Dasari L. V. K. Prasad

Localisation of Plasmodium falciparum uroporphyrinogen III decarboxylase of the heme-biosynthetic pathway in the apicoplast and characterisation of its catalytic properties

Uroporphyrinogen decarboxylase (UROD) is a key enzyme in the heme-biosynthetic pathway and in Plasmodium falciparum it occupies a strategic position in the proposed hybrid pathway for heme biosynthesis involving shuttling of intermediates between different subcellular compartments in the parasite. In the present study, we demonstrate that an N-terminally truncated recombinant P. falciparum UROD (r(Delta)PfUROD) over-expressed and purified from Escherichia coli cells, as well as the native enzyme from the parasite were catalytically less efficient compared with the host enzyme, although they were similar in other enzyme parameters. Molecular modeling of PfUROD based on the known crystal structure of the human enzyme indicated that the protein manifests a distorted triose phosphate isomerase (TIM) barrel fold which is conserved in all the known structures of UROD. The parasite enzyme shares all the conserved or invariant amino acid residues at the active and substrate binding sites, but is rich in lysine residues compared with the host enzyme. Mutation of specific lysine residues corresponding to residues at the dimer interface in human UROD enhanced the catalytic efficiency of the enzyme and dimer stability indicating that the lysine rich nature and weak dimer interface of the wild-type PfUROD could be responsible for its low catalytic efficiency. PfUROD was localised to the apicoplast, indicating the requirement of additional mechanisms for transport of the product coproporphyrinogen to other subcellular sites for its further conversion and ultimate heme formation.

Mitochondrial localization of functional ferrochelatase from Plasmodium falciparum.

In the malarial parasite, enzymes of heme-biosynthetic pathway are distributed in different cellular compartments. The site of localization of ferrochelatase in the malarial parasite is crucial, since it will decide the ultimate site of heme synthesis. Earlier results have differed in terms of localization, being the mitochondrion or apicoplast and the functional enzyme has not been cloned, expressed and characterized. The present study reveals that Plasmodium falciparum ferrochelatase (PfFC) gene encodes multiple transcripts of which the one encoding the full length functional protein (PfFC) has been cloned and the recombinant protein over-expressed and purified from E. coli cells. The enzyme shows maximum activity with iron, while zinc is a poor substrate. Immunofluorescence studies with antibodies to functional ferrochelatase reveal that the native enzyme is localized to the mitochondrion of the parasite indicating that this organelle is the ultimate site of heme synthesis.

Protoporphyrinogen IX oxidase from Plasmodium falciparum is anaerobic and is localized to the mitochondrion

Earlier studies in this laboratory had shown that the malarial parasite can synthesize heme de novo and inhibition of the pathway leads to death of the parasite. It has been proposed that the pathway for the biosynthesis of heme in Plasmodium falciparum is unique involving three different cellular compartments, namely mitochondrion, apicoplast and cytosol. Experimental evidences are now available for the functionality and localization of all the enzymes of this pathway, except protoporphyrinogen IX oxidase (PfPPO), the penultimate enzyme. In the present study, PfPPO has been cloned, expressed and shown to be localized to the mitochondrion by immunofluorescence microscopy. Interestingly, the enzyme has been found to be active only under anaerobic conditions and is dependent on electron transport chain (ETC) acceptors for its activity. The native enzyme present in the parasite is inhibited by the ETC inhibitors, atovaquone and antimycin. Atovaquone, a well known inhibitor of parasite dihydroorotate dehydrogenase, dependent on the ETC, inhibits synthesis of heme as well in P. falciparum culture. A model is proposed to explain the ETC dependence of both the pyrimidine and heme-biosynthetic pathways in P. falciparum.

Characterization of coproporphyrinogen III oxidase in Plasmodium falciparum cytosol.

A unique hybrid pathway has been proposed for de novo heme biosynthesis in Plasmodium falciparum involving three different compartments of the parasite, namely mitochondrion, apicoplast and cytosol. While parasite mitochondrion and apicoplast have been shown to harbor key enzymes of the pathway, there has been no experimental evidence for the involvement of parasite cytosol in heme biosynthesis. In this study, a recombinant P. falciparum coproporphyrinogen III oxidase (rPfCPO) was produced in E. coli and confirmed to be active under aerobic conditions. rPfCPO behaved as a monomer of 61kDa molecular mass in gel filtration analysis. Immunofluorescence studies using antibodies to rPfCPO suggested that the enzyme was present in the parasite cytosol. These results were confirmed by detection of enzyme activity only in the parasite soluble fraction. Western blot analysis with anti-rPfCPO antibodies also revealed a 58kDa protein only in this fraction and not in the membrane fraction. The cytosolic presence of PfCPO provides evidence for a hybrid heme-biosynthetic pathway in the malarial parasite.

Silicon monoxide at 1 atm and elevated pressures: Crystalline or amorphous?

