Novel ATPase activity of the polyprotein intermediate, Viral Protein genome-linked-Nuclear Inclusion-a protease, of Pepper vein banding potyvirus

Potyviruses temporally regulate their protein function by polyprotein processing. Previous studies have shown that VPg (Viral Protein genome-linked) of Pepper vein banding virus interacts with the NIa-Pro (Nuclear Inclusion-a protease) domain, and modulates the kinetics of the protease. In the present study, we report for the first time that VPg harbors the Walker motifs A and B, and the presence of NIa-Pro, especially in cis (cleavage site (E191A) VPg-Pro mutant), is essential for manifestation of the ATPase activity. Mutation of Lys47 (Walker motif A) and Asp88:Glu89 (Walker motif B) to alanine in E191A VPg-Pro lead to reduced ATPase activity, confirming that this activity was inherent to VPg. We propose that potyviral VPg, established as an intrinsically disordered domain, undergoes plausible structural alterations upon interaction with globular NIa-Pro which induces the ATPase activity. (C) 2012 Elsevier Inc. All rights reserved.

Effect of pouring temperature on cooling slope casting of semi-solid Al-Si-Mg alloy

Present trend of semi-solid processing is directed towards rheocasting route which allows manufacturing of near-net-shape cast components directly from the prepared semi-solid slurry. Generation of globular equi-axed grains during solidification of rheocast components, compared to the columnar dendritic structure of conventional casting routes, facilitates the manufacturing of components with improved mechanical properties and structural integrity. In the present investigation, a cooling slope has been designed and indigenously fabricated to produce semi solid slurry of Al-Si-Mg (A356) alloy and successively cast in a metallic mould. The scope of the present work discusses about development of a numerical model to simulate the liquid metal flow through cooling slope using Eulerian two-phase flow approach and to investigate the effect of pouring temperature on cooling slope semi-solid slurry generation process. The two phases considered in the present model are liquid metal and air. Solid fraction evolution of the solidifying melt is tracked at different locations of the cooling slope, following Schiel's equation. The continuity equation, momentum equation and energy equation are solved considering thin wall boundary condition approach. During solidification of the liquid metal, a modified temperature recovery scheme has been employed taking care of the latent heat release and change of fraction of liquid. The results obtained from simulations are compared with experimental findings and good agreement has been found.

Diel variation in fig volatiles across syconium development: making sense of scents

Plants produce volatile organic compounds (VOCs) in a variety of contexts that include response to abiotic and biotic stresses, attraction of pollinators and parasitoids, and repulsion of herbivores. Some of these VOCs may also exhibit diel variation in emission. In Ficus racemosa, we examined variation in VOCs released by fig syconia throughout syconium development and between day and night. Syconia are globular enclosed inflorescences that serve as developing nurseries for pollinating and parasitic fig wasps. Syconia are attacked by gallers early in their development, serviced by pollinators in mid phase, and are attractive to parasitoids in response to the development of gallers at later stages. VOC bouquets of the different development phases of the syconium were distinctive, as were their day and night VOC profiles. VOCs such as alpha-muurolene were characteristic of the pollen-receptive diurnal phase, and may serve to attract the diurnally-active pollinating wasps. Diel patterns of release of volatiles could not be correlated with their predicted volatility as determined by Henry's law constants at ambient temperatures. Therefore, factors other than Henry's law constant such as stomatal conductance or VOC synthesis must explain diel variation in VOC emission. A novel use of weighted gene co-expression network analysis (WGCNA) on the volatilome resulted in seven distinct modules of co-emitted VOCs that could be interpreted on the basis of syconium ecology. Some modules were characterized by the response of fig syconia to early galling by parasitic wasps and consisted largely of green leaf volatiles (GLVs). Other modules, that could be characterized by a combination of syconia response to oviposition and tissue feeding by larvae of herbivorous galler pollinators as well as of parasitized wasps, consisted largely of putative herbivore-induced plant volatiles (HIPVs). We demonstrated the usefulness of WGCNA analysis of the volatilome in making sense of the scents produced by the syconia at different stages and diel phases of their development.

Study of dendrite growth in a rotational flow field

A numerical model to study the growth of dendrites in a pure metal solidification process with an imposed rotational flow field is presented. The micro-scale features of the solidification are modeled by the well-known enthalpy technique. The effect of flow changing the position of the dendrite is captured by the Volume of Fluid (VOF) method. An imposed rigid-body rotational flow is found to gradually transform the dendrite into a globular microstructure. A parametric study is carried out for various angular velocities and the time for merger of dendrite arms is compared with the order estimate obtained from scaling.

