The conformational features of three 2-sulphur-substituted cyclohexanone derivatives, which differ in the number of sulphur-bound oxygen atoms, i.e. zero (I), one (II) and two (III), were investigated by single crystal X-ray crystallography and geometry optimized structures determined using Hartree-Fock method. In each of (I)-(III) an intramolecular S center dot center dot center dot O(carbonyl) interaction is found with the magnitude correlated with the oxidation state of the sulphur atom, i.e. 2.838(3) angstrom in (I) to 2.924(2) angstrom in (II) to 3.0973(18) angstrom in (III). There is an inverse relationship between the strength of this interaction and the magnitude of the carbonyl bond. The supramolecular aggregation patterns are primarily determined by C-H center dot center dot center dot O contacts and are similarly influenced by the number of oxygen atoms in the molecular structures. Thus, a supramolecular chain is found in the crystal structure of (I). With an additional oxygen atom available to participate in C-H center dot center dot center dot O interactions, as in (II), a two-dimensional array is found. Finally, a three-dimensional network is found for (III). Despite there being differences in conformations between the experimental structures and those calculated in the gas-phase...
Foram analisados, por difração de raios X, dois materiais policristalinos: uma liga de Heusler (C02ScSn), onde amostras originárias da mesma preparação foram submetidas a vários tratamentos térmicos distintos, e um material biocerâmico. Para o refinamento utilizou-se o Método de Rietveld. Na análise feita com a liga de Heusler (C02ScSn) tornou-se evidente uma segunda fase: C02Sn, e que não foi refinada por não haver um modelo de estrutura para a mesma. Assim, o refinamento foi efetuado, apenas para a estrutura conhecida, escolhendo algumas alternativas de função perfil, tais como as funções Gaussiana, pseudo-Voigt e Thompson¬-Cox-Hastings pseudo-Voigt modificada. A radiação de fundo também foi refinada utilizando o polinômio de quinta ordem. Os resultados obtidos foram equivalentes. Dos resultados obtidos nos refinamentos, conclui-se que as condições de preparação das amostras Fl17 (proveniente da amostra original, tratada a 600°C por 60 horas, em seguida moída, tratada a 200°C por 80 horas e submetida a resfriamento lento) e Al17 (proveniente da amostra original, tratada a 800°C por 48 horas e submetida a resfriamento lento), foram as mais satisfatórias. As amostras Fl17 e Al17 foram mais satisfatórias...
Esta dissertação consiste de duas partes: Parte I: Descrição teórica suscinta dos fundamentos da cristalografia de raios-X. Parte II: Resolução de quatro estruturas cristalinas, três complexos de rutênio (capítulos V, VI, VII) e um ligante comumente encontrado em complexos de rutênio, o C28H28O2P2. As estruturas resolvidas foram: 1) C28H28O2P2, Mr= 458.48, triclínico, PI a= 5.826(1), b= 8.862(1), c= 12.517(2)Å, α= 100.29(1), β= 102.67(1), Υ= 104.22(1)°, V= 592.5(3), Z=1, Dx=1.285g.cm-3, λ(MοKα)=0,71073Å, μ= 2.00cm-1, F(000)=242, T=296K, Rint=0.01, R=0.031, Rw=0.030 para 1390 reflexões independentes observadas [I> 3 ο (I)]. Os átomos P estão a 0.126(1)Å do plano formado pelo grupo (CH2)4-. Os anéis fenil são planares dentro da margem de erro experimental. Os átomos P têm uma configuração tetraédrica distorcida. 2) PyH[RuCl4(CO)Py], Mr=430.11, monoclínico, P21/n, a= 7.821(1), b= 10.337(3), c= 19.763(3)Å, β=93.07(1)°, V= 1595.5(5), Z=4, Dx=1.791g.cm-3, λ(MοKα)=0,71073Å, μ= 14.86cm-1, F(000)=843.9, T=296K, Rint=0.03, R=0.062, Rw=0.063 para 1478 reflexões independentes observadas [I> 3ο (I)]. A estrutura é composta essencialmente por dois planos perpendiculares entre si; um formado pelos quatro átomos de cloro (com ângulo de aproximadamente 90° entre si)...