The absence of a crystalline SiO phase under ordinary conditions is an anomaly in the sequence of group 14 monoxides. We explore theoretically ordered ground-state and amorphous structures for SiO at P = 1 atm, and crystalline phases also at pressures up to 200 GPa. Several competitive ground-state P = 1 atm structures are found, perforce with Si-Si bonds, and possessing Si-O-Si bridges similar to those in silica (SiO2) polymorphs. The most stable of these static structures is enthalpically just a little more stable than a calculated random bond model of amorphous SiO. In that model we find no segregation into regions of amorphous Si and amorphous SiO2. The P = 1 atm structures are all semiconducting. As the pressure is increased, intriguing new crystalline structures evolve, incorporating Si triangular nets or strips and stishovite-like regions. A heat of formation of crystalline SiO is computed; it is found to be the most negative of all the group 14 monoxides. Yet, given the stability of SiO2, the disproportionation 2SiO(s) → Si(s)+SiO2(s) is exothermic, falling right into the series of group 14 monoxides, and ranging from a highly negative ΔH of disproportionation for CO to highly positive for PbO. There is no major change in the heat of disproportionation with pressure, i.e., no range of stability of SiO with respect to SiO2. The high-pressure SiO phases are metallic.

Lithium amide (LiNH2) under pressure.

Static high pressure lithium amide (LiNH(2)) crystal structures are predicted using evolutionary structure search methodologies and intuitive approaches. In the process, we explore the relationship of the structure and properties of solid LiNH(2) to its molecular monomer and dimer, as well as its valence-isoelectronic crystalline phases of methane, water, and ammonia all under pressure. A NaNH(2) (Fddd) structure type is found to be competitive for the ground state of LiNH(2) above 6 GPa with the P = 1 atm I4[overline] phase. Three novel phases emerge at 11 (P4[overline]2(1)m), 13 (P4(2)/ncm), and 46 GPa (P2(1)2(1)2(1)), still containing molecular amide anions, which begin to form N-H···N hydrogen bonds. The P2(1)2(1)2(1) phase remains stable over a wide pressure range. This phase and another Pmc2(1) structure found at 280 GPa have infinite ···(H)N···H···N(H)···H polymeric zigzag chains comprising symmetric N···H···N hydrogen bonds with one NH bond kept out of the chain, an interesting general feature found in many of our high pressure (>280 GPa) LiNH(2) structures, with analogies in high pressure H(2)O-ices. All the predicted low enthalpy LiNH(2) phases are calculated to be enthalpically stable with respect to their elements but resist metallization with increasing pressure up to several TPa. The possibility of Li sublattice melting in the intermediate pressure range structures is raised.

Stuffed fullerenelike boron carbide nanoclusters

Viable stuffed fullerenelike boron carbide nanoclusters, C50B34, C48B36−2, and their isomers based on an icosahedral B84 fragment of elemental β-rhombohedral boron have been investigated using density functional theory calculations. The structure and the stability of these clusters are rationalized using the polyhedral skeletal electron counting and ring-cap orbital overlap compatibility rules. The curvature of the fullerene was found to play a vital role in achieving the most stable isomer C50B34(3B). The large highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps, three dimensional aromaticity, and electron detachment energies support their high stability. Further, the IR and Raman active modes were recognized.

Electronic structure and bonding studies on triple‐decker sandwich complexes with a P6 middle ring

DFT and hybrid HF‐DFT studies of structure and bonding of CpMP6MCp triple‐decker sandwich complexes, ranging from 18–28 valence electrons (VE) with M = Sc, Y, Ti, Zr, Hf, V, Nb, Ta, Cr, Mo, and W, show that the middle P6 ring complexes adopt symmetric planar (28 valence electron count [VEC]), asymmetric planar (26 VEC), and puckered (24 VEC) geometries. According to the mno Rule, 50 skeletal electrons are needed for these triple‐decker cluster frameworks. For 28 VEC, this corresponds to 10 electrons more than the 50 electrons of the mno Rule if all VE of the metal are included. These additional electrons control the distortion of a P6 middle ring and other finer structural details. Completely filled 2a* and 2b* orbitals in 28 VE complexes lead to a planar symmetrical P6 middle ring, while the occupancy in either 2a* or 2b* alone explains the in‐plane distortions (asymmetric) in 26 VE complexes. In comparison with 28 VE complexes, the puckering of P6 middle ring in 24 VE complexes is due to the greater stabilization of 5a and the extra stabilization of the +4 oxidation state of Ti. The quintet state of 22 VE complexes is planar as 2a* and 2b* are half filled. Similar geometrical and bonding patterns of CpScP6ScCp and C2P3H2ScC3P3H3ScC2P3H2 support the carbon–phosphorus analogy further. The 18 VE systems, CpScC3B3H6ScCp+ and CpScP3B3H3ScCp+, have the 50 skeletal electrons as stipulated by the mno Rule. Corresponding anions have 52 skeletal electrons (20 VE); the middle rings here are distorted in the plane.

Squaroglitter: A 3,4-Connected Carbon Net

Theoretical calculations are presented on a new hypothetical 3,4-connected carbon net (called squaroglitter) incorporating 1,4 cyclohexadiene units. The structure has tetragonal space group P4/mmm (No. 123) symmetry. The optimized geometry shows normal distances, except for some elongated bonds in the cyclobutane ring substructures in the network. Squaroglitter has an indirect bandgap of about 1.0 eV. The hypothetical lattice, whose density is close to graphite, is more stable than other 3,4-connected carbon nets. A relationship to a (4,4)nanotube is explored, as is a potential threading of the lattice with metal needles.