A classification of homogeneous operators in the Cowen-Douglas class

An explicit construction of all the homogeneous holomorphic Hermitian vector bundles over the unit disc D is given. It is shown that every such vector bundle is a direct sum of irreducible ones. Among these irreducible homogeneous holomorphic Hermitian vector bundles over D, the ones corresponding to operators in the Cowen-Douglas class B-n(D) are identified. The classification of homogeneous operators in B-n(D) is completed using an explicit realization of these operators. We also show how the homogeneous operators in B-n(D) split into similarity classes. (C) 2011 Elsevier Inc. All rights reserved.

Ultrafast underdamped solvation: Agreement between computer simulation and various theories of solvation dynamics

A theoretical analysis of the three currently popular microscopic theories of solvation dynamics, namely, the dynamic mean spherical approximation (DMSA), the molecular hydrodynamic theory (MHT), and the memory function theory (MFT) is carried out. It is shown that in the underdamped limit of momentum relaxation, all three theories lead to nearly identical results when the translational motions of both the solute ion and the solvent molecules are neglected. In this limit, the theoretical prediction is in almost perfect agreement with the computer simulation results of solvation dynamics in the model Stockmayer liquid. However, the situation changes significantly in the presence of the translational motion of the solvent molecules. In this case, DMSA breaks down but the other two theories correctly predict the acceleration of solvation in agreement with the simulation results. We find that the translational motion of a light solute ion can play an important role in its own solvation. None of the existing theories describe this aspect. A generalization of the extended hydrodynamic theory is presented which, for the first time, includes the contribution of solute motion towards its own solvation dynamics. The extended theory gives excellent agreement with the simulations where solute motion is allowed. It is further shown that in the absence of translation, the memory function theory of Fried and Mukamel can be recovered from the hydrodynamic equations if the wave vector dependent dissipative kernel in the hydrodynamic description is replaced by its long wavelength value. We suggest a convenient memory kernel which is superior to the limiting forms used in earlier descriptions. We also present an alternate, quite general, statistical mechanical expression for the time dependent solvation energy of an ion. This expression has remarkable similarity with that for the translational dielectric friction on a moving ion.

Using Correlated Parameters for Improved Ranking of Protein-Protein Docking Decoys

A successful protein-protein docking study culminates in identification of decoys at top ranks with near-native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near-native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface and the significant variation of the nonbonding and solvation energies based on the chemical composition of the protein-protein interface. In this work, we describe a novel method combining an interface-size filter, a regression model for geometric compatibility (based on two correlated surface and packing parameters), and normalized interaction energy (calculated from correlated nonbonded and solvation energies), to effectively rank decoys from a set of 10,000 decoys. Tests on 30 unbound binary protein-protein complexes show that in 16 cases we can identify at least one decoy in top three ranks having <= 10 angstrom backbone root mean square deviation from true binding geometry. Comparisons with other state-of-art methods confirm the improved ranking power of our method without the use of any experiment-guided restraints, evolutionary information, statistical propensities, or modified interaction energy equations. Tests on 118 less-difficult bound binary protein-protein complexes with <= 35% sequence redundancy at the interface showed that in 77% cases, at least 1 in 10,000 decoys were identified with <= 5 angstrom backbone root mean square deviation from true geometry at first rank. The work will promote the use of new concepts where correlations among parameters provide more robust scoring models. It will facilitate studies involving molecular interactions, including modeling of large macromolecular assemblies and protein structure prediction. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 787-796, 2011.

Studies on molecular evolution and structural features of double-headed inhibitors of ?-amylase and trypsin in plants

Plant seeds usually have high concentrations of proteinase and amylase inhibitors. These inhibitors exhibit a wide range of specificity, stability and oligomeric structure. In this communication, we report analysis of sequences that show statistically significant similarity to the double-headed alpha-amylase/trypsin inhibitor of ragi (Eleusine coracana). Our aim is to understand their evolutionary and structural features. The 14 sequences of this family that are available in the SWISSPROT database form three evolutionarily distinct branches. The branches relate to enzyme specificities and also probably to the oligomeric state of the proteins and not to the botanical class of the plant from which the enzymes are derived. This suggests that the enzyme specificities of the inhibitors evolved before the divergence of commercially cultivated cereals. The inhibitor sequences have three regions that display periodicity in hydrophobicity. It is likely that this feature reflects extended secondary structure in these segments. One of the most variable regions of the polypeptide corresponds to a loop, which is most probably exposed in the native structure of the inhibitors and is responsible for the inhibitory property.