lantanídeos, visando a determinação da simetria de coordenação ao redor dos íons e sua comparação com prévias previsões espectroscópicas. As medidas de difração foram realizadas com um difratômetro de quatro círculos de geometria Kappa. Os dados cristalinos relevantes são: [Eu (TMU)6] (AsF6)3, TMU = C5H12N2O. Fórmula química: EuC30H72N12O6As3F18; cela unitária é cúbica, a = 18,000 (3)Åe V = 5832 (3) grupo espacial: F23 número - 196 da Internacional Tables For X-Ray Crystallography; número de moléculas por cela unitária: Z = 4; coeficiente de absorção de massa para radiação de molibdênio: µ (MoKα)=27,4 cm-1; densidade calculada: Dc = 1,60 g.cm-3 Para um cristal de tamanho aproximadamente 0,25 x 0,25 x 0,30mm foram medidas 2309 reflexões. A média das intensidades das reflexões equivalentes por simetria de Laue foi calculada obtendo-se um total de 841 independentes, das quais, apenas 277 resultaram maiores que três vezes o desvio padrão estimado de contagem estatística. A estrutura se mostrou altamente desordenada e o modelo proposto refinou a um fator-R final de 13.8%. Os átomos de európio e arsênio estão localizados em posições especiais de simetria pontual local 23 (T) O Eu3+ está hexacoordenado através dos oxigênios das moléculas de TMU formando um octaedro regular de simetria pontual Oh. A distância európio-oxigênio é de aproximadamente 2...
A cruzaína, principal cisteíno protease do Trypanosoma cruzi, é um alvo terapêutico validado para o tratamento da doença de Chagas. Grande parte dos inibidores desta enzima é constituída de peptídeo-miméticos do tipo covalente irreversível cujo desenvolvimento, entretanto, tem sido evitado devido ao potencial efeito off target e ao perfil farmacocinético indesejável. O grupo de química medicinal NEQUIMED/ IQSC/USP vêm utilizando métodos avançados em quimioinformática para a identificação de inibidores reversíveis da cruzaína e de outras cisteíno proteases. Contudo, para que estes inibidores se desenvolvam a compostos matrizes mais eficientes, informações computacionais e estruturais de seus Modos de Interação (MOB) com a proteína alvo tornam-se fundamentais. Neste trabalho, a cristalografia de raios X foi utilizada para descrever em detalhes o MOB de três importantes inibidores reversíveis da cruzaína identificados pelo NEQUIMED: a dipeptidil-nitrila Neq0409 e os dois fragmentos moleculares Neq0147 e Neq0176. De modo a evitar a auto-proteólise experimentada pela cruzaína nativa que torna desafiadora a cristalização com inibidores de baixa afinidade como os fragmentos reversíveis...
Importin-alpha is the nuclear import receptor that recognizes cargo proteins with nuclear localization sequences (NLSs). Tile study of NLS peptidomimetics can provide a better understanding of the requirements for the molecular recognition of cargo proteins by importin-alpha, and potentially engender a large number of applications in medicine. Importin-a was crystallized with a set of six NLS peptidomimetics, and X-ray diffraction data were collected in the range 2.1-2.5 angstrom resolution. Preliminary electron density calculations show that the ligands are present in the crystals. (c) 2005 Elsevier B.V All rights reserved.
J Biol Inorg Chem (2007) 12:353–366
DOI 10.1007/s00775-006-0191-9; Two arsenite-inhibited forms of each of the aldehyde oxidoreductases from Desulfovibrio gigas and Desulfovibrio desulfuricans have been studied by X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy. The molybdenum site of these enzymes shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. Arsenite addition to active as-prepared enzyme or to a reduced desulfo form yields two different species called A and B, respectively, which show different Mo(V) EPR signals. Both EPR signals show strong hyperfine and quadrupolar couplings with an arsenic nucleus, which suggests that arsenic interacts with molybdenum through an equatorial ligand. X-ray data of single crystals prepared from EPR-active samples show in both inhibited forms that the arsenic atom interacts with the molybdenum ion through an oxygen atom at the catalytic labile site and that the sulfido ligand is no longer present. EPR and X-ray data indicate that the main difference between both species is an equatorial ligand to molybdenum which was determined to be an oxo ligand in species A and a hydroxyl/water ligand in species B. The conclusion that the sulfido ligand is not essential to determine the EPR properties in both Mo-As complexes is achieved through EPR measurements on a substantial number of randomly oriented chemically reduced crystals immediately followed by X-ray studies on one of those crystals. EPR saturation studies show that the electron transfer pathway...
ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best fitting ligand from a “cocktail”; and finding ordered water molecules. All protocols are easy to handle by a non-expert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours.
This article reports the characterization of thin SiGe/Si(100) epilayers using reciprocal space maps measured by a laboratory X-ray instrument and a high-resolution X-ray diffraction study of partially relaxed SiGe/Si thin films.
Neutron crystallography and sub-atomic X-ray crystallography complement each other in defining hydrogen positions in macromolecules. Significant advances have been made but much effort is still required if neutron crystallography is to become a mainstream activity.
The Energy Dispersive X-ray Diffraction System at Brock
University has been used to measure the intensities of the diffraction lines
of aluminum powder sample as a function of temperature. At first,
intensity measurements at high temperature were not reproducible. After
some modifications have been made, we were able to measure the
intensities of the diffraction lines to 815K, with good accuracy and
reproducibility. Therefore the changes of the Debye-Waller factor from
room temperature up to 815K for aluminum were determined with
precision. Our results are in good agreement with those previously
Using the energy dispersive x ...ray diffraction (EDXD)
technique, the room temperature diffraction pattern of Al powder was
obtained at diffraction angles ~ 30° and 50°. From the small angle
diffraction pattern the average relative intensities (IR) of the (111), (200),
and (220) lines were measured to be equal to 100, 62, and 32 respectively.
From the large diffraction angle IR for the (220), (311+222), (400),
(331+420), and (422) lines were measured to be 100,201,17,90, and 19.5
The diffraction pattern at those two angles were obtained at
several higher temperatures to measure the change in the intensities of the
Al lines. From the intensity changes the increase of the Debye- Waller
temperature factor, i.e ~B(T), with respect to the value at room
temperature was determined to be 0.6+0.1 at 250°C, 1.10+0.15 at 350°C,
1.45+0.20 at 450°C, and 2.20±0.35 at 550°C.
Dissertação para obtenção do Grau de Doutor em Bioquímica, Especialidade Bioquímica Estrutural; Heme is essential to all aerobic organisms, as it is involved in several biological processes. Due to its toxicity and high insolubility, several proteins transiently bind this molecule, ensuring the transport and insertion into heme proteins. A structural study of three heme-binding proteins, human SOUL protein and human and murine p22HBP is described in this dissertation.
In chapter 1, an introduction to heme and its biological importance is performed and all the information related to the proteins previously mentioned is summarized. The basic principles of X-ray Crystallography and Nuclear Magnetic Resonance (NMR), the techniques used in the structural characterization of these proteins, are described.
For the studies described in this thesis large amounts of pure protein are required. For this reason, hSOUL protein was cloned, and the overexpression and purification of hSOUL optimized – chapter 2.
The overall structure of hSOUL is very similar to murine p22HBP solution structure. hSOUL protein structure determined by X-ray Crystallography is described in chapter 3 and the possible biological consequences are discussed.
Understanding the heme interaction with hSOUL was an important objective of this work. For that...
The high flux and coherence produced at long synchrotron beamlines makes them well suited to performing phase-contrast X-ray imaging of the airways and lungs of live small animals. Here, findings of the first live-animal imaging on the Imaging and Medical Beamline (IMBL) at the Australian Synchrotron are reported, demonstrating the feasibility of performing dynamic lung motion measurement and high-resolution micro-tomography. Live anaesthetized mice were imaged using 30 keV monochromatic X-rays at a range of sample-to-detector propagation distances. A frame rate of 100 frames s(-1) allowed lung motion to be determined using X-ray velocimetry. A separate group of humanely killed mice and rats were imaged by computed tomography at high resolution. Images were reconstructed and rendered to demonstrate the capacity for detailed, user-directed display of relevant respiratory anatomy. The ability to perform X-ray velocimetry on live mice at the IMBL was successfully demonstrated. High-quality renderings of the head and lungs visualized both large structures and fine details of the nasal and respiratory anatomy. The effect of sample-to-detector propagation distance on contrast and resolution was also investigated, demonstrating that soft tissue contrast increases...