Structural Integrity of the Greek Key Motif in beta gamma-Crystallins Is Vital for Central Eye Lens Transparency

Background: We highlight an unrecognized physiological role for the Greek key motif, an evolutionarily conserved super-secondary structural topology of the beta gamma-crystallins. These proteins constitute the bulk of the human eye lens, packed at very high concentrations in a compact, globular, short-range order, generating transparency. Congenital cataract (affecting 400,000 newborns yearly worldwide), associated with 54 mutations in beta gamma-crystallins, occurs in two major phenotypes nuclear cataract, which blocks the central visual axis, hampering the development of the growing eye and demanding earliest intervention, and the milder peripheral progressive cataract where surgery can wait. In order to understand this phenotypic dichotomy at the molecular level, we have studied the structural and aggregation features of representative mutations. Methods: Wild type and several representative mutant proteins were cloned, expressed and purified and their secondary and tertiary structural details, as well as structural stability, were compared in solution, using spectroscopy. Their tendencies to aggregate in vitro and in cellulo were also compared. In addition, we analyzed their structural differences by molecular modeling in silico. Results: Based on their properties, mutants are seen to fall into two classes. Mutants A36P, L45PL54P, R140X, and G165fs display lowered solubility and structural stability, expose several buried residues to the surface, aggregate in vitro and in cellulo, and disturb/distort the Greek key motif. And they are associated with nuclear cataract. In contrast, mutants P24T and R77S, associated with peripheral cataract, behave quite similar to the wild type molecule, and do not affect the Greek key topology. Conclusion: When a mutation distorts even one of the four Greek key motifs, the protein readily self-aggregates and precipitates, consistent with the phenotype of nuclear cataract, while mutations not affecting the motif display `native state aggregation', leading to peripheral cataract, thus offering a protein structural rationale for the cataract phenotypic dichotomy ``distort motif, lose central vision''.

Rheological characterization of semi-solid A356 aluminium alloy

Rheological behavior of semi-solid slurries forms the backbone of semi-solid processing of metallic alloys. In particular, the effects of several process and metallurgical parameters such as shear rate, shear time, temperature, rest time and size, distribution and morphology of the primary phase on the viscosity of the slurry needs in-depth characterization. In the present work, rheological behaviour of the semisolid aluminium alloy (A356) slurry is investigated by using a high temperature Searle type Rheometer using concentric cylinders. Three different types of experiment are carried out: isothermal test, continuous cooling test and steady state test. Continuous decrease in viscosity is observed with increasing shear rate at a fixed temperature (isothermal test). It is also found that the viscosity increases with decreasing temperature for a particular shear rate due to increasing solid fraction (continuous cooling test). Thixotropic nature of the slurry is confirmed from the hysteresis loops obtained during experimentation. Time dependence of slurry viscosity has been evaluated from the steady state tests. After a longer shearing time under isothermal conditions the starting dendritic structure of the said alloy is transformed into globular grains due to abrasion, agglomeration, welding and ripening.

Numerical study of the impact of inoculant and grain transport on macrosegregation and microstructure formation during solidification of an Al-22%Cu alloy

We investigate the impact of the nucleation law for nucleation on Al-Ti-B inoculant particles, of the motion of inoculant particles and of the motion of grains on the predicted macrosegregation and microstructure in a grain-refined Al-22 wt.% Cu alloy casting. We conduct the study by numerical simulations of a casting experiment in a side-cooled 76×76×254 mm sand mould. Macrosegregation and microstructure formation are studied with a volume-averaged two-phase model accounting for macroscopic heat and solute transport, melt convection, and transport of inoculant particles and equiaxed grains. On the microscopic scale it accounts for nucleation on inoculant particles with a given size distribution (and corresponding activation undercooling distribution)and for the growth of globular solid grains. The growth kinetics is described by accounting for limited solute diffusion in both liquid and solid phases and for convective effects. We show that the consideration of a size distribution of the inoculants has a strong impact on the microstructure(final grain size) prediction. The transport of inoculants significantly increases the microstructure heterogeneities and the grain motion refines the microstructure and reduces the microstructure heterogeneities.

