The first mononuclear PtIII complex. Molecular structures of (NBu4)[PtIII(C6Cl5)4] and of its parent compound {NBu4}2[PtII(C6Cl5)4]·2CH2Cl2

(NBu4)[PtIII(C6Cl5)4], fully characterized by crystallographic, spectral, and magnetic measurements has been isolated by oxidation with halogens or TICl3 of the parent compound (NBu4)2[PtII(C6CL5)4], which has also been analysed by X-ray crystallography

Synthesis and reactivity of [NBu4]+[Pt(III)(C6Cl5)4]-: molecular structures of [NBu4]2+[Pt(C6Cl5)4]2-.cntdot.2CH2Cl2, [NBu4]+[Pt(III)(C6Cl5)4]- and [NBu4]+[Pt(C6Cl5)4(NO)]-

The synthesis and chemical and spectral characterizations of compounds [ N B ~ ~ ] ~ + [ P t ( c ~(lc)l,~ ) ~ ] ~ - [NBu ~ ]+[ P ~ (C~(C21~, [~N)B~ ]u-~ ]+[P~(C~CI~)(~31N, aOn]d- [NBU~]+[P~(C~C~,)~(4() ParPe~ d~es)c]ri-be d in this paper. By far the most intriguing complex is 2, the first mononuclear Pt(II1) complex ever reported. [NBu4]+[Pt(C&l5),]-( 2) can be prepared by reacting [NBu4]2+[Pt(C,C15)4]2(-1 ) with various oxidants such as C12, Br2, 12, or T1C13 and also by the electrochemical oxidation of 1 at 0.7 V in CH2C12. Compound 2 is stable to air and moisture, shows very limited reactivity, and has magnetic properties consistent with a 1/2 spin system. Complex 2 reacts with NO gas to give the adduct [NBu4]'[Pt(C6Cl5),(NO)]- (3), which can also be made directly from 1 by reaction with [NO]+[ClO,]- under an atmosphere at NO. Attempts to make the corresponding fluorine analogue of the Pt(II1) complex [NBu4]+[Pt(C6F,),]w- ere unsuccessful. The X-ray structures of complexes 1-3 have been determined and are also reported in this aper. Complex 3 crystallizes in the tetragonal space group P4,lnbc (no. 1331, with a = b = 14.948 (6) c = 23.488 (9) 8, V = 5248 (3) %r3, and p(calcd) = 1.85 g cm-3 for 2 = 4. The structure has been refined to a final agreement factor of R = 6.6%

Irrigation from the Sixties: Flumen-Monegros

53 Pags.- Tabls.- Maps.In arid and semiarid areas, agricultural land use is mainly restricted, in the first place, by the availability of water for crop growth. The transformation to irrigation of about 600 000 ha in the Ebro Valley has led to high increases in yield and in diversity of crops. After the Spanish Civil War (1936-39), which was followed by II World War, the Spanish food production system was heavily disrupted and food shortages appeared. This put high pressure on the development of new irrigated schemes which had been planned many years ago. In the Flumen-Monegros area, the technology available in the late fifties was based on flood-irrigation systems, with no previous soil studies, an empirical land evaluation, no control of saltinization risk and, finally, levelling without topsoil preservation. The extension of salinity and/or sodicity-affected soils in the Ebro Valley (IRYDA, 1977) was 200 000 ha, from which 160 000 were located in Aragon, mainly in Bardenas, Cinca and Flumen-Monegros area. But Alberto et al. (1984) reckron this data in 300 000 ha. As a result of these studies, ILACO (1975) designed two experimental drainage plots. Although the existence of salt-affected soils was known, information about the extent, location and general functioning at landscape level of those soils was lacking in the area. Some of the problems related to land use and soil management which are present now in the area or can be expected in the near future are:- Salinity-Sodicity: Diagnosis, monitoring and rehabilitation of salt-affected soils. - Soil structural degradation and surface crust formation. - Need for improved efficiency in water use: irrigation technology, water reuse, ... - Control of drainage-system degradation: open-air drains as well as underground drains. Several approaches at different scales have been adopted to work on these issues. Satellite images have been used to monitor land use and its temporal variability. Classical soil mapping at 1: 100000 level have been performed; in addition various detailed studies have been undertaken in model areas using the electromagnetic and four electrode sensors, micromorphological techniques, scanning electronic microscopy, and land evaluation procedures. The results have been presented in several papers: about salinity-sodicity trends in the Flumen sector (Herrero, 1987); about parameters related to water behaviour (Aragues, 1986); about soil porosity in plough horizons (Rodriguez-Ochoa, 1998); about translocation of solid materials (Rodriguez-Ochoa, et al. 1989; Porta and Rodriguez-Ochoa, 1991; Rodriguez-Ochoa, 1998); about degradation of underground drainage systems by mineral siltation (Herrero et al. 1989; Rodriguez-Ochoa, et al. 1989; Munoz, 1991; RodriguezOchoa, 1998).Other studies performed in the area include: Soil-vegetation relationships (Herrero, 1981); laboratory trials with different amendments in the drainage trench infilling material (Porta et al. 1996); dispersive processes because of soil structural instability (Amezketa and Aragues, 1990; Aragues and Amezketa, 1991; Amezketa and Aragues, 1995) and degradation of the hydraulic conductivity of soils (Amezketa and Aragues, 1989; Aragues and Amezketa, 1991; Amezketa and Aragues, 1995). The trip to the Flumen-Monegros area undertakes some of these points, and the stops are located in some of the main soil units. Discussion will be centered on aspects of soil genesis, classification and mapping, land use and soil conservation.Peer reviewe

ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation.

