Structural Studies on the Second Mycobacterium smegmatis Dps: Invariant and Variable Features of Structure, Assembly and Function

A second DNA binding protein from stationary-phase cells of Mycobacterium smegmatis (MsDps2) has been identified from the bacterial genome. It was cloned, expressed and characterised and its crystal structure was determined. The core dodecameric structure of MsDps2 is the same as that of the Dps from the organism described earlier (MsDps1). However, MsDps2 possesses a long N-terminal tail instead of the C-terminal tail in MsDps1. This tail appears to be involved in DNA binding. It is also intimately involved in stabilizing the dodecamer. Partly on account of this factor, MsDps2 assembles straightway into the dodecamer, while MsDps1 does so on incubation after going through an intermediate trimeric stage. The ferroxidation centre is similar in the two proteins, while the pores leading to it exhibit some difference. The mode of sequestration of DNA in the crystalline array of molecules, as evidenced by the crystal structures, appears to be different in MsDps1 and MsDps2, highlighting the variability in the mode of Dps–DNA complexation. A sequence search led to the identification of 300 Dps molecules in bacteria with known genome sequences. Fifty bacteria contain two or more types of Dps molecules each, while 195 contain only one type. Some bacteria, notably some pathogenic ones, do not contain Dps. A sequence signature for Dps could also be derived from the analysis.

Structure and Bonding in Cyclic Isomers of B2AlHnm (n = 3−6, m = −2 to +1): A Comparative Study with B3Hnm, BAl2Hnm and Al3Hnm†

The structure, bonding and energetics of B2AlHnm (n = 3−6, m = −2 to +1) are compared with corresponding homocyclic boron, aluminum analogues and BAl2Hnm using density functional theory (DFT). Divalent to hexacoordinated boron and aluminum atoms are found in these species. The geometrical and bonding pattern in B2AlH4− is similar to that for B2SiH4. Species with lone pairs on the divalent boron and aluminum atoms are found to be minima on the potential energy surface of B2AlH32−. A dramatic structural diversity is observed in going from B3Hnm to B2AlHnm, BAl2Hnm and Al3Hnm and this is attributable to the preference of lower coordination on aluminum, higher coordination on boron and the higher multicenter bonding capability of boron. The most stable structures of B3H6+, B2AlH5 and BAl2H4− and the trihydrogen bridged structure of Al3H32− show an isostructural relationship, indicating the isolobal analogy between trivalent boron and divalent aluminum anion.

Structure and bonding of MCB5H7 and its sandwiched dimer CB5H6M–MCB5H6 (M = Si, Ge, Sn): Isomer stability and preference for slip distorted structure

We find sandwiched metal dimers CB5H6M–MCB5H6 (M = Si, Ge, Sn) which are minima in the potential energy surface with a characteristic M–M single bond. The NBO analysis and the M–M distances (Å) (2.3, 2.44 and 2.81 for M = Si, Ge, Sn) indicate substantial M–M bonding. Formal generation of CB5H6M–MCB5H6 has been studied theoretically. Consecutive substitution of two boron atoms in B7H−27 by M (Si, Ge, Sn) and carbon, respectively followed by dehydrogenation may lead to our desired CB5H6M–MCB5H6. We find that the slip distorted geometry is preferred for MCB5H7 and its dehydrogenated dimer CB5H6M–MCB5H6. The slip-distortion of M–M bond in CB5H6M–MCB5H6 is more than the slip distortion of M–H bond in MCB5H7. Molecular orbital analysis has been done to understand the slip distortion. Larger M–M bending (CB5H6M–MCB5H6) in comparison with M–H bending (MCB5H7) is suspected to be encouraged by stabilization of one of the M–M π bonding MO’s. Preference of M to occupy the apex of pentagonal skeleton of MCB5H7 over its icosahedral analogue MCB10H11 has been observed.

