Topological mimicry and epitope duplication in the guanylyl cyclase C receptor

Guanylyl cyclase C (GCC) is the receptor for the gastrointestinal hormones, guanylin, and uroguanylin, in addition to the bacterial heat-stable enterotoxins, which are one of the major causes of watery diarrhea the world over. GCC is expressed in intestinal cells, colorectal tumor tissue and tumors originating from metastasis of the colorectal carcinoma. We have earlier generated a monoclonal antibody to human GCC, GCC:B10, which was useful for the immunohistochemical localization of the receptor in the rat intestine (Nandi A et al., 1997, J Cell Biochem 66:500-511), and identified its epitope to a 63-amino acid stretch in the intracellular domain of GCC. In view of the potential that this antibody has for the identification of colorectal tumors, we have characterized the epitope for GCC:B10 in this study. Overlapping peptide synthesis indicated that the epitope was contained in the sequence HIPPENIFPLE. This sequence was unique to GCC, and despite a short stretch of homology with serum amyloid protein and pertussis toxin, no cross reactivity was detected. The core epitope was delineated using a random hexameric phage display library, and two categories of sequences were identified, containing either a single, or two adjacent proline residues. No sequence identified by phage display was identical to the epitope present in GCC, indicating that phage sequences represented mimotopes of the native epitope. Alignment of these sequences with HIPPENIFPLE suggested duplication of the recognition motif, which was confirmed by peptide synthesis. These studies allowed us not only to define the requirements of epitope recognition by GCC:B10 monoclonal antibody, but also to describe a novel means of epitope recognition involving topological mimicry and probable duplication of the cognate epitope in the native guanylyl cyclase C receptor sequence.

Simultaneous observation of positive and negative nuclear Overhauser effects in oligopeptides due to segmental motio

Nuclear Overhauser effect (NOE) studies of the symmetrical cystine peptides (Formula: see text) (n = 1-3) in dimethylsulfoxide, have resulted in the simultaneous observation of both positive and negative NOEs. Positive NOEs are observed on the Trp C2H and C4H protons of the indole ring upon irradiation of Trp C alpha H and C beta H2 resonances in the peptides where n = 1 and 2. Negative NOEs are observed between backbone NH and C alpha H protons. The magnitudes of the observed NOEs are sensitive to changes in molecular size and solvent viscosity. The results demonstrate that NOEs may be a useful probe of sidechain segmental motion in oligopeptides.

Main chain and segmental dynamics of semi interpenetrating based on polyisoprene and poly(methyl methacrylate)

Main chain and segmental dynamics of polyisoprene (PI) and poly(methyl methacrylate)(PMMA) chains in semi IPNs were systematically studied over a wide range of temperatures (above and below T-g of both polymers) as a function of composition, crosslink density, and molecular weight. The immiscible polymers retained most of its characteristic molecular motion; however, the semi IPN synthesis resulted in dramatic changes in the motional behavior of both polymers due to the molecular level interpenetration between two polymer chains. ESR spin probe method was found to be sensitive to the concentration changes of PMMA in semi IPNs. Low temperature spectra showed the characteristics of rigid limit spectra, and in the range of 293-373 K.complex spectra were obtained with the slow component mostly arisingout of the PMMA rich regions and fast component from the PI phase. We found that the rigid PMMA chains closely interpenetrated into thehighly mobile PI network imparts motional restriction in nearby PI chains, and the highly mobile PI chains induce some degree of flexibility in highly rigid PMMA chains. Molecular level interchain mixing was found to be more efficient at a PMMA concentration of 35 wt.%. Moreover, the strong interphase formed in the above mentionedsemi IPN contributed to the large slow component in the ESR spectra at higher temperature. The shape of the spectra along with the data obtained from the simulations of spectra was correlated to the morphology of the semi IPNs. The correlation time measurement detected the motional region associated with the glass transition of PI and PMMA, and these regions were found to follow the same pattern of shifts in a-relaxation of PI and PMMA observed in DMA analysis. Activation energies associated with the T-g regions were also calculated. T-50G was found to correlate with the T-g of PMMA, and the volume of polymer segments undergoing glass transitional motion was calculated to be 1.7 nm(3).C-13 T-1 rho measurements of PMMA carbons indicate that the molecular level interactions were strong in semi IPN irrespective of the immiscible nature of polymers. The motional characteristics of H atoms attached to carbon atoms in both polymers were analyzed using 2D WISE NMR. Main relaxations of both components shifted inward, and both SEM and TEM analysis showed the development of a nanometer sized morphology in the case of highly crosslinked semi IPN. (C) 2010 Elsevier Ltd. All rights reserved.

