Structure-function relationships of icosahedral plant

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary organization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.

Singularity and controllability analysis of parallel manipulators and closed-loop mechanisms

This paper presents a study of kinematic and force singularities in parallel manipulators and closed-loop mechanisms and their relationship to accessibility and controllability of such manipulators and closed-loop mechanisms, Parallel manipulators and closed-loop mechanisms are classified according to their degrees of freedom, number of output Cartesian variables used to describe their motion and the number of actuated joint inputs. The singularities in the workspace are obtained by considering the force transformation matrix which maps the forces and torques in joint space to output forces and torques ill Cartesian space. The regions in the workspace which violate the small time local controllability (STLC) and small time local accessibility (STLA) condition are obtained by deriving the equations of motion in terms of Cartesian variables and by using techniques from Lie algebra.We show that for fully actuated manipulators when the number ofactuated joint inputs is equal to the number of output Cartesian variables, and the force transformation matrix loses rank, the parallel manipulator does not meet the STLC requirement. For the case where the number of joint inputs is less than the number of output Cartesian variables, if the constraint forces and torques (represented by the Lagrange multipliers) become infinite, the force transformation matrix loses rank. Finally, we show that the singular and non-STLC regions in the workspace of a parallel manipulator and closed-loop mechanism can be reduced by adding redundant joint actuators and links. The results are illustrated with the help of numerical examples where we plot the singular and non-STLC/non-STLA regions of parallel manipulators and closed-loop mechanisms belonging to the above mentioned classes. (C) 2000 Elsevier Science Ltd. All rights reserved.

High-Resolution Magic Angle Spinning Nmr-Studies Of P-31 And B-11 In Fast Ion Conducting Agi-Ag2o-P2o5 And Agi-Ag2o-B2o3 Glasses

Silver iodide-based fast ion conducting glasses containing silver phosphate and silver borate have been studied. An attempt is made to identify the interaction between anions by studying the chemical shifts of31P and11B atoms in high resolution (HR) magic angle spinning (MAS) NMR spectra. Variation in the chemical shifts of31P or11B has been observed which is attributed to the change in the partial charge on the31P or11B. This is indicative of the change in the electronegativity of the anion matrix as a whole. This in turn is interpreted as due to significant interaction among anions. The significance of such interaction to the concept of structural unpinning of silver ions in fast ion conducting glasses is discussed.

Interaction between the Z-type DNA duplex and 1,3-propanediamine:crystal structure of d(CACGTG)(2) at 1.2 angstrom resolution

The crystal structure of a hexamer duplex d(CACGTG)(2) has been determined and refined to an R-factor of 18.3% using X-ray data up to 1.2 angstrom resolution. The sequence crystallizes as a left-handed Z-form double helix with Watson-Crick base pairing. There is one hexamer duplex, a spermine molecule, 71 water molecules, and an unexpected diamine (Z-5, 1,3-propanediamine, C3H10N2)) in the asymmetric unit. This is the high-resolution non-disordered structure of a Z-DNA hexamer containing two AT base pairs in the interior of a duplex with no modifications such as bromination or methylation on cytosine bases. This structure does not possess multivalent cations such as cobalt hexaammine that are known to stabilize Z-DNA. The overall duplex structure and its crystal interactions are similar to those of the pure-spermine form of the d(CGCGCG)(2) structure. The spine of hydration in the minor groove is intact except in the vicinity of the T5A8 base pair. The binding of the Z-5 molecule in the minor grove of the d(CACGTG)(2) duplex appears to have a profound effect in conferring stability to a Z-DNA conformation via electrostatic complementarity and hydrogen bonding interactions. The successive base stacking geometry in d(CACGTG)(2) is similar to the corresponding steps in d(CG)(3). These results suggest that specific polyamines such as Z-5 could serve as powerful inducers of Z-type conformation in unmodified DNA sequences with AT base pairs. This structure provides a molecular basis for stabilizing AT base pairs incorporated into an alternating d(CG) sequence.