Finding hidden females in a crowd: Mate recognition in fig wasps

Multi-species mating aggregations are crowded environments within which mate recognition must occur. Mating aggregations of fig wasps can consist of thousands of individuals of many species that attain sexual maturity simultaneously and mate in the same microenvironment, i.e, in syntopy, within the close confines of an enclosed globular inflorescence called a syconium - a system that has many signalling constraints such as darkness and crowding. All wasps develop within individual galled flowers. Since mating mostly occurs when females are still confined within their galls,, male wasps have the additional burden of detecting conspecific females that are ``hidden'' behind barriers consisting of gall walls. In Ficus racemosa, we investigated signals used by pollinating fig wasp males to differentiate conspecific females from females of other syntopic fig wasp species. Male Ceratosolen fusciceps could detect conspecific females using cues from galls containing females, empty galls, as well as cues from gall volatiles and gall surface hydrocarbons. In many figs, syconia are pollinated by single foundress wasps, leading to high levels of wasp inbreeding due to sibmating. In F. racemosa, as most syconia contain many foundresses, we expected male pollinators to prefer non-sib females to female siblings to reduce inbreeding. We used galls containing females from non-natal figs as a proxy for non-sibs and those from natal figs as a proxy for sibling females. We found that males preferred galls of female pollinators from natal figs. However, males were undecided when given a choice between galls containing non-pollinator females from natal syconia and pollinator females from non-natal syconia, suggesting olfactory imprinting by the natal syconial environment. (C) 2013 Elsevier Masson SAS. All rights reserved.

DEFINING alpha-HELIX GEOMETRY BY C-alpha ATOM TRACE vs (phi-psi) TORSION ANGLES: A COMPARATIVE ANALYSIS

A regular secondary structure is described by a well defined set of values for the backbone dihedral angles (phi,psi and omega) in a polypeptide chain. However in real protein structures small local variations give rise to distortions from the ideal structures, which can lead to considerable variation in higher order organization. Protein structure analysis and accurate assignment of various structural elements, especially their terminii, are important first step in protein structure prediction and design. Various algorithms are available for assigning secondary structure elements in proteins but some lacunae still exist. In this study, results of a recently developed in-house program ASSP have been compared with those from STRIDE, in identification of alpha-helical regions in both globular and membrane proteins. It is found that, while a combination of hydrogen bond patterns and backbone torsional angles (phi-psi) are generally used to define secondary structure elements, the geometry of the C-alpha atom trace by itself is sufficient to define the parameters of helical structures in proteins. It is also possible to differentiate the various helical structures by their C-alpha trace and identify the deviations occurring both at mid-positions as well as at the terminii of alpha-helices, which often lead to occurrence of 3(10) and pi-helical fragments in both globular and membrane proteins.

INDUCTION OF FOLDED STRUCTURES IN DESIGNED PEPTIDES USING CONFORMATIONALLY CONSTRAINED RESIDUES

Folding into compact globular structures, with well-defined modules of secondary structure, appears to be a characteristic of long polypeptide chains, with a specific patterning of coded amino acid residues along the length of sequence. Cooperative hydrogen bond driven secondary structure formation and solvent forces, which contribute favorably to the entropy of folding, by promoting compaction of the polymeric chain, have long been discussed as major determinants of the folding process. First principles design approaches, which use non-coded amino acids, employ an alternative structure directing strategy, by using amino acid residues which exhibit a strong conformational bias for specific regions of the Ramachandran map. This overview of ongoing studies in the authors' laboratory, attempts to explore the use of conformationally restricted amino acid residues in the design of peptides with well-defined secondary structures. Short peptides composed of 20 genetically coded amino acids usually exist in solution as an ensemble of equilibrating conformations. Apolar peptide sequences, which are readily soluble in organic solvents like chloroform and methanol, facilitate formation of structures which are predominately driven by intramolecular hydrogen bond formation. The choice of sequences containing residues with a limited range of conformational choices strongly favors formation of local turn structures, stabilized by short range intramolecular hydrogen bonds. Two residue beta-turns can nucleate either helical or hairpin folding, depending on the precise conformation of the turn segment Restriction of the conformational space available to amino acid residues is easily achieved by introduction of an additional alkyl group at the C alpha carbon atom or by side chain backbone cyclization, as in proline. Studies of synthetic sequences incorporating two prototype residues alpha-aminoisobutyric acid (Aib) and D-proline (DPro) illustrate the utility of the strategy in construction of helices and hairpins. Extensions to the design of conformationally switchable sequences and structurally defined hybrid peptides containing backbone homologated residues are also surveyed.