Carbon-13 relaxation study of chain segmental motion and side-chain internal rotations of poly(isobutyl methacrylate) in solution

The dynamics of poly(isobutyl methacrylate) in toluene solution has been examined by C-13 spin-lattice relaxation time and NOE measurements as a function of temperature. The experiments were performed at 50.3 and 100.6 MHz. The backbone carbon relaxation data have been analyzed using the Dejean-Laupretre-Monnerie (DLM) model, which describes the dynamical processes in the backbone in terms of conformational transitions and bond librations. The relaxation data of the side chain nuclei have been analyzed by assuming different motional models, namely, unrestricted rotational diffusion, three site jumps, and restricted rotational diffusion. The different models have been compared for their ability to reproduce the experimental spin-lattice relaxation times and also to predict the behavior of NOE as a function of temperature. Conformational energy calculations have been carried out on a model compound by using the semiempirical quantum chemical method, AM1, and the results confirm the validity of the motional models used to describe the side-chain motion.

Segmental relaxations and crystallization-induced phase separation in PVDF/PMMA blends in the presence of surface-functionalized multiwall carbon nanotubes

Crystallization-induced phase separation and segmental relaxations in poly(vinylidene fluoride)/poly(methyl methacrylate) (PVDF/PMMA) blends was systematically investigated by melt-rheology and broadband dielectric spectroscopy in the presence of multiwall carbon nanotubes (MWNTs). Different functionalized MWNTs (amine, -NH2; acid, -COOH) were incorporated in the blends by melt-mixing above the melting temperature of PVDF, where the blends are miscible, and the crystallization induced phase separation was probed in situ by shear rheology. Interestingly, only -NH2 functionalized MWNTs (a-MWNTs) aided in the formation of beta-phase (trans-trans) crystals in PVDF, whereas both the neat blends and the blends with -COOH functionalized MWNTs (c-MWNTs) showed only alpha-phase (trans-gauche-trans-gauche') crystals as inferred from wide-angle X-ray diffraction (WXRD) and Fourier transform infrared (FTIR). Furthermore, blends with only a-MWNTs facilitated in heterogeneous nucleation in the blends manifesting in an increase in the calorimetric crystallization temperature and hence, augmented the theologically determined crystallintion induced phase separation temperature. The dielectric relaxations associated with the crystalline phase of PVDF (alpha(c)) was completely absent in the blends with a-MWNTs in contrast to neat blends and the blends with c-MWNTs in the dielectric loss spectra. The relaxations in the blends investigated here appeared to follow Havriliak-Negami (HN) empirical equations, and, more interestingly, the dynamic heterogeneity in the system could be mapped by an extra relaxation at higher frequency at the crystallization-induced phase separation temperature. The mean relaxation time (tau(HN)) was evaluated and observed to be delayed in the presence of MWNTs in the blends, more prominently in the case of blends with a-MWNTs. The latter also showed a significant increase in the dielectric relaxation strength (Delta epsilon). Electron microscopy and selective etching was used to confirm the localization of MWNTs in the amorphous phases of the interspherulitic regions as observed from scanning electron microscopy (SEM). The evolved crystalline morphology, during crystallization-induced phase separation, was observed to have a strong influence on the charge transport processes in the blends. These observations were further supported by the specific interactions (like dipole induced dipole interaction) between a-MWNTs and PVDF, as inferred from FTIR, and the differences in the crystalline morphology as observed from WXRD and polarized optical microscopy (POM).

