Evolution, Homology Conservation, and Identification of Unique Sequence Signatures in GH19 Family Chitinases

The discovery of GH (Glycoside Hydrolase) 19 chitinases in Streptomyces sp. raises the possibility of the presence of these proteins in other bacterial species, since they were initially thought to be confined to higher plants. The present study mainly concentrates on the phylogenetic distribution and homology conservation in GH19 family chitinases. Extensive database searches are performed to identify the presence of GH19 family chitinases in the three major super kingdoms of life. Multiple sequence alignment of all the identified GH19 chitinase family members resulted in the identification of globally conserved residues. We further identified conserved sequence motifs across the major sub groups within the family. Estimation of evolutionary distance between the various bacterial and plant chitinases are carried out to better understand the pattern of evolution. Our study also supports the horizontal gene transfer theory, which states that GH19 chitinase genes are transferred from higher plants to bacteria. Further, the present study sheds light on the phylogenetic distribution and identifies unique sequence signatures that define GH19 chitinase family of proteins. The identified motifs could be used as markers to delineate uncharacterized GH19 family chitinases. The estimation of evolutionary distance between chitinase identified in plants and bacteria shows that the flowering plants are more related to chitinase in actinobacteria than that of identified in purple bacteria. We propose a model to elucidate the natural history of GH19 family chitinases.

Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types

The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.

Nucleotide-sequence of 5S RNA from mycobacterium-smegmatis

32P labelled 5S RNA isolated fromMycobacterium smegmatis was digested withT 1 and pancreatic ribonucleases separately and fingerprinted by two dimensional high voltage electrophoresis on thin-layer DEAE-cellulose plates. The radioactive spots were sequenced and their molar yields were determined. The chain length of the 5S RNA was found to be 120. It showed resemblances to both prokaryotic and eukaryotic 5S RNAs.

Sequence specificity in spermine-induced structural changes in CG-oligomers

The role of spermine in inducing A-DNA conformation in deoxyoligonucleotides has been studied using CCGG and GGCC as model sequences. It has been found that while CCGG adopts an alternating B-DNA conformation in low salt solution at low temperature, addition of spermine to this medium induces a B --greater than A transition. In contrast, the A-DNA-like structure of GGCC in low salt solution at low temperature does not change under the influence of spermine. This suggests a sequence-dependent behaviour of spermine. Further these results suggest that the A-DNA conformation observed in the crystals of d(iCCGG) and d(GGCC)2 might have been due to the presence of spermine in the crystallization cocktail.

Crystal structure of 2-thiophene-2-yl-3(thiophene-2-carboxylideneamino)-1,2-dihydroquinazolin-4(3H)-one and the synthesis, spectral and thermal studies of its transition metal(II) complexes

The synthesis of manganese(II), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes of a new ligand 2-thiophene-2-yl-3(thiophene-2-carboxylidene-amino)-1,2-dihydroquinazolin-4(3H)-one (TTCADQ) is described. The ligand and metal complexes were characterized by elemental analysis, conductivity measurements, spectral (u.v.-vis., i.r., 1D n.m.r., 2D hetcor and e.p.r.) and thermal studies. The formation of 1,2-dihydroquinazolin-4(3H)-one rather than hydrazone, in the reaction of aromatic aldehyde and o-aminobenzoylhydrazide is proved by single crystal X-ray diffraction and 2D hetcor n.m.r. studies. On the basis of elemental analysis, u.v.-vis.spectroscopy and magnetic moment studies, six coordinate geometry for all the complexes was proposed. The i.r. spectral studies reveal the bidentate behaviour of the ligand.

Wave propagation analysis in carbon nanotube embedded composite using wavelet based spectral finite elements

