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Patel D.K.,University of Granada | Dominguez-Martin A.,University of Granada | Brandi-Blanco M.D.P.,University of Granada | Choquesillo-Lazarte D.,Laboratorio Of Estudios Cristalograficos | And 2 more authors.
Coordination Chemistry Reviews | Year: 2012

The metal coordination patterns of hypoxanthine, xanthine and related oxy-purines have been reviewed on the basis of the structural information available in the Cambridge Structural Database (CSD), including also the most recent reports founded in SciFinder. Attention is paid to the metal ion binding modes and interligand interactions in mixed-ligand metal complexes, as well as the possibilities of metal binding of the exocyclic-O atoms. The information in CSD is also reviewed for the complexes of adenine in cationic, neutral and anionic forms with every metal ion. In contrast to the scarce structural information about hypoxanthine and related complexes, large structural information is available for adenine complexes with a variety of metals that reveals some correlations between the crystal-chemical properties of metal ions. Three aspects are studied in deep: the coordination patterns, the interligand interactions influencing the molecular recognition in mixed-ligand metal complexes and the connectivity between metals for different adenine species, thus supporting its unique versatility as ligand. When possible, the overall behaviour showed by adenine metal complexes is discussed according to the HSAB Pearson criteria and the tautomeric behaviour observed for each protonated species of adenine. The differences between the roles of adenine and the referred oxypurines ligands are underlined. © 2011 Elsevier B.V.


Gavira J.A.,Laboratorio Of Estudios Cristalograficos
Archives of Biochemistry and Biophysics | Year: 2015

Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented. Synopsis: Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale. © 2015 Elsevier Inc.


Gavira J.A.,Laboratorio Of Estudios Cristalograficos | Van Driessche A.E.S.,Laboratorio Of Estudios Cristalograficos | Garcia-Ruiz J.-M.,Laboratorio Of Estudios Cristalograficos
Crystal Growth and Design | Year: 2013

Protein crystals were obtained in a wide range of silica gel concentrations, 2.0-22.0% (v/v), using the counter-diffusion technique. The protein crystal lattice incorporates silica fibers during their growth, making the crystal appear optically translucent while maintaining the diffraction quality. The effect of the silica fibers on the nucleation and growth morphology is discussed, and the amount of incorporated silica matrix is quantified. The practical implications of the presence of a high hygroscope phase on the crystal properties are discusse, and the improvement of the mechanical properties and stability of the crystals is shown. These reinforced protein crystals, able to include large amounts of silica, open a new range of possibilities for the characterization of protein crystals and the application in the biotechnological industry. © 2013 American Chemical Society.


Sleutel M.,Vrije Universiteit Brussel | Van Driessche A.E.S.,Laboratorio Of Estudios Cristalograficos
Crystal Growth and Design | Year: 2013

We report on the failure of the Cabrera-Vermilyea (CV) step pinning model to reproduce the elementary step kinetics for the case of tetragonal lysozyme crystals growing from contaminated solutions. We measured the supersaturation dependency of the step velocity using confocal microscopy for three different commercially available lysozyme batches with varying levels of impurity content, that is, Seikagaku, Fluka, and Sigma. Strong nonlinear dependencies are obtained in the high to intermediate supersaturation range and near-linear dependencies at lower driving forces. The clear absence of a dead zone for the Fluka and Seikagaku data is in direct contradiction to the CV model. As such, we developed a time-dependent impurity model based on Bliznakov kinetics assuming Langmuir adsorption. Admissible fits are obtained for Fluka and Seikagaku lysozyme corroborating the self-purification interpretation due to the diminishing terrace exposure times at higher supersaturation levels. The steeper recovery toward pure kinetics for Sigma lysozyme than predicted by Langmuir adsorption prompted us to expand the model to allow for impurity-impurity interaction. The resultant kinetic model, which assumes a Kisliuk-like mode of impurity adsorption, did yield acceptable fits with Sigma step kinetics. This Bliznakov-Kisliuk model also predicts clustering of impurity molecules on the surface, which is corroborated by our in situ experimental atomic force microscopy observations. © 2013 American Chemical Society.


Glaab F.,University of Regensburg | Kellermeier M.,University of Konstanz | Kunz W.,University of Regensburg | Morallon E.,University of Alicante | Garcia-Ruiz J.M.,Laboratorio Of Estudios Cristalograficos
Angewandte Chemie - International Edition | Year: 2012

Silica gardens are well-known examples for the self-assembly of inorganic material (see figure). The growth of hollow tubes results in