Multiwalled-carbon-nanotube-induced miscibility in near-critical PS/PVME blends: assessment through concentration fluctuations and segmental relaxation

The effects of multiwalled carbon nanotubes (MWNTs) on the concentration fluctuations, interfacial driven elasticity, phase morphology, and local segmental dynamics of chains for near-critical compositions of polystyrene/poly(vinyl to methyl ether) (PS/PVME) blends were systematically investigated using dynamic shear rheology and dielectric spectroscopy. The contribution of the correlation length (xi) of the concentration fluctuations to the evolving stresses was monitored in situ to probe the different stages of demixing in the blends. The classical upturn in the dynamic moduli was taken as the rheological demixing temperature (T-rheo), which was also observed to be in close agreement with those obtained using concentration fluctuation variance, <(delta phi)(2)>, versus temperature curves. Further, Fredrickson and Larson's approach involving the mean-field approximation and the double-reptation self-concentration (DRSC) model was employed to evaluate the spinodal decomposition temperature (T-s). Interestingly, the values of both T-rheo and T-s shifted upward in the blends in the presence of MWNTs, manifesting in molecular-level miscibility. These phenomenal changes were further observed to be a function of the concentration of MWNTs. The evolution of morphology as a function of temperature was studied using polarized optical microscopy (POM). It was observed that PVME, which evolved as an interconnected network during the early stages of demixing, coarsened into a matrix-droplet morphology in the late stages. The preferential wetting of PVME onto MWNTs as a result of physicochemical interactions retained the interconnected network of PVME for longer time scales, as supported by POM and atomic force microscopy (AFM) images. Microscopic heterogeneity in macroscopically miscible systems was studied by dielectric relaxation spectroscopy. The slowing of segmental relaxations in PVME was observed in the presence of both ``frozen'' PS and MWNTs interestingly at temperatures much below the calorimetric glass transition temperature (T-g). This phenomenon was observed to be local rather than global and was addressed by monitoring the evolution of the relaxation spectra near and above the demixing temperature.

Concentration Fluctuations and Segmental Dynamics in Weakly Dynamic Asymmetric Blends in the Presence of Surface-Functionalized Multiwall Carbon Nanotubes

Surface-functionalized multiwall carbon nanotubes (MWCNTs) are incorporated in poly(methyl methacrylate)/styrene acrylonitrile (PMMA/SAN) blends and the pretransitional regime is monitored in situ by melt rheology and dielectric spectroscopy. As the blends exhibit weak dynamic asymmetry, the obvious transitions in the melt rheology due to thermal concentration fluctuations are weak. This is further supported by the weak temperature dependence of the correlation length ( approximate to 10-12 angstrom) in the vicinity of demixing. Hence, various rheological techniques in both the temperature and frequency domains are adopted to evaluate the demixing temperature. The spinodal decomposition temperature is manifested in an increase in the miscibility gap in the presence of MWCNTs. Furthermore, MWCNTs lead to a significant slowdown of the segmental dynamics in the blends. Thermally induced phase separation in the PMMA/SAN blends lead to selective localization of MWCNTs in the PMMA phase. This further manifests itself in a significant increase in the melt conductivity.