The cDNA sequence of cytochrome b5 associated with cytokinin-induced haustoria formation in Cuscuta reflexa

A cDNA clone isolated by differentially screening a cytokinin-induced haustorial cDNA library of Cuscuta reflexa was sequenced and identified as the gene coding for cytochrome b(5), based on the similarity of the deduced amino-acid sequence with that of the cauliflower (60% identity) and tobacco (78% identity) proteins. The 5'-UTR is unusually long (720 bp) and contains 14 potential start codons (ATG) and 10 short ORFs.

Normal state tunneling conductance of perovskite oxides: Implications for high-Tc superconductors

We have investigated tunneling conductances in disordered, normally conducting perovskite oxides close to the metal�insulator transition. We show that the normal state tunneling conductance of perovskite oxides can be cast in a general form G(V) = G0[1 + curly logical orV/V*curly logical orn] with 1?n?0.5 and where V* is an intrinsic energy scale. The exponent n graduall y increases from 0.5 to 1 as the metal-insulator (M-I) transition is approached. In the high-Tc Bi(2212) cuprates, the normally observed, linear G(V)(n=1) can be made sub-linear (n<1) by substitution of Ca with Y. From the similarity of the linear conductances, we suggest proximity to the M-I transition as a likely cause for this G(V)logical or, bar below V dependence. In systems showing linear conductances (nreverse similar, equals1), we find that ?G/?Vreverse similar, equalsG?0 with ?reverse similar, equals 1 and the intrinsic energy scale V*reverse similar, equals25�75 meV in the different oxides investigated.

Identification of the active-site peptide of 2,3-dihydroxybenzoic acid decarboxylase from Aspergillus oryzae

The non-oxidative decarboxylation of aromatic acids is a poorly understood reaction. The transformation of 2,3-dihydroxybenzoic acid to catechol in the fungal metabolism of indole is a prototype of such a reaction. 2,3-Dihydroxybenzoic acid decarboxylase (EC 4.1.1.46) which catalyzes this reaction was purified to homogeneity from anthranilate induced cultures of Aspergillus oryzae using affinity chromatography. The enzyme did not require cofactors like NAD(+), PLP, TPP or metal ions for its activity. There was no spectral evidence for the presence of enzyme bound cofactors. The preparation, which was adjudged homogeneous by the criteria of SDS-PAGE, sedimentation analysis and N-terminal analysis, was characterized for its physicochemical and kinetic parameters. The enzyme was inactivated by group-specific modifiers like diethyl pyrocarbonate (DEPC) and N-ethylmaleimide (NEM). The kinetics of inactivation by DEPC suggested the presence of a single class of essential histidine residues, the second order rate constant of inactivation for which was 12.5 M(-1) min(-1). A single class of cysteine residues was modified by NEM with a second order rate constant of 33 M(-1) min(-1). Substrate analogues protected the enzyme against inactivation by both DEPC and NEM, suggesting the Location of the essential histidine and cysteine to be at the active site of the enzyme. The incorporation of radiolabelled NEM in a differential labelling experiment was 0.73 mol per mol subunit confirming the presence of a single essential cysteine per active-site. Differentially labelled enzyme was enzymatically cleaved and the peptide bearing the label was purified and sequenced. The active-site peptide LLGLAETCK and the N-terminal sequence MLGKIALEEAFALPRFEEKT did not bear any similarity to sequences reported in the Swiss-Prot Protein Sequence Databank, a reflection probably of the unique primary structure of this novel enzyme. The sequences reported in this study will appear in the Swiss-Prot Protein Sequence Databank under the accession number P80402.