Structural, dielectric and ferroelectric properties of four-layer Aurivillius phase Na0.5La0.5Bi4Ti4O15

Monophasic Na0.5La0.5Bi4Ti4O15 powders were synthesized via the conventional solid-state reaction route. The X-ray powder diffraction (XRD), selected area electron diffraction (SAED) and high resolution transmission electron microscopy (HRTEM) studies carried out on the as synthesized powdered samples confirmed the phase to be a four-layer Aurivillius that crystallizes in an orthorhombic A2(1)am space group. The microstructure and the chemical composition of the sintered sample were examined by scanning electron microscope (SEM) equipped with an energy dispersive X-ray analyzer (EDX). The dielectric properties of the ceramics have been studied in the 27-700 degrees C temperature range at various frequencies (100 Hz to 1 MHz). A sharp dielectric anomaly was observed at 580 degrees C for all the frequencies corresponding to the ferroelectric to paraelectric phase transition. Saturated ferroelectric hysteresis loops were observed at 200 degrees C and the associated remnant polarization (P-r) and coercive field (E-c) were found to be 7.4 mu C/cm(2) and 34.8 kV/cm, respectively. AC conductivity analysis confirmed the existence of two different conduction mechanisms in the ferroelectric region. Activation energies calculated from the Arrhenius plots were similar to 0.24 eV and similar to 0.84 eV in the 300-450 degrees C and 450-580 degrees C temperature ranges, respectively. (C) 2010 Elsevier B.V. All rights reserved.

Identification of corona discharge-induced SF6 oxidation mechanisms using SF6/18O2/H216O and SF6/16O2/H218O gas mixtures

The absolute yields of gaseous oxyfluorides SOF2, SO2F2, and SOF4 from negative, point-plane corona discharges in pressurized gas mixtures of SF6 with O2 and H2O enriched with18O2 and H2 18O have been measured using a gas chromatograph-mass spectrometer. The predominant SF6 oxidation mechanisms have been revealed from a determination of the relative18O and16O isotope content of the observed oxyfluoride by-product. The results are consistent with previously proposed production mechanisms and indicate that SOF2 and SO2F2 derive oxygen predominantly from H2O and O2, respectively, in slow, gas-phase reactions involving SF4, SF3, and SF2 that occur outside of the discharge region. The species SOF4 derives oxygen from both H2O and O2 through fast reactions in the active discharge region involving free radicals or ions such as OH and O, with SF5 and SF4.

Successive refinement of structures with data of increasing resolution: a theoretical study for triclinic space groups

The method of least squares could be used to refine an imperfectly related trial structure by adoption of one of the following two procedures: (i) using all the observed at one time or (ii) successive refinement in stages with data of increasing resolution. While the former procedure is successful in the case of trial structures which are sufficiently accurate, only the latter has been found to be successful when the mean positional error (i.e.<|[Delta]r|>) for the atoms in the trial structure is large. This paper makes a theoretical study of the variation of the R index, mean phase-angle error, etc. as a function of <|[Delta]r|> for data corresponding to different esolutions in order to find the best refinement procedure [i.e. (i) or (ii)] which could be successfully employed for refining trial structures in which <|[Delta]r|> has large, medium and low values. It is found that a trial structure for which the mean positional error is large could be refined only by the method of successive refinement with data of increasing resolution.

cis-trans Enantiomerism in the Diels-Alder cycloadducts of 6-arylfulvenes with maleic anhydride: resolution of the exo adducts via the N-((1S)-1-(naphth-1-yl)ethyl)imide derivatives: assignment of the absolute configurations based on the crystal structure of an imide diastereomer

A new case of the uncommon cis-trans enantiomerism is presented. The titled anhydride adducts were prepared in good yields by the known reaction of three 6-arylfulvenes with maleic anhydride (aryl = phenyl, p-tolyl and p-anisyl). The exo adducts were converted to the corresponding imides by reaction with (1S)-1-(naphth-1-yl)ethylamine in similar to 80% yields, and the resulting diastereomeric imides separated by silica gel column chromatography. They were hydrolysed and recyclised to the chiral anhydrides, in `one-pot' with 10% NaOH-EtOH, followed by treatment with 2 M HCl, in similar to 40% yields. The titled anhydrides were thus obtained in homochiral form, in enantiomeric purities (generally) of similar to 90% as indicated by chiral HPLC. The chiral anhydrides were also converted to the corresponding imides (presumably stereospecifically), by treatment with ammonia solution in excellent yields. The crystal structure of one of the above diastereomeric imides (derived from 6-phenylfulvene) was determined, and based on the known (S)-configuration of the naphthylethylamine moiety, the `configurations' of the original anhydride adducts were assigned. (c) 2005 Elsevier Ltd. All rights reserved.