Non-equilibrium segmental dynamics driven by multiwall carbon nanotubes in PS/PVME blends

The present paper discusses the effect of multiwall carbon nanotubes (MWNTs) on the structural relaxation and the intermolecular cooperativity in dynamically asymmetric blends of PS/PVME (polystyrene/poly(vinyl methyl ether)). The temperature regime where chain connectivity effects dominate the thermodynamic concentration fluctuation (T/T-g > 0.75, T-g is the glass transition temperature of the blends) was studied using dielectric spectroscopy (DS). Interestingly, in the blends with MWNTs a bimodal distribution of relaxation was obtained in the loss modulus spectra. This plausibly is due to different environments experienced by the faster component (PVME) in the presence of MWNTs. The segmental dynamics of PVME was observed to be significantly slowed down in the presence of MWNTs and an Arrhenius-type behavior, weakly dependent on temperature, is observed at higher frequencies. This non-equilibrium dynamics of PVME is presumed to be originating from interphase regions near the surface of MWNTs. The length scale of the cooperative rearranging region (xi CRR) at T-g, assessed by calorimetric measurements, was observed to be higher in the case of blends with MWNTs. An enhanced molecular level miscibility driven by MWNTs in the blends corroborates with the larger xi CRR and comparatively more number of segments in CRR (in contrast to neat blends) around T-g. The configurational entropy and length scale of the cooperative volume was mapped as a function of temperature in the temperature regime, Tg < T < T-g + 60 K. The blends phase separated by spinodal decomposition which further led to an interconnected PVME network in PS. This further led to materials with very high electrical conductivity upon demixing.

Flow behavior of long chain plasticizing liquids: Segment size calculations in carboxylate esters

This is the first comprehensive report on the calculation of segment size, which signifies the asic unit of flow in long chain plasticizing liquids, by a novel multi-pronged approach. Unlike,low molecular weight liquids and high polymer melts these complex long chain liquids encompasses the least understood domain of the liquid state. In the present work the flow behaviour of carboxylate ester (300-900 Da) has been explained through segmental motion taking into account the independence of molecular weight region. The segment size have been calculated by various methods based on satistical thermodynamics, molecular dynamics and group additivity nd their merits analysed.

Ionic transport in (PEG)x LiBr systems

Ionic conductivity in (PEG)(x)LiBr systems is measured using the complex impedance method in the temperature range -20 degrees C to 100 degrees C. For x = 6 and 10, above a certain concentration dependent temperature T-c, a power law fit based on mode coupling theory is seen to better explain the data than the Vogel-Tamman-Fulcher (VTF) expression. Li-7 NMR linewidth measurements indicate two regions of motional narrowing, one attributable to segmental motion and the other to translational diffusion.

Structural mobility and transformations in globular proteins

Although globular proteins are endowed with well defined three-dimensional structures, they exhibit substantial mobility within the framework of the given threedimensional structure. The different types of mobility found in proteins by and large correspond to the different levels of organisational hierarchy in protein architecture. They are of considerable structural and functional significance, and can be broadly classified into(a) thermal and conformational fluctuations, (b) segmental mobility, (c) interdomain mobility and (d) intersubunit mobility. Protein crystallographic studies has provided a wealth of information on all of them. The temperature factors derived from X-ray diffraction studies provide a measure of atomic displacements caused by thermal and conformational fluctuations. The variation of displacement along the polypeptide chain have provided functionally significant information on the flexibility of different regions of the molecule in proteins such as myoglobin, lysozyme and prealbumin. Segmental mobility often involves the movement of a region or a segment of a molecule with respect to the rest, as in the transition between the apo and the holo structures of lactate dehydrogenase. It may also involve rigidification of a disordered region of the molecule as in the activation of the zymogens of serine proteases. Transitions between the apo and the holo structures of alcohol dehydrogenase,and between the free and the sugar bound forms of hexokinase, are good examples of interdomain mobility caused by hinge-bending. The capability of different domains to move semi-independently contributes greatly to the versatility of immunoglobulin molecules. Interdomain mobility in citrate synthase appears to be more complex and its study has led to an alternative description of domain closure. The classical and the most thoroughly studied case of intersubunit mobility is that in haemoglobin. The stereochemical mechanism of the action of this allosteric protein clearly brings out the functional subtilities that could be achieved through intersubunit movements. In addition to ligand binding and activation,environmental changes also often cause structural transformations. The reversible transformation between 2 Zn insulin and 4 Zn insulin is caused by changes in the ionic strength of the medium. Adenylate Kinase provides a good example for functionally significant reversible conformational transitions induced by variation in pH. Available evidences indicate that reversible structural transformations in proteins could also be caused by changes in the aqueous environment, including those in the amount of water surrounding protein molecules.

