X-ray diffraction and theoretical investigation of the Gedunin crystal structure

The Gedunin compound (C28H34O6) is a natural product extracted from Trichilia pallida that has shown a wide activity. The crystallographic structure shows two conformers in the asymmetric unit, which differ in a rotation of the furan group. To understand this molecular arrangement, the density functional calculations. Molecular Electrostatic Potential (MEP) and thermodynamic function calculation have been performed at the B3LYP/6-311++g(d,p) level. Both conformers were optimized and the agreement with the experimental structure was very good, making possible further theoretical analysis of the structure. The inter-conversion between two conformers depends on the energy barrier. This process is studied in the vacuum and shows two transition states with a low energetic barrier for a potential energy curve scanning rigid around furan group: 4.37 kcal/mol and 16.52 kcal/mol. As the first transition state has a notably lower energetic barrier, the preferred inter-conversion pathway between the conformers involves the first rather than the second transition state. Understanding this transition state in detail led us to perform its optimization, showing an energetic barrier around 3.66 kcal/mol. The negative free energy and low enthalpy confirm that the process is spontaneous and exothermic. The results show that this requirement makes the existence of the two conformers in the asymmetric unit possible. The structure of molecules in the asymmetric unit is better understood when the MEP is used on the interaction between molecules. For Gedunin, both molecules have shown MEP with well-defined regions, and this behavior contributes to the observed link between molecules and for the negative regions complementing positive regions of another molecule. (C) 2011 Elsevier B.V. All rights reserved.

Crystallization and preliminary X-ray diffraction of malate dehydrogenase from Plasmodium falciparum

The expression, purification, crystallization and preliminary X-ray diffraction characterization of malate dehydrogenase (MDH) from the malarial parasite Plasmodium falciparum (PfMDH) are reported. In order to gain a deeper understanding of the function and role of PfMDH, the protein was purified to homogeneity. The purified protein crystallized in space group P1, with unit-cell parameters a = 72, b = 157, c = 159 angstrom, a = 105, beta = 101, ? = 95 degrees. The resulting crystals diffracted to a maximal resolution of 2.24 angstrom and the structure has been solved by molecular replacement, with 16 monomers in the asymmetric unit. The 16 monomers are arranged into four independent tetramers, in agreement with previous reports demonstrating the tetrameric solution state of PfMDH. The X-ray structure of PfMDH is expected to clarify the differences in catalysis by PfMDH compared with other MDH family members and to provide a basis for the structure-based design of specific PfMDH inhibitors as well as general MDH inhibitors.

Crystallization and preliminary X-ray diffraction analysis of three myotoxic phospholipases A2 from Bothrops brazili venom

Two myotoxic and noncatalytic Lys49-phospholipases A2 (braziliantoxin-II and MT-II) and a myotoxic and catalytic phospholipase A2 (braziliantoxin-III) from the venom of the Amazonian snake Bothrops brazili were crystallized. The crystals diffracted to resolutions in the range 2.562.05 angstrom and belonged to space groups P3121 (braziliantoxin-II), P6522 (braziliantoxin-III) and P21 (MT-II). The structures were solved by molecular-replacement techniques. Both of the Lys49-phospholipases A2 (braziliantoxin-II and MT-II) contained a dimer in the asymmetric unit, while the Asp49-phospholipase A2 braziliantoxin-III contained a monomer in its asymmetric unit. Analysis of the quaternary assemblies of the braziliantoxin-II and MT-II structures using the PISA program indicated that both models have a dimeric conformation in solution. The same analysis of the braziliantoxin-III structure indicated that this protein does not dimerize in solution and probably acts as a monomer in vivo, similar to other snake-venom Asp49-phospholipases A2.

Reactive sputter magnetron reactor for preparation of thin films and simultaneous in-situ structural study by X-ray diffraction.

Reactive Sputter Magnetron (RSM) is a widely used technique to thin films growing of compounds both, in research laboratories and in industrial processes. The nature of the deposited compound will depend then on the nature of the magnetron target and the nature of the ions generated in the plasma. One important aspect of the problem is the knowledge of the evolution of the film during the process of growing itself. In this work, we present the design, construction of a chamber to be installed in the Huber goniometer in the XRD2 line of LNLS in Campinas, which allows in situ growing kinetic studies of thin films.

Crystallization and preliminary X-ray diffraction analysis of selenophosphate synthetases from Trypanosoma brucei and Leishmania major

Selenophosphate synthetase (SPS) plays an indispensable role in selenium metabolism, being responsible for catalyzing the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential selenium donor for selenocysteine synthesis. Recombinant full-length Leishmania major SPS (LmSPS2) was recalcitrant to crystallization. Therefore, a limited proteolysis technique was used and a stable N-terminal truncated construct (ΔN-LmSPS2) yielded suitable crystals. The Trypanosoma brucei SPS orthologue (TbSPS2) was crystallized by the microbatch method using paraffin oil. X-ray diffraction data were collected to resolutions of 1.9 Å for ΔN-LmSPS2 and 3.4 Å for TbSPS2.

