Cloning, expression, purification and preliminary X-ray diffraction studies of a putative Mycobacterium smegmatis thiolase

Thiolases are important in fatty-acid degradation and biosynthetic pathways. Analysis of the genomic sequence of Mycobacterium smegmatis suggests the presence of several putative thiolase genes. One of these genes appears to code for an SCP-x protein. Human SCP-x consists of an N-terminal domain (referred to as SCP2 thiolase) and a C-terminal domain (referred as sterol carrier protein 2). Here, the cloning, expression, purification and crystallization of this putative SCP-x protein from M. smegmatis are reported. The crystals diffracted X-rays to 2.5 angstrom resolution and belonged to the triclinic space group P1. Calculation of rotation functions using X-ray diffraction data suggests that the protein is likely to possess a hexameric oligomerization with 32 symmetry which has not been observed in the other six known classes of this enzyme.

Nature and strength of C-H center dot center dot center dot O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes

Structural and electronic properties of C-H center dot center dot center dot O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of a-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H center dot center dot center dot O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H center dot center dot center dot O interactions in the crystal packing of formyl compounds.

(4aR, 8aS, 9aR, 10aS)-8a, 9a-Difluoro-1,4,4a, 5,8,8a, 9,9a, 10,10a-decahydroanthracene-4a, 10a-diol hemihydrate

The title compound, C(14)H(18)F(2)O(2)center dot 0.5H(2)O, a hemihydrate of a C(s)-symmetric unsaturated difluorodiol, crystallizes in the centrosymmetric space group P2/m (Z = 4). The asymmetric unit contains two crystallographically independent difluorodiol half-molecules, occupying the mirror planes at (x, 0, z) and (x, 1/2, z), and half a molecule of water, lying on the twofold axis at (0, y, 0). Four difluorodiol molecules self-assemble around each solvent water molecule via O-H center dot center dot center dot O hydrogen bonds in a near tetrahedral symmetry to generate a cylindrical column-like architecture.

Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C–H⋯F and C–H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C–H⋯F and C–H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O–H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

Location and conformation of pantothenate and its derivatives in Mycobacterium tuberculosis pantothenate kinase: insights into enzyme action

Previous studies of complexes of Mycobacterium tuberculosis PanK (MtPanK) with nucleotide diphosphates and non-hydrolysable analogues of nucleoside triphosphates in the presence or the absence of pantothenate established that the enzyme has dual specificity for ATP and GTP, revealed the unusual movement of ligands during enzyme action and provided information on the effect of pantothenate on the location and conformation of the nucleotides at the beginning and the end of enzyme action. The X-ray analyses of the binary complexes of MtPanK with pantothenate, pantothenol and N-nonylpantothenamide reported here demonstrate that in the absence of nucleotide these ligands occupy, with a somewhat open conformation, a location similar to that occupied by phosphopantothenate in the `end' complexes, which differs distinctly from the location of pantothenate in the closed conformation in the ternary `initiation' complexes. The conformation and the location of the nucleotide were also different in the initiation and end complexes. An invariant arginine appears to play a critical role in the movement of ligands that takes place during enzyme action. The work presented here completes the description of the locations and conformations of nucleoside diphosphates and triphosphates and pantothenate in different binary and ternary complexes, and suggests a structural rationale for the movement of ligands during enzyme action. The present investigation also suggests that N-alkylpantothenamides could be phosphorylated by the enzyme in the same manner as pantothenate.

3-(2-Bromoacetyl)-6-fluoro-2H-chromen-2-one

The non-H atoms of the title compound, C(11)H(6)BrFO(3), are essentially coplanar (r.m.s. deviation for all non-H atoms = 0.074 angstrom). In the crystal, the molecules are linked by C-H center dot center dot center dot O and C-H center dot center dot center dot Br interactions.