Design of Single-Input-Single-Output Compliant Mechanisms for Practical Applications Using Selection Maps

We present an interactive map-based technique for designing single-input-single-output compliant mechanisms that meet the requirements of practical applications. Our map juxtaposes user-specifications with the attributes of real compliant mechanisms stored in a database so that not only the practical feasibility of the specifications can be discerned quickly but also modifications can be done interactively to the existing compliant mechanisms. The practical utility of the method presented here exceeds that of shape and size optimizations because it accounts for manufacturing considerations, stress limits, and material selection. The premise for the method is the spring-leverage (SL) model, which characterizes the kinematic and elastostatic behavior of compliant mechanisms with only three SL constants. The user-specifications are met interactively using the beam-based 2D models of compliant mechanisms by changing their attributes such as: (i) overall size in two planar orthogonal directions, separately and together, (ii) uniform resizing of the in-plane widths of all the beam elements, (iii) uniform resizing of the out-of-plane thick-nesses of the beam elements, and (iv) the material. We present a design software program with a graphical user interface for interactive design. A case-study that describes the design procedure in detail is also presented while additional case-studies are posted on a website. DOI:10.1115/1.4001877].

Improved retrieval of aerosol size-resolved properties from moderate resolution imaging spectroradiometer over India: Role of aerosol model and surface reflectance

We have compared the total as well as fine mode aerosol optical depth (tau and tau(fine)) retrieved by Moderate Resolution Imaging Spectroradiometer (MODIS) onboard Terra and Aqua (2001-2005) with the equivalent parameters derived by Aerosol Robotic Network (AERONET) at Kanpur (26.45 degrees N, 80.35 degrees E), northern India. MODIS Collection 005 (C005)-derived tau(0.55) was found to be in good agreement with the AERONET measurements. The tau(fine) and eta (tau(fine)/tau) were, however, biased low significantly in most matched cases. A new set of retrieval with the use of absorbing aerosol model (SSA similar to 0.87) with increased visible surface reflectance provided improved tau and tau(fine) at Kanpur. The new derivation of eta also compares well qualitatively with an independent set of in situ measurements of accumulation mass fraction over much of the southern India. This suggests that though MODIS land algorithm has limited information to derive size properties of aerosols over land, more accurate parameterization of aerosol and surface properties within the existing C005 algorithm may improve the accuracy of size-resolved aerosol optical properties. The results presented in this paper indicate that there is a need to reconsider the surface parameterization and assumed aerosol properties in MODIS C005 algorithm over the Indian region in order to retrieve more accurate aerosol optical and size properties, which are essential to quantify the impact of human-made aerosols on climate.

High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination

Three-dimensional (3D) structure determination of proteins is benefitted by long-range distance constraints comprising the methyl groups, which constitute the hydrophobic core of proteins. However, in methyl groups (of Ala, Ile, Leu, Met, Thr and Val) there is a significant overlap of C-13 and H-1 chemical shifts. Such overlap can be resolved using the recently proposed (3,2)D HCCH-COSY, a G-matrix Fourier transform (GFT) NMR based experiment, which facilitates editing of methyl groups into distinct spectral regions by combining their C-13 chemical shifts with that of the neighboring, directly attached, C-13 nucleus. Using this principle, we present three GFT experiments: (a) (4,3)D NOESY-HCCH, (b) (4,3)D H-1-TOCSY-HCCH and (c) (4,3)D C-13-TOCSY-HCCH. These experiments provide unique 4D spectral information rapidly with high sensitivity and resolution for side-chain resonance assignments and NOE analysis of methyl groups. This is exemplified by (4,3)D NOESY-HCCH data acquired for 17.9 kDa non-deuterated cytosolic human J-protein co-chaperone, which provided crucial long-range distance constraints for its 3D structure determination.

Influence of cross-correlation between dipolar and chemical shift anisotropy relaxation mechanisms upon the transverse relaxation rates of 15N in macromolecules

Heteronuclear multiple-quantum coherence relaxation rate are calculated for the individual transitions of the S spin in an AIS nuclear spin system assuming that the heteronucleus (S spin) has relaxation contributions from both intramolecular dipole-dipole and chemical shift anisotropy relaxation. The individual multiplet components of the heteronuclear zero- and double-quantum coherences are shown to have different transverse relaxation rates. The cross-correlation between the two relaxation mechanisms is shown to be the dominant cause of the calculated differential line broadening. Experimental data are presented using as an example a uniformly 15N labelled sample of human epidermal growth factor.