Three-dimensional structure of heat shock protein 90 from Plasmodium falciparum: molecular modelling approach to rational drug design against malaria

We have recently implicated heat shock protein 90 from Plasmodium falciparum (PfHsp90) as a potential drug target against malaria. Using inhibitors specific to the nucleotide binding domain of Hsp90, we have shown potent growth inhibitory effects on development of malarial parasite in human erythrocytes. To gain better understanding of the vital role played by PfHsp90 in parasite growth, we have modeled its three dimensional structure using recently described full length structure of yeast Hsp90. Sequence similarity found between PfHsp90 and yeast Hsp90 allowed us to model the core structure with high confidence. The superimposition of the predicted structure with that of the template yeast Hsp90 structure reveals an RMSD of 3.31 angstrom. The N-terminal and middle domains showed the least RMSD (1.76 angstrom) while the more divergent C-terminus showed a greater RMSD (2.84 angstrom) with respect to the template. The structure shows overall conservation of domains involved in nucleotide binding, ATPase activity, co-chaperone binding as well as inter-subunit interactions. Important co-chaperones known to modulate Hsp90 function in other eukaryotes are conserved in malarial parasite as well. An acidic stretch of amino acids found in the linker region, which is uniquely extended in PfHsp90 could not be modeled in this structure suggesting a flexible conformation. Our results provide a basis to compare the overall structure and functional pathways dependent on PfHsp90 in malarial parasite. Further analysis of differences found between human and parasite Hsp90 may make it possible to design inhibitors targeted specifically against malaria.

Vegetation structure and floristic composition of a tropical dry deciduous forest in Bhadra Wildlife Sanctuary, Karnataka, India

A permanent 2 ha (200 m x 100 m) plot was established for long-term monitoring of plant diversity and dynamics in a tropical dry deciduous forest of Bhadra Wildlife Sanctuary, Karnataka, southern India. Enumeration of all woody plants >= 1 cm DBH (diameter at breast height) yielded a total of 1766 individuals that belonged to 46 species, 37 genera and 24 families. Combretaceae was the most abundant family in the forest with a family importance value of 68.3. Plant density varied from 20 - 90 individuals with an average 35 individuals/quadrat (20 m x 20 m). Randia dumetorum, with 466 individuals (representing 26.7 % of the total density 2 ha(-1)) with species importance value of 36.25, was the dominant species in the plot. The total basal area of the plot was 18.09 m(2) ha(-1) with a mean of 0.72 m(2) quadrat(-1). The highest basal area of the plot was contributed by Combretaceae (12.93 m(2) 2 ha(-1)) at family level and Terminalia tomentosa (5.58 m(2) 2 ha(-1)) at species level. The lowest diameter class (1-10 cm) had the highest density (1054 individuals 2 ha(-1)), but basal area was highest in the 80 - 90 cm diameter class (5.03m(2) 2 ha(-1)). Most of the species exhibited random or aggregated distribution over the plot. This study provides a baseline information on the dry forests of Bhadra Wildlife Sanctuary.

Interlayer structure of iodide intercalated layered double hydroxides (LDHs)

The iodide-containing layered double hydroxides (LDHs) of Mg and Zn with AI crystallize by the inclusion of extensive positional disorder of I- ions in the interlayer region. I- ion given its poor charge to size ratio can neither screen effectively the positive charge nor participate in H-bonding with the metal hydroxide layers. Thereby the I- ions are not stabilized in sites close to the seat of positive charge of the metal hydroxide layers (6c), nor in sites that facilitate H-bonding (3b or 18h). On the other hand, OH- from water can do both and effectively displaces I- from the interlayer. (C) 2010 Elsevier Inc. All rights reserved.

Structure and assembly of Sesbania mosaic virus

Sesbania mosaic virus (SeMV) is a ss-RNA (4149 nt) plant sobemovirus isolated from farmer's field around Tirupathi, Andhra Pradesh. The viral capsid (30 nm diameter) consists of 180 copies of protein subunits (MW 29 kDa) organized with icosahedral symmetry. In order to understand the mechanism of assembly of SeMV, a large number of deletion and substitution mutants of the coat protein (CP) were constructed. Recombinant SeMV CP (rCP) as well as the N-terminal rCP deletion mutant Delta N22 were found to assemble in E. coli into virus-like particles (VLPs). Delta N36 and Delta N65 mostly formed smaller particles consisting of 60 protein subunits. Although particlem assembly was not affected due to the substitution of aspartates (D14 and D149) that coordinate calcium ions by asparagines, the stability of the resulting capsids was drastically reduced. Deletion of residues forming a characteristic beta-annulus at the icosahedral 3-folds did not affect the assembly of VLPs. Mutation of a single tryptophan, which occurs near the icosahedral fivefold axis to glutamate or lysine, resulted in the disruption of the capsid leading to soluble dimers that resembled the quasi-dimer structure of the native virus. Replacement of positively charged residues in the amino terminal segment of CP resulted in the formation of empty shells. Based on these observations, a plausible mechanism of assembly is proposed.