A comparative study of speaker adaptation methods

For the problem of speaker adaptation in speech recognition, the performance depends on the availability of adaptation data. In this paper, we have compared several existing speaker adaptation methods, viz. maximum likelihood linear regression (MLLR), eigenvoice (EV), eigenspace-based MLLR (EMLLR), segmental eigenvoice (SEV) and hierarchical eigenvoice (HEV) based methods. We also develop a new method by modifying the existing HEV method for achieving further performance improvement in a limited available data scenario. In the sense of availability of adaptation data, the new modified HEV (MHEV) method is shown to perform better than all the existing methods throughout the range of operation except the case of MLLR at the availability of more adaptation data.

Analysis of the amino acid sequences of plant Bowman-Birk inhibitors

Plant seeds contain a large number of protease inhibitors of animal, fungal, and bacterial origin. One of the well-studied families of these inhibitors is the Bowman-Birk family(BBI). The BBIs from dicotyledonous seeds are 8K, double-headed proteins. In contrast, the 8K inhibitors from monocotyledonous seeds are single headed. Monocots also have a 16K, double-headed inhibitor. We have determined the primary structure of a Bowman-Birk inhibitor from a dicot, horsegram, by sequential edman analysis of the intact protein and peptides derived from enzymatic and chemical cleavage. The 76-residue-long inhibitor is very similar to that ofMacrotyloma axillare. An analysis of this inhibitor along with 26 other Bowman-Birk inhibitor domains (MW 8K) available in the SWISSPROT databank revealed that the proteins from monocots and dicots belong to related but distinct families. Inhibitors from monocots show larger variation in sequence. Sequence comparison shows that a crucial disulphide which connects the amino and carboxy termini of the active site loop is lost in monocots. The loss of a reactive site in monocots seems to be correlated to this. However, it appears that this disulphide is not absolutely essential for retention of inhibitory function. Our analysis suggests that gene duplication leading to a 16K inhibitor in monocots has occurred, probably after the divergence of monocots and dicots, and also after the loss of second reactive site in monocots.

Hydrogel membrane electrolyte for electrochemical capacitors

Polymer electrolytes are known to possess excellent physicochemical properties that are very useful for electrochemical energy systems. The mobility in polymer electrolytes is understood to be mainly due to the segmental motion of polymer chains and the ion transport is generally restricted to the amorphous phase of the polymer. Gel polymer electrolytes (GPE) that are formed using plastizicers and polymers along with ionic salts are known to exhibit liquid-like ionic conductivity while maintaining the dimensional stability of a solid matrix. In the present study, the preparation and characterization of poly(vinyl alcohol)-based hydrogel membranes (PHMEs) as electrolyte for electrochemical capacitors have been reported. VaryingHClO4 dopant concentration leads to different characteristics of the capacitors. The EC comprising PHME doped with 2 M HClO4 and black pearl carbon (BPC) electrodes has been found to exhibit a maximum specific capacitance value of 97 F g(-1), a phase angle value of 78A degrees, and a maximum charge-discharge coulombic efficiency of 88%.

Evolution of sequence specificity in a restriction endonuclease by a point mutation

Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed with exquisite sequence specificity. REases have originated from the ancestral proteins and evolved new sequence specificities by genetic recombination, gene duplication, replication slippage, and transpositional events. They are also speculated to have evolved from nonspecific endonucleases, attaining a high degree of sequence specificity through point mutations. We describe here an example of generation of exquisitely site-specific REase from a highly-promiscuous one by a single point mutation.