The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation of a given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes

Evaluation of Wedged Arterial Injection as a New Technique for Delivery of Experimental Therapeutic Sustances into the Porcine Pancreas

Objectives. To prospectively evaluate the technical feasibility and efficacy of wedged arterial injection (WAI) as a potential route for experimental selective therapy to the pancreas of healthy pigs. Materials and Methods. Selective angiographies were completed in ten pigs under general anaesthesia. By superselective angiography, the catheter was inserted and wedged into the major pancreatic artery, blocking the blood flow. In order to evaluate the efficacy of the WAI method, a DNA-specific fluorescent dye (Hoechst 33258) was used. Results. Histological study revealed a uniform distribution of the fluorescent dye within the nuclei of the endocrine and exocrine pancreatic cells. Pancreatic and liver enzymes as well as histopathology of the pancreas were normal. Conclusion. WAI is a highly effective minimally invasive methodology to target the porcine pancreas. The findings suggest that WAI may contribute to developing preclinical assays of pancreas gene or cell-transfer therapies in swine model

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER.

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE. The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER.

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE. The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose

SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses.

Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force approach through side-chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main-chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content

Plasmodium falciparum Apicomplexan-Specific Glucosamine-6-Phosphate <i>N</i>-Acetyltransferase Is Key for Amino Sugar Metabolism and Asexual Blood Stage Development.

--- - i: - N - N - O - N - Plasmodium falciparum - Cryptosporidium parvum - P. falciparum - N - N - P. falciparum - C. parvum b: - IMPORTANCE content: - UDP- - "-acetylglucosamine (UDP-GlcNAc), the main product of the hexosamine biosynthetic pathway, is an important metabolite in protozoan parasites since its sugar moiety is incorporated into glycosylphosphatidylinositol (GPI) glycolipids and " - "- and " - "-linked glycans. Apicomplexan parasites have a hexosamine pathway comparable to other eukaryotic organisms, with the exception of the glucosamine-phosphate " - "-acetyltransferase (GNA1) enzymatic step that has an independent evolutionary origin and significant differences from nonapicomplexan GNA1s. By using conditional genetic engineering, we demonstrate the requirement of GNA1 for the generation of a pool of UDP-GlcNAc and for the development of intraerythrocytic asexual " - " parasites. Furthermore, we present the 1.95\xE2\x80\x89\xC3\x85 resolution structure of the GNA1 ortholog from " - ", an apicomplexan parasite which is a leading cause of diarrhea in developing countries, as a surrogate for " - " GNA1. The in-depth analysis of the crystal shows the presence of specific residues relevant for GNA1 enzymatic activity that are further investigated by the creation of site-specific mutants. The experiments reveal distinct features in apicomplexan GNA1 enzymes that could be exploitable for the generation of selective inhibitors against these parasites, by targeting the hexosamine pathway. This work underscores the potential of apicomplexan GNA1 as a drug target against malaria." - " Apicomplexan parasites cause a major burden on global health and economy. The absence of treatments, the emergence of resistances against available therapies, and the parasite's ability to manipulate host cells and evade immune systems highlight the urgent need to characterize new drug targets to treat infections caused by these parasites. We demonstrate that glucosamine-6-phosphate " - -acetyltransferase (GNA1), required for the biosynthesis of UDP- - "-acetylglucosamine (UDP-GlcNAc), is essential for " - " asexual blood stage development and that the disruption of the gene encoding this enzyme quickly causes the death of the parasite within a life cycle. The high-resolution crystal structure of the GNA1 ortholog from the apicomplexan parasite " - ", used here as a surrogate, highlights significant differences from human GNA1. These divergences can be exploited for the design of specific inhibitors against the malaria parasite.

Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER

11 pags., 5 figs., 3 tabsStructure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the removal of unstructured polypeptide, hierarchical decomposition of structural units from domains to local folds and systematically probing the model against the experimental data will ensure the optimal use of the model in phasing. Concomitantly, the exhaustive use of models and stereochemistry in phasing, refinement and validation raises the concern of crystallographic model bias and the need to critically establish the information contributed by the experiment. Therefore, in its predicted_model mode ARCIMBOLDO_SHREDDER will first determine whether the input model already constitutes a solution or provides a straightforward solution with Phaser. If not, extracted fragments will be located. If the landscape of solutions reveals numerous, clearly discriminated and consistent probes or if the input model already constitutes a solution, model-free verification will be activated. Expansions with SHELXE will omit the partial solution seeding phases and all traces outside their respective masks will be combined in ALIXE, as far as consistent. This procedure completely eliminates the molecular replacement search model in favour of the inferences derived from this model. In the case of fragments, an incorrect starting hypothesis impedes expansion. The predicted_model mode has been tested in different scenarios.We are grateful to the Spanish MICINN/AEI/FEDER/UE for support through the PGC2018-101370-B-100 project to IU, PID2020-115331GB-I00 to JH, a scholarship (PRE2019-087953) to EJ and a scholarship (BES-2017-080368) associated with the Structural Biology Maria de Maeztu Unit of Excellence (MDM2014-0435-01) to AM. Support from STFC-UK/ CCP4 ‘Agreement for the integration of methods into the CCP4 software distribution, ARCIMBOLDO_LOW’ is gratefully acknowledged.Peer reviewe