Evaluation of methods to estimate foliage density in the understorey of a tropical evergreen forest

Foliage density and leaf area index are important vegetation structure variables. They can be measured by several methods but few have been tested in tropical forests which have high structural heterogeneity. In this study, foliage density estimates by two indirect methods, the point quadrat and photographic methods, were compared with those obtained by direct leaf counts in the understorey of a wet evergreen forest in southern India. The point quadrat method has a tendency to overestimate, whereas the photographic method consistently and ignificantly underestimates foliage density. There was stratification within the understorey, with areas close to the ground having higher foliage densities.

Structure and optical properties of Cd-substituted ZnO (Zn1-xCdxO) nanostructures synthesized by the high-pressure solution route

We report the synthesis of Cd-substituted ZnO nanostructures (Zn1-xCdxO with x up to approximate to 0.09) by the high-pressure solution growth method. The synthesized nanostructures comprise nanocrystals that are both particles (similar to 10-15 nm) and rods which grow along the [002] direction as established by transmission electron microscope (TEM) and x-ray diffraction (XRD) analysis. Rietveld analysis of the XRD data shows a monotonic increase of the unit cell volume with the increase of Cd concentration. The optical absorption, as well as the photoluminescence (PL), shows a red shift on Cd substitution. The line width of the PL spectrum is related to the strain inhomogeneity and it peaks in the region where the CdO phase separates from the Zn1-xCdxO nanostructures. The time-resolved photoemission showed a long-lived (similar to 10 ns) component. We propose that the PL behaviour of the Zn1-xCdxO is dominated by strain in the sample with the red shift of the PL linked to the expansion of the unit cell volume on Cd substitution.

Negative nuclear Overhauser effects as probes of macromolecular structure

Nuclear Overhauser effects (NOE) and circular dichroism (CD) techniques have been used to probe @-turn conformations in acyclic and cyclic peptides containingPro-Xsequences. The model peptides studied are of the type Piv-Pro-X-NHMe (X = Aib, D-Ala, Gly, Val, and Leu) and Boc-Cys-Pro-X-C s NHMe (X = Aib, L-Ala, D-Ala, Gly, and Leu). In the acyclic series, observation of NOES between Pro C"H and X-NH, together with solvent and temperature dependence of NH chemical shifts, establishes a 4 - 1 hydrogen bond stabilized type I1 @-turn in the Gly, D-Ala, and Aib peptides, in CDC13 and (CD3)2S0. A positive n-r* CD band at -225-230 nm appears to be characteristic of this structure. For the acyclic Pro-Leu peptide the observation of NOE's for both Pro and Leu C"H resonances on saturation of Leu NH is compatible with a type V bend or consecutive y-turn conformation. In the cyclic disulfide series the Pro-Aib and Pro-D-Ala peptides favor type I1 @-turns, whereas all other peptides adopt type I (111) conformations. All the cyclic disulfides exhibit an intense negative CD band at -228-230 nm. The results suggest thatgeneralcorrelations between CD spectral type and specific 0-turn conformations may not be obtained. Evidence for solvent-dependent structural changes in the Pro-Aib sequence in both cyclic and acyclic peptides is presented.

An asymptotic analysis of a simple model for the structure and dynamics of the Ramdas layer

This paper presents a complete asymptotic analysis of a simple model for the evolution of the nocturnal temperature distribution on bare soil in calm clear conditions. The model is based on a simplified flux emissivity scheme that provides a nondiffusive local approximation for estimating longwave radiative cooling near ground. An examination of the various parameters involved shows that the ratio of the characteristic radiative to the diffusive timescale in the problem is of order 10(-3), and can therefore be treated as a small parameter (mu). Certain other plausible approximations and linearization lead to a new equation whose asymptotic solution as mu --> 0 can be written in closed form. Four regimes, consishttp://eprints.iisc.ernet.in/cgi/users/home?screen=EPrint::Edit&eprintid=27192&stage=core#tting of a transient at nominal sunset, a radiative-diffusive boundary ('Ramdas') layer on ground, a boundary layer transient and a radiative outer solution, are identified. The asymptotic solution reproduces all the qualitative features of more exact numerical simulations, including the occurrence of a lifted temperature minimum and its evolution during night, ranging from continuing growth to relatively sudden collapse of the Ramdas layer.