Studies of Inorganic Layer and Framework Structures Using Time-, Temperature- and Pressure-Resolved Powder Diffraction Techniques

This thesis is concerned with in-situ time-, temperature- and pressure-resolved synchrotron X-ray powder diffraction investigations of a variety of inorganic compounds with twodimensional layer structures and three-dimensional framework structures. In particular, phase stability, reaction kinetics, thermal expansion and compressibility at non-ambient conditions has been studied for 1) Phosphates with composition MIV(HPO4)2·nH2O (MIV = Ti, Zr); 2) Pyrophosphates and pyrovanadates with composition MIVX2O7 (MIV = Ti, Zr and X = P, V); 3) Molybdates with composition ZrMo2O8. The results are compiled in seven published papers and two manuscripts. Reaction kinetics for the hydrothermal synthesis of α-Ti(HPO4)2·H2O and intercalation of alkane diamines in α-Zr(HPO4)2·H2O was studied using time-resolved experiments. In the high-temperature transformation of γ-Ti(PO4)(H2PO4)·2H2O to TiP2O7 three intermediate phases, γ'-Ti(PO4)(H2PO4)·(2-x)H2O, β-Ti(PO4)(H2PO4) and Ti(PO4)(H2P2O7)0.5 were found to crystallise at 323, 373 and 748 K, respectively. A new tetragonal three-dimensional phosphate phase called τ-Zr(HPO4)2 was prepared, and subsequently its structure was determined and refined using the Rietveld method. In the high-temperature transformation from τ-Zr(HPO4)2 to cubic α-ZrP2O7 two new orthorhombic intermediate phases were found. The first intermediate phase, ρ-Zr(HPO4)2, forms at 598 K, and the second phase, β-ZrP2O7, at 688 K. Their respective structures were solved using direct methods and refined using the Rietveld method. In-situ high-pressure studies of τ-Zr(HPO4)2 revealed two new phases, tetragonal ν-Zr(HPO4)2 and orthorhombic ω-Zr(HPO4)2 that crystallise at 1.1 and 8.2 GPa. The structure of ν-Zr(HPO4)2 was solved and refined using the Rietveld method. The high-pressure properties of the pyrophosphates ZrP2O7 and TiP2O7, and the pyrovanadate ZrV2O7 were studied up to 40 GPa. Both pyrophosphates display smooth compression up to the highest pressures, while ZrV2O7 has a phase transformation at 1.38 GPa from cubic to pseudo-tetragonal β-ZrV2O7 and becomes X-ray amorphous at pressures above 4 GPa. In-situ high-pressure studies of trigonal α-ZrMo2O8 revealed the existence of two new phases, monoclinic δ-ZrMo2O8 and triclinic ε-ZrMo2O8 that crystallises at 1.1 and 2.5 GPa, respectively. The structure of δ-ZrMo2O8 was solved by direct methods and refined using the Rietveld method.

Single meson production in proton diffraction at 190 GeV/c at COMPASS

The quark model successfully describes all ground state bary-ons as members of $SU(N)$ flavour multiplets. For excited baryon states the situation is totally different. There are much less states found in the experiment than predicted in most theoretical calculations. This fact has been known for a long time as the 'missing resonance problem'. In addition, many states found in experiments are only poorly measured up to now. Therefore, further experimental efforts are needed to clarify the situation.rnrnAt mbox{COMPASS}, reactions of a $190uskgigaeVperclight$ hadron beam impinging on a liquid hydrogen target are investigated.rnThe hadron beam contains different species of particles ($pi$, $K$, $p$). To distinguish these particles, two Cherenkov detectors are used. In this thesis, a new method for the identification of particles from the detector information is developed. This method is based on statistical approaches and allows a better kaon identification efficiency with a similar purity compared to the method, which was used before.rnrnThe reaction $pprightarrow ppX$ with $X=(pi^0,~eta,~omega,~phi)$ is used to study different production mechanisms. A previous analysis of $omega$ and $phi$ mesons is extended to pseudoscalar mesons. As the resonance contributions in $peta$ are smaller than in $ppi^0$ a different behaviour of these two final states is expected as a function of kinematic variables. The investigation of these differences allows to study different production mechanisms and to estimate the size of the resonant contribution in the different channels.rnrnIn addition, the channel $pprightarrow ppX$ allows to study baryon resonances in the $pX$ system.rnIn the mbox{COMPASS} energy regime, the reaction is dominated by Pomeron exchange. As a Pomeron carries vacuum quantum numbers, no isospin is transferred between the target proton and the beam proton. Therefore, the $pX$ final state has isospin $textstylefrac{1}{2}$ and all baryon resonances in this channel are $N^ast$ baryons. This offers the opportunity to do spectroscopy without taking $Delta$ resonances into account. rnrnTo disentangle the contributions of different resonances a partial wave analysis (PWA) is used. Different resonances have different spin and parity $J^parity$, which results in different angular distributions of the decay particles. These angular distributions can be calculated from models and then be fitted to the data. From the fit the contributions of the single resonances as well as resonance parameters -- namely the mass and the width -- can be extracted. In this thesis, two different approaches for a partial wave analysis of the reaction $pprightarrow pppi^0$ are developed and tested.

The macromolecular complex of ICP and falcipain-2 from Plasmodium: preparation, crystallization and preliminary X-ray diffraction analysis

The malaria parasite Plasmodium depends on the tight control of cysteine-protease activity throughout its life cycle. Recently, the characterization of a new class of potent inhibitors of cysteine proteases (ICPs) secreted by Plasmodium has been reported. Here, the recombinant production, purification and crystallization of the inhibitory C-terminal domain of ICP from P. berghei in complex with the P. falciparum haemoglobinase falcipain-2 is described. The 1:1 complex was crystallized in space group P4(3), with unit-cell parameters a = b = 71.15, c = 120.09 A. A complete diffraction data set was collected to a resolution of 2.6 A.