Cellulosomes are the most efficient plant cell wall degradation machines discovered to date. All cellulosomal components contain protein modules connected by linkers of varying lengths, which are predicted to be flexible. Consequently, structural studies of the cellulosome have employed a “dissect and build” strategy, whereby individual modules are studied in isolation with the hope to later model the intact complex. However, representative individual structures are now available for all of the cellulosome modules and many questions still remain. The studies described in this thesis depart from the ‘dissection’ stage and enter the ‘build’ stage of cellulosome structural studies of the cellulosome from Clostridium thermocellum.
We first describe the crystal structure of a heterodimeric complex comprising the type-II cohesin (CohII) from cell surface anchoring protein SdbA and a trimodular C-terminal truncation of the CipA scaffoldin protein containing the ninth type-I cohesin module (CohI9), a linker, the X-module (X), and the type-II dockerin module (DocII). This structure revealed novel intertwining of scaffoldin molecules and extensive reciprocal contacts between the CohI9 and the X-module of another scaffoldin molecule. Sedimentation velocity experiments indicate dimerization also occurs in solution.
We have carried out the crystallization and structural analysis of a heterotrimeric complex containing the CohI9—X-DocII:CohII complex bound to the type-I dockerin module (DocI) from the Cel9D enzyme...
In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint with the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.
The HAD superfamily contains enzymes that catalyze carbon or phosphate transfer
reactions. One family within the HAD superfamily is the p-nitrophenyl phosphatase (PNPPase)
family. Members of this family are all phosphatases that cleave the substrate analog pnitrophenyl
phosphate, in addition to their biologically significant substrate. Interestingly,
among the small number of family members that have been characterized, there is a wide variety
of biologically relevant activities. YZGD from Paenibacillus thiaminolyticus has pyridoxal
phosphatase activity, catalyzed by a HAD superfamily domain, as well as a CDP-alcohol/sugar
nucleotide hydrolase activity, catalyzed by a Nudix hydrolase domain. Determining the structure
of this enzyme would result in valuable information to contribute to our knowledge and
understanding of the HAD superfamily and the Nudix hydrolase superfamily. Sufficient
quantities of sufficiently pure YZGD are necessary to perform x-ray crystal structure
determination. A histidine tag was added to the enzyme so that it can be purified by nickel
affinity chromatography. This was done by cloning the gene into pET19b, a plasmid containing
a sequence encoding a string of ~10 histidines, and expressing the protein in Escherichia coli
BLR(DE3). The tagged YZGD expresses well...
Ditopic symmetrical bis(pyridyl) ligands incorporating the chiral dibenzobicyclo[b,f][3.3.1]nona-5a,6a-diene-6,12-dione cleft have been synthesised and characterised by NMR spectroscopy, mass spectrometry and X-ray crystallography. The ligands, which incorporate pyridyl groups directly connected to the carbocyclic cleft core or via alkyne or phenyl linkers were accessed from palladium-catalysed coupling reactions of 2,8-dibromodibenzobicyclo[b,f][3.3.1]nona-5a,6a-diene-6,12-dione. X-ray crystal analyses show the interplanar angles between the two cleft aromatic rings in these molecules, which range from 97.80(3) to 109.80(4)°.
The heterovalentgold(I)/gold(III)complex [(C6F 5)AuI(μ-2-Ph2PC6H 3-6-Me)AuIII(C6F5)(η 2-(6-MeC6H3-2-PPh2)}] has been prepared and structurally characterized by X-ray crystallography. It shows square planar stereochemistry at AuIII incorporating a four-m
P-glycoprotein (ABCB1) is an ATP-binding cassette protein that is associated with the acquisition of multi-drug resistance in cancer and the failure of chemotherapy in humans. Structural insights into this protein are described using a combination of small angle X-ray scattering data and cryo-electron crystallography data. We have compared the structures with bacterial homologues, and discuss the development of homology models for P-glycoprotein based on the bacterial Sav1866 structure.