Conformationally restricted formyl methionyl tripeptide chemoattractants: a three-dimensional structure-activity study of analogs incorporating a C alpha,alpha-dialkylated glycine at position 2

The conformationally restricted CHO-L-Met-Xxx-L-Phe-OY (where Xxx = Aib, Ac3c, Ac5c, Ac6c, and Ac7c; Y = H, Me) tripeptides, analogs of the chemoattractant CHO-L-Met-L-Leu-L-Phe-OH, have been synthesized in solution by classical methods and fully characterized. Compounds were compared to determine the combined effect of backbone conformational preferences and side-chain bulkiness on the relation of three-dimensional structure to biological activity. Each peptide was tested for its ability to induce granule enzyme secretion from rabbit peritoneal polymorphonuclear leukocytes. In parallel, a conformational analysis on the CHO-blocked peptide and their tertbutyloxycarbonylated synthetic precursors was performed in the crystal state and in solution using X-ray diffraction, infrared absorption, and 1H nuclear magnetic resonance. The biological and conformational data are discussed in relation to the proposed model of the chemotactic peptide receptor of rabbit neutrophils.

Modular design of synthetic protein mimics. Crystal structure of two seven-residue helical peptide segments linked by .epsilon.-aminocaproic acid

Two seven-residue helical segments, Val-Ala-Leu-Aib-Val-Ala-Leu, were linked synthetically with an epsilon-aminocaproic acid (Acp) linker with the intention of making a stable antiparallel helix-helix motif. The crystal structure of the linked peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Acp-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe (1) shows the two helices displaced laterally from each other by the linker, but the linker has not folded the molecule into a close-packed antiparallel conformation. Two strong intermolecular NH...O = C hydrogen bonds are formed between the top of the lower helix of one molecule and the bottom of the upper helix in a laterally adjacent molecule to give the appearance of an extended single helix. The composite peptide with Boc and OMe end groups, C76H137N15O18.H2O, crystallize in space group P2(1) with a = 8.802 (1) angstrom, b = 20.409 (4) angstrom, c = 26.315 (3) angstrom, and beta = 90.72 (1)degrees; overall agreement R = 7.86% for 5030 observed reflections (\F(o)\ > 3-sigma(F)); resolution = 0.93 angstrom. Limited evidence for a more compact conformation in solution consistent with an antiparallel helix arrangement is obtained by comparison of the HPLC retention times and CD spectra of peptide 1 with well-characterized continuous helices of similar length and sequence.

Electronic structure and bonding of beta-rhombohedral boron using cluster fragment approach

Theoretical studies using density functional theory are carried out to understand the electronic structure and bonding and electronic properties of elemental beta-rhombohedral boron. The calculated band structure of ideal beta-rhombohedral boron (B-105) shows valence electron deficiency and depicts metallic behavior. This is in contrast to the experimental result that it is a semiconductor. To understand this ambiguity we discuss the electronic structure and bonding of this allotrope with cluster fragment approach using our recently proposed mno rule. This helps us to comprehend in greater detail the structure of B-105 and materials which are closely related to beta-rhombohedral boron. The molecular structures B12H12-2, B28H21+1, BeB27H21, LiB27H21-1, CB27H21+2, B57H36+3, Be3B54H36, and Li2CB54H36, and corresponding solids Li8Be3B102 and Li10CB102 are arrived at using these ideas and studied using first principles density functional theory calculations.

Peptide-lanthanide interactions. Crystal structure of a europium(III)-triglycine complex

Crystals of Eu-(Gly-Gly-Gly).(H2O)5.(ClO4)3 are triclinic, spacegroup P1BAR with a = 9.123 (2), b = 11.185 (5), c = 11.426 (2) angstrom; alpha = 90.79 (2), beta = 98.08 (1), gamma = 98.57 (2)-degrees; Z = 2. The europium cation is surrounded by four oxygens from three different peptide units and four oxygens from water molecules. The geometry around the metal is a distorted bi-capped trigonal prism. The peptide backbone conformation in this complex is compared with those in the free peptide and in various metal complexes. Considerable differences are observed between Eu(III) and Ca(II) complexes of triglycine. (C) Munksgaard 1994.