Dependence of giant magnetoresistance on oxygen stoichiometry and magnetization in polycrystalline La0.67Ba0.33MnOz

We have studied resistivity, magnetization, and magnetoresistance in polycrystalline La0.67Ba0.33MnOz by reducing the oxygen stoichiometry from z=2.99 to 2.80. As the oxygen content decreases, the resistivity of La0.67Ba0.33 MnOz increases and the magnetic transition temperature shifts to lower temperature. A large magnetoresistance effect was observed over a wide temperature range for all samples except the insulating z=2.80 sample. The similarity between our results on oxygen-deficient polycrystalline La0.67 Ba0.33MnOz and films previously reported to have a very large intrinsic magnetoresistance is discussed. At low temperature the magnetoresistance was observed to be strongly dependent on the magnetization. A possible mechanism for this effect is discussed.

Self-similar solutions of laser produced blast waves

The aerodynamics of the blast wave produced by laser ablation is studied using the piston analogy. The unsteady one-dimensional gasdynamic equations governing the flow an solved under assumption of self-similarity. The solutions are utilized to obtain analytical expressions for the velocity, density, pressure and temperature distributions. The results predict. all the experimentally observed features of the laser produced blast waves.

Substitution of chromium for univalent copper in superconducting Pb2Sr2(Ca,Y)Cu3O8+delta

Following considerations of geometry and the similarity between chromate and carbonate groups in terms of size and charge, we have investigated the possibility of replacing the two-coordinate Cu-I in superconducting lead cuprates of the general formula Pb2Sr2(Ca, Y)CU3O8 by Cr. A high-resolution electron microscopy study coupled with energy dispersive X-ray analysis on small crystals of the title phases suggests that between 10 and 15% of the Cu-I can be replaced by Cr. While from the present structural study using HRTEM and Rietveld refinement of X-ray powder data we are unable to precisely obtain the oxidation state and oxygen coordination of Cr, we suggest in analogy with Cr substitution in other similar cuprates that in the title phases (CuO2)-O-I rods are partially replaced by tetrahedral CrO42- groups. Infrared spectroscopy supports the presence of CrO42- groups. The phases Pb1.75Sr2Ca0.2Y0.8O8+delta and Pb1.75Sr2Ca0.2Y0.8CCu2.85Cr0.15O8+delta are superconducting as-prepared, but the substitution of Cr for Cu-I results in a decrease of the Te as well as the superconducting volume fraction. (C) 1996 Academic Press, lnc.

Observation of Water-Mediated Helix-Terminating Conformation in a Dehydrophenylalanine Peptide: Crystal and Solution Structure of the Octapeptide Ac-.DELTA.Phe-Val-.DELTA.Phe-Phe-Ala-Val-.DELTA.Phe-Gly-OMe

We have synthesised and determined the solution conformation and X-ray crystal structure of the octapeptide Ac-Delta Phe(1)-Val(2)-Delta Phe(3)-Phe(4)-Ala(5)-Val(6)-Delta Phe(7)-Gly(8)-OCH3 (Delta Phe = alpha,beta-dehydrophenylalanine) containing three Delta Phe residues as conformation constraining residues. In the solid state, the peptide folds into (i) an N-terminal (3)10(R)-helical pentapeptide segment, (ii) a middle non-helical segment, and (iii) a C-terminal incipient (3)10(L)-helical segment. The results of H-1 NMR data also suggest that a similar multiple-turn conformation for the peptide is largely maintained in solution. Though the C-terminal helix is incipient, the overall conformation of the octapeptide matches well with the conformation of the hairpins reported. Comparison of the pi-turn seen in the octapeptide molecule with those observed in proteins at the C-terminal end of helixes shows the structural similarity among them. A water molecule mediates the 5 --> 2 hydrogen bond in the pi-turn region. This is the first example of a water-inserted pi-turn in oligopeptides reported so far. Comparison between the present octapeptide and another (3)10(R)-helical dehydro nonapeptide Boc-Val-Delta Phe-Phe-Ala-Phe-Delta Phe-Val-Delta Phe-Gly-OCH3 solved by us recently, demonstrates the possible sequence-dependent conformational variations in alpha,beta-dehydrophenylalanine-containing oligopeptides.

