigidity to polypeptide scaffolds. The assignment of disulfide connectivity in multiple crosslinked systems is often difficult to achieve. Here, we show that rapid unambiguous characterisation of disulfide connectivity can be achieved through direct mass spectrometric CID fragmentation of the disulfide intact polypeptides. The method requires a direct mass spectrometric fragmentation of the native disulfide bonded polypeptides and subsequent analysis using a newly developed program, DisConnect. Technical difficulties involving direct fragmentation of proteins are surmounted by an initial proteolytic nick and subsequent determination of the structures of these proteolytic peptides through DisConnect. While the connectivity in proteolytic fragments containing one cystine is evident from the MS profile alone, those with multiple cystines are subjected to subsequent mass spectrometric fragmentation. The wide applicability of this method is illustrated using examples of peptide hormones, peptide toxins, proteins, and disulfide foldamers of a synthetic analogue of a marine peptide toxin. The method, coupled with DisConnect, provides an unambiguous, straightforward approach, especially useful for the rapid screening of the disulfide crosslink fidelity in recombinant proteins, determination of disulfide linkages in natural peptide toxins and characterization of folding intermediates encountered in oxidative folding pathways.

``On-the-fly'' kinetics of enzymatic racemization using deuterium NMR in DNA-based chiral oriented media

We report the in situ and real-time monitoring of the interconversion of L- and D-alanine-d(3) by alanine racemase from Bacillus stearothermophilus directly observed by H-2 NMR spectroscopy in anisotropic phase. The enantiomers are distinguished by the difference of their H-2 quadrupolar splittings in a chiral liquid crystal containing short DNA fragments. The proof-of-principle, the reliability, and the robustness of this new method is demonstrated by the determination of the turnover rates of the enzyme using the Michaelis Menten model.

Metal doped nanosized titania used for the photocatalytic degradation of rhodamine B dye under visible-light

Metal-doped anatase nanosized titania photocatalysts were successfully synthesized using a sal gel process. Different amounts of the dopants (0.2, 0.4, 0.6, 0.8 and 1.0%) of the metals (Ag, Ni, Co and Pd) were utilized. The UV-Vis spectra (solid state diffuse reflectance spectra) of the doped nanoparticles exhibited a red shift in the absorption edge as a result of metal doping. The metal-doped nanoparticles were investigated for their photocatalytic activity under visible-light irradiation using Rhodamine B (Rh B) as a control pollutant. The results obtained indicate that the metal-doped titania had the highest activity at 0.4% metal loading. The kinetic models revealed that the photodegradation of Rh B followed a pseudo first order reaction. From ion chromatography (IC) analysis the degradation by-products Rhodamine B fragments were found to be acetate, chloride, nitrite, carbonate and nitrate ions.

Fragment-based real-time object tracking: a sparse representation approach

Real-time object tracking is a critical task in many computer vision applications. Achieving rapid and robust tracking while handling changes in object pose and size, varying illumination and partial occlusion, is a challenging task given the limited amount of computational resources. In this paper we propose a real-time object tracker in l(1) framework addressing these issues. In the proposed approach, dictionaries containing templates of overlapping object fragments are created. The candidate fragments are sparsely represented in the dictionary fragment space by solving the l(1) regularized least squares problem. The non zero coefficients indicate the relative motion between the target and candidate fragments along with a fidelity measure. The final object motion is obtained by fusing the reliable motion information. The dictionary is updated based on the object likelihood map. The proposed tracking algorithm is tested on various challenging videos and found to outperform earlier approach.

Intravenous immunoglobulin expands regulatory T cells via induction of cyclooxygenase-2-dependent prostaglandin E2 in human dendritic cells

CD4(+)CD25(+)FoxP3(+) regulatory T cells (Tregs) play a critical role in the maintenance of immune tolerance. Intravenous immunoglobulin (IVIg), a therapeutic preparation of normal pooled human IgG, expands Tregs in various experimental models and in patients. However, the cellular and molecular mechanisms by which IVIg expands Tregs are relatively unknown. As Treg expansion in the periphery requires signaling by antigen-presenting cells such as dendritic cells (DCs) and IVIg has been demonstrated to modulate DC functions, we hypothesized that IVIg induces distinct signaling events in DCs that subsequently mediate Treg expansion. We demonstrate that IVIg expands Tregs via induction of cyclooxygenase (COX)-2-dependent prostaglandin E2 (PGE(2)) in human DCs. However, costimulatory molecules of DCs such as programmed death ligands, OX40 ligand, and inducible T-cell costimulator ligands were not implicated. Inhibition of PGE(2) synthesis by COX-2 inhibitors prevented IVIg-mediated Treg expansion in vitro and significantly diminished IVIg-mediated Treg expansion in vivo and protection from disease in experimental autoimmune encephalomyelitis model. IVIg-mediated COX-2 expression, PGE(2) production, and Treg expansion were mediated in part via interaction of IVIg and F(ab('))(2) fragments of IVIg with DC-specific intercellular adhesion molecule-3-grabbing nonintegrin. Our results thus uncover novel cellular and molecular mechanism by which IVIg expands Tregs.

Optimisation of an asymmetric polymerase chain reaction assay for the amplification of single-stranded DNA from Wuchereria bancrofti for electrochemical detection

Single-stranded DNA (ssDNA) is a prerequisite for electrochemical sensor-based detection of parasite DNA and other diagnostic applications. To achieve this detection, an asymmetric polymerase chain reaction method was optimised. This method facilitates amplification of ssDNA from the human lymphatic filarial parasite Wuchereria bancrofti. This procedure produced ssDNA fragments of 188 bp in a single step when primer pairs (forward and reverse) were used at a 100:1 molar ratio in the presence of double-stranded template DNA. The ssDNA thus produced was suitable for immobilisation as probe onto the surface of an Indium tin oxide electrode and hybridisation in a system for sequence-specific electrochemical detection of W. bancrofti. The hybridisation of the ssDNA probe and target ssDNA led to considerable decreases in both the anodic and the cathodic currents of the system's redox couple compared with the unhybridised DNA and could be detected via cyclic voltammetry. This method is reproducible and avoids many of the difficulties encountered by conventional methods of filarial parasite DNA detection; thus, it has potential in xenomonitoring.