In this paper, elastic wave propagation is studied in a nanocomposite reinforced with multiwall carbon nanotubes (CNTs). Analysis is performed on a representative volume element of square cross section. The frequency content of the exciting signal is at the terahertz level. Here, the composite is modeled as a higher order shear deformable beam using layerwise theory, to account for partial shear stress transfer between the CNTs and the matrix. The walls of the multiwall CNTs are considered to be connected throughout their length by distributed springs, whose stiffness is governed by the van der Waals force acting between the walls of nanotubes. The analyses in both the frequency and time domains are done using the wavelet-based spectral finite element method (WSFEM). The method uses the Daubechies wavelet basis approximation in time to reduce the governing PDE to a set of ODEs. These transformed ODEs are solved using a finite element (FE) technique by deriving an exact interpolating function in the transformed domain to obtain the exact dynamic stiffness matrix. Numerical analyses are performed to study the spectrum and dispersion relations for different matrix materials and also for different beam models. The effects of partial shear stress transfer between CNTs and matrix on the frequency response function (FRF) and the time response due to broadband impulse loading are investigated for different matrix materials. The simultaneous existence of four coupled propagating modes in a double-walled CNT-composite is also captured using modulated sinusoidal excitation.

Structural and spectral perspectives of a novel thiosemicarbazone synthesized from di-2-pyridyl ketone and 4-phenyl-3-thiosemicarbazide

A new thiosemicarbazone, HL is synthesized from di-2-pyridyl ketone and 4-phenyl-3-thiosemicarbazide and structurally and spectrochemically characterized. H-1 NMR, C-13 NMR, COSY, HMQC and IR spectra of the compound are studied and the proton magnetic resonance spectrum reveals some unprecedented observations. The thione form is predominant in the solid state, as supported by the crystal structure and IR data, while a thiol-thione equilibrium is proposed in the solution state by NMR studies. The compound crystallizes into a monoclinic lattice with space group C2/c and the ZE conformation is exhibited by the thiosemicarbazone. Intra- and intermolecular hydrogen-bonding interactions give rise to a two-dimensional packing in the crystal lattice

Sequence specificity of Z-DNA formation in oligonucleotides

The sequence specific requirement for B----Z transition in solution was examined in d(CGTGCGCACG), d(CGTACGTACG), d(ACGTACGT) in presence of various Z-inducing factors. Conformational studies show that inspite of the alternating nature of purines and pyrimidines, the aforementioned sequences do not undergo B----Z transition under the influence of NaCl, hexamine cobalt chloride and ethanol. A comparison with the crystal structures of an assorted array of purine and pyrimidine sequences show that the sequence requirement for B----Z transition is much more stringent in solution as compared to the solid state. The disruptive influence of AT base pairs in B to Z transition is discussed.

Spectral assignments based on the 13C NMR spectra of mixed liquid crystals of opposite diamagnetic anisotropies

The proton-decoupled 13C NMR spectra of mixtures of liquid crystals with opposite diamagnetic anisotropies have been studied in the natural abundance of 13C. A new method to assign the spectral lines to specific carbons in the liquid crystalline phase has been developed. For this purpose, the assignments of lines in the isotropic media are required, and they were obtained from two-dimensional hetero-COSY experiments. From the spectra in the �critical� mixtures where both the orientations of the liquid crystal directors, with the alignments along and perpendicular to the direction of the magnetic field, �coexist,� the 13C chemical-shift anisotropies have been determined, assuming uniaxial symmetry.

Spectral studies on pyridinium hexafluorotitanate(IV)

Pure samples of pyridinium hexafluorotitanate(IV) [(C5H5N+H)2TiF=6] were prepared by the reaction of pyridinium poly(hydrogen fluoride) and titanium tetrachloride. The i.r. spectral data in the range 4000–200 cm−1 and 1H, 19F, and 13CNMR spectra for this compound are reported.

Structural and spectral perspectives of a novel thiosemicarbazone synthesized from di-2-pyridyl ketone and 4-phenyl-3-thiosemicarbazide

A new thiosemicarbazone, HL is synthesized from di-2-pyridyl ketone and 4-phenyl-3-thiosemicarbazide and structurally and spectrochemically characterized. H-1 NMR, C-13 NMR, COSY, HMQC and IR spectra of the compound are studied and the proton magnetic resonance spectrum reveals some unprecedented observations. The thione form is predominant in the solid state, as supported by the crystal structure and IR data, while a thiol-thione equilibrium is proposed in the solution state by NMR studies. The compound crystallizes into a monoclinic lattice with space group C2/c and the ZE conformation is exhibited by the thiosemicarbazone. Intra- and intermolecular hydrogen-bonding interactions give rise to a two-dimensional packing in the crystal lattice. (c) 2005 Elsevier B.V. All rights reserved.