Experimental and numerical studies on friction welding of thixocast A356 aluminum alloy

This paper highlights the role of globular microstructure on the weldability of semi-solid processed aluminum alloys via high temperature flow behavior. The investigation was carried out on the joining of thixocast A356 aluminum alloy components by friction welding. A thermomechanical model was developed to predict the temperature and stress distributions, as well as to identify the suitable and safe range of parameters. Good comparisons between numerical and experimental results were observed. In addition, metallographic examinations and hardness and tensile tests of the welded samples were carried out. It was found that the tensile strength of the joint is higher than the tensile strength of the parent material for the optimum set of parameters. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Processing-microstructure-yield strength correlation in a near beta Ti alloy, Ti-5Al-5Mo-5V-3Cr

A combined set of thermo-mechanical steps recommended for high strength beta Ti alloy are homogenization, deformation, recrystallization, annealing and ageing steps in sequence. Recrystallization carried out above or below beta transus temperature generates either beta annealed (lath type morphology of alpha) or bimodal (lath+globular morphology of alpha) microstructure. Through variations in heat treatment parameters at these processing steps, wide ranges of length scales of features have been generated in both types of microstructures in a near beta Ti alloy, Ti-5Al-5Mo-5V-3Cr (Ti-5553). 0.2% Yield strength (YS) has been correlated to various microstructural features and associated heat treatment parameters. Relative importance of microstructural features in influencing YS has been identified. Process parameters at different steps have been identified and recommended for attaining different levels of YS for this near beta Ti alloy. (C) 2014 Elsevier B.V. All rights reserved.

Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness

The protein folding funnel paradigm suggests that folding and unfolding proceed as directed diffusion in a multidimensional free energy surface where a multitude of pathways can be traversed during the protein's sojourn from initial to final state. However, finding even a single pathway, with the detail chronicling of intermediates, is an arduous task. In this work we explore the free energy surface of unfolding pathway through umbrella sampling, for a small globular a-helical protein chicken-villin headpiece (HP-36) when the melting of secondary structures is induced by adding DMSO in aqueous solution. We find that the unfolding proceeds through the initial separation or melting of aggregated hydrophobic core that comprises of three phenylalanine residues (Phe7, Phe11, and Phe18). This separation is accompanied by simultaneous melting of the second helix. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hydrophobic grooves to stabilize the intermediate states. We identify the configuration of the intermediates and correlate the intermediates with those obtained in our previous works. We also give an estimate of the barriers for different transition states and observe the softening of the barriers with increasing DMSO concentration. We show that higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of a solvent modified, less rugged pathway. The prime outcome of this work is the demonstration that mixed solvents can profoundly transform the nature of the energy landscape and induce unfolding via a modified route. A successful application of Kramer's rate equation correlating the free energy simulation results shows faster rate of unfolding with increasing DMSO concentration. This work perhaps presents the first systematic theoretical study of the effect of a chemical denaturant on the microscopic free energy surface and rates of unfolding of HP-36. (C) 2014 AIP Publishing LLC.

Sequence and conformational preferences at termini of alpha-helices in membrane proteins: Role of the helix environment

-helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These -helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze -helices in a high-resolution dataset of integral -helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. Proteins 2014; 82:3420-3436. (c) 2014 Wiley Periodicals, Inc.

Influence of melt pouring temperature and plate inclination on solidification and microstructure of A356 aluminum alloy produced using oblique plate

The preparation of semisolid slurry of A356 aluminum alloy using an oblique plate was investigated. A356 alloy melt undergoes partial solidification when it flows down on an oblique plate cooled from underneath by counter flowing water. It results in continuous formation of columnar dendrites on plate wall. Due to forced convection, these dendrites are sheared off into equiaxed/fragmented grains and then washed away continuously to produce semisolid slurry at plate exit. Melt pouring temperature provides required condition of solidification whereas plate inclination enables necessary shear for producing semisolid slurry of desired quality. Slurry obtained was solidified in metal mould to produce semisolid-cast billets of desired microstructure. Furthermore, semisolid-cast billets were heat treated to improve surface quality. Microstructures of both semisolid-cast and heat-treated billets were analyzed. Effects of melt pouring temperature and plate inclination on solidification and microstructure of billets produced using oblique plate were described. The investigations involved four different melt pouring temperatures (620, 625, 630 and 635 degrees C) associated with four different plate inclinations (30 degrees, 45 degrees, 60 degrees and 75 degrees). Melt pouring temperature of 625 degrees C with plate inclination of 60 degrees shows fine and globular microstructures and it is the optimum.