The effect of surface mass transfer on buoyancy induced flow in a variable porosity medium adjacent to a vertical heated plate

The effect of surface mass transfer on buoyancy induced flow in a variable porosity medium adjacent to a heated vertical plate is studied for high Rayleigh numbers. Similarity solutions are obtained within the frame work of boundary layer theory for a power law variation in surface temperature,T Wpropx lambda and surface injectionv Wpropx(lambda–1/2). The analysis incorporates the expression connecting porosity and permeability and also the expression connecting porosity and effective thermal diffusivity. The influence of thermal dispersion on the flow and heat transfer characteristics are also analysed in detail. The results of the present analysis document the fact that variable porosity enhances heat transfer rate and the magnitude of velocity near the wall. The governing equations are solved using an implicit finite difference scheme for both the Darcy flow model and Forchheimer flow model, the latter analysis being confined to an isothermal surface and an impermeable vertical plate. The influence of the intertial terms in the Forchheimer model is to decrease the heat transfer and flow rates and the influence of thermal dispersion is to increase the heat transfer rate.

Cloning, expression, purification, crystallization and preliminary X-ray studies of the mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis

The mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis has been cloned, expressed, purified and crystallized and the crystals have been characterized using X-ray diffraction. The Matthews coefficient suggests the possibility of two lectin domains in the triclinic cell. The amino-acid sequence of the domain indicates structural similarity to well characterized beta-prism II fold lectins.

Structure of sesbania mosaic virus at 3 å resolution

Background: Sobemoviruses are a group of RNA plant viruses that have a narrow host range. They are characterized in vitro by their stability, high thermal inactivation point and longevity. The three-dimensional structure of only one virus belonging to this group, southern bean mosaic virus (SBMV), is known. Structural studies on sesbania mosaic virus (SMV), which is closely related to SBMV, will provide details of the molecular interactions that are likely to be important in the stability and assembly of sobemoviruses. Results: We have determined the three-dimensional structure of SMV at 3 Angstrom resolution. The polypeptide fold and quaternary organization are very similar to those of SBMV. The capsid consists of sixty icosahedral asymmetric units, each comprising three copies of a chemically identical coat protein subunit, which are designated as A, B and C and are in structurally different environments. Four cation-binding sites have been located in the icosahedral asymmetric unit. Of these, the site at the quasi-threefold axis is not found in SBMV. Structural differences are observed in loops and regions close to this cation-binding site. Preliminary studies on ethylene diamine tetra acetic acid (EDTA) treated crystals suggest asymmetry in removal of the quasi-equivalent cations at the AB, BC, and AC subunit interfaces. Conclusions: Despite the overall similarity between SMV and SBMV in the nature of the polypeptide fold, these viruses show a number of differences in intermolecular interactions. The polar interactions at the quasi-threefold axis are substantially less in SMV and positively charged residues on the RNA-facing side of the protein and in the N-terminal arm are not particularly well conserved. This suggests that protein-RNA interactions are likely to be different between the two viruses.

Vortex sheet simulation of a plane �canonical� mixing layer

Discrete vortex simulations of the mixing layer carried out in the past have usually involved large induced velocity fluctuations, and thus demanded rather long time-averaging to obtain satisfactory values of Reynolds stresses and third-order moments. This difficulty has been traced here, in part, to the use of discrete vortices to model what in actuality are continuous vortex sheets. We propose here a novel two-dimensional vortex sheet technique for computing mixing layer flow in the limit of infinite Reynolds number. The method divides the vortex sheet into constant-strength linear elements, whose motions are computed using the Biot-Savart law. The downstream far-field is modelled by a steady vorticity distribution derived by application of conical similarity from the solution obtained in a finite computational domain. The boundary condition on the splitter plate is satisfied rigorously using a doublet sheet. The computed large-scale roll-up of the vortex sheet is qualitatively similar to experimentally obtained shadow-graphs of the plane turbulent mixing layer. The mean streamwise velocity profile and the growth rate agree well with experimental data. The presently computed Reynolds stresses and third-order moments are comparable with experimental and previous vortex-dynamical results, without using any external parameter (such as the vortex core-size) of the kind often used in the latter. The computed autocorrelations are qualitatively similar to experimental results along the top and bottom edges of the mixing layer, and show a well-defined periodicity along the centreline. The accuracy of the present computation is independently established by demonstrating negligibly small changes in the five invariants (including the Hamiltonian) in vortex dynamics.