(2E)-1-(5-Chlorothiophen-2-yl)-3-(2,4,5-trimethoxyphenyl)prop-2-en-1-one

In the title molecule, C(16)H(15)ClO(4)S, the chlorothiophene and trimethoxyphenyl rings make a dihedral angle of 31.12 (5)degrees. The C = C double bond exhibits an E conformation. In the crystal, C-H center dot center dot center dot O interactions generate bifurcated bonds, linking the molecules into chains along the b axis.

4-(4-Chlorophenyl)-N-[(E)-4-(dimethylamino)benzylidene]-1,3-thiazol-2- amine

The title compound, C(18)H(16)ClN(3)S, adopts an extended molecular structure. The thiazole ring is inclined by 9.2 (1) and 15.3 (1)degrees with respect to the chlorophenyl and 4-(dimethylamino)phenyl rings, respectively, while the benzene ring planes make an angle of 19.0 (1)degrees. A weak intermolecular C-H center dot center dot center dot pi contact is observed in the crystal structure.

Intruder detection over sensor placement in a hexagonal lattice

The problem of intrusion detection and location identification in the presence of clutter is considered for a hexagonal sensor-node geometry. It is noted that in any practical application,for a given fixed intruder or clutter location, only a small number of neighboring sensor nodes will register a significant reading. Thus sensing may be regarded as a local phenomenon and performance is strongly dependent on the local geometry of the sensor nodes. We focus on the case when the sensor nodes form a hexagonal lattice. The optimality of the hexagonal lattice with respect to density of packing and covering and largeness of the kissing number suggest that this is the best possible arrangement from a sensor network viewpoint. The results presented here are clearly relevant when the particular sensing application permits a deterministic placement of sensors. The results also serve as a performance benchmark for the case of a random deployment of sensors. A novel feature of our analysis of the hexagonal sensor grid is a signal-space viewpoint which sheds light on achievable performance.Under this viewpoint, the problem of intruder detection is reduced to one of determining in a distributed manner, the optimal decision boundary that separates the signal spaces SI and SC associated to intruder and clutter respectively. Given the difficulty of implementing the optimal detector, we present a low-complexity distributive algorithm under which the surfaces SI and SC are separated by a wellchosen hyperplane. The algorithm is designed to be efficient in terms of communication cost by minimizing the expected number of bits transmitted by a sensor.

An O(mn) Gomory-Hu Tree Construction Algorithm for Unweighted Graphs

We present a fast algorithm for computing a Gomory-Hu tree or cut tree for an unweighted undirected graph G = (V,E). The expected running time of our algorithm is Õ(mc) where |E| = m and c is the maximum u-vedge connectivity, where u,v ∈ V. When the input graph is also simple (i.e., it has no parallel edges), then the u-v edge connectivity for each pair of vertices u and v is at most n-1; so the expected running time of our algorithm for simple unweighted graphs is Õ(mn).All the algorithms currently known for constructing a Gomory-Hu tree [8,9] use n-1 minimum s-t cut (i.e., max flow) subroutines. This in conjunction with the current fastest Õ(n20/9) max flow algorithm due to Karger and Levine [11] yields the current best running time of Õ(n20/9n) for Gomory-Hu tree construction on simpleunweighted graphs with m edges and n vertices. Thus we present the first Õ(mn) algorithm for constructing a Gomory-Hu tree for simple unweighted graphs.We do not use a max flow subroutine here; we present an efficient tree packing algorithm for computing Steiner edge connectivity and use this algorithm as our main subroutine. The advantage in using a tree packing algorithm for constructing a Gomory-Hu tree is that the work done in computing a minimum Steiner cut for a Steiner set S ⊆ V can be reused for computing a minimum Steiner cut for certain Steiner sets S' ⊆ S.

Limits of Data Level Parallelism

Abstract—A new breed of processors like the Cell Broadband Engine, the Imagine stream processor and the various GPU processors emphasize data-level parallelism (DLP) and threadlevel parallelism (TLP) as opposed to traditional instructionlevel parallelism (ILP). This allows them to achieve order-ofmagnitude improvements over conventional superscalar processors for many workloads. However, it is unclear as to how much parallelism of these types exists in current programs. Most earlier studies have largely concentrated on the amount of ILP in a program, without differentiating DLP or TLP. In this study, we investigate the extent of data-level parallelism available in programs in the MediaBench suite. By packing instructions in a SIMD fashion, we observe reductions of up to 91 % (84 % on average) in the number of dynamic instructions, indicating a very high degree of DLP in several applications. I.

2-{[{2-Hydroxy-3-[2-methyl-5-(propan-2-yl)phenoxy]propyl}(pyridin -2-ylmethyl)amino]methyl}phenol

In the title racemic compound, C(26)H(32)N(2)O(3), an intramolecular O-H center dot center dot center dot N hydrogen bond is formed between the phenolic OH group and the tertiary amine N atom. Another O-H center dot center dot center dot N hydrogen bond that is formed between the OH group and the pyridine N atom links the molecules into a polymeric chain extending along the a axis. The structure is further stabilized by intramolecular and intermolecular C-H center dot center dot center dot O interactions.

Weak C-H center dot center dot center dot O hydrogen bonds in anisaldehyde, salicylaldehyde and cinnamaldehyde

In situ cryocrystallization has been employed to grow single crystals of 4-methoxybenzaldehyde (anisaldehyde), C(8)H(8)O(2), 2-hydroxybenzaldehyde (salicylaldehyde), C(7)H(6)O(2), and (2E)-3-phenylprop-2-enal (cinnamaldehyde), C(9)H(8)O, all of which are liquids at room temperature. Several weak C-H center dot center dot center dot O interactions of the types C(aryl)-H center dot center dot center dot O, C(formyl)-H center dot center dot center dot O and Csp(3)-H center dot center dot center dot O are present in these related crystal structures.

Single Particle and Packed Bed Combustion in Modern Gasifier Stoves—Density Effects

This article is concerned with a study of an unusual effect due to density of biomass pellets in modern stoves based on close-coupled gasification-combustion process. The two processes, namely, flaming with volatiles and glowing of the char show different effects. The mass flux of the fuel bears a constant ratio with the air flow rate of gasification during the flaming process and is independent of particle density; char glowing process shows a distinct effect of density. The bed temperatures also have similar features: during flaming, they are identical, but distinct in the char burn (gasification) regime. For the cases, wood char and pellet char, the densities are 350, 990 kg/m(3), and the burn rates are 2.5 and 3.5 g/min with the bed temperatures being 1380 and 1502 K, respectively. A number of experiments on practical stoves showed wood char combustion rates of 2.5 +/- 0.5 g/min and pellet char burn rates of 3.5 +/- 0.5 g/min. In pursuit of the resolution of the differences, experimental data on single particle combustion for forced convection and ambient temperatures effects have been obtained. Single particle char combustion rate with air show a near-d(2) law and surface and core temperatures are identical for both wood and pellet char. A model based on diffusion controlled heat release-radiation-convection balance is set up. Explanation of the observed results needs to include the ash build-up over the char. This model is then used to explain observed behavior in the packed bed; the different packing densities of the biomass chars leading to different heat release rates per unit bed volume are deduced as the cause of the differences in burn rate and bed temperatures.

(2E)-1-(5-Chlorothiophen-2-yl)-3-(2,3-dimethoxyphenyl)prop-2-en-1-one

In the title compound, C(15)H(13)ClO(3)S, the chlorothiophene and dimethoxyphenyl groups are linked by a prop-2-en-1-one group. The C=C double bond exhibits an E conformation. The molecule is non-planar, with a dihedral angle of 31.12 (5)degrees between the chlorothiophene and dimethoxyphenyl rings. The methoxy group at position 3 is coplanar with the benzene ring to which it is attached, with a C-O-C-C torsion angle of -3.8 (3)degrees. The methoxy group attached at position 2 of the benzene ring is in a (+)synclinal conformation, as indicated by the C-O-C-C torsion angle of -73.6 (2)degrees. In the crystal, two different C-H center dot center dot center dot O intermolecular interactions generate chains of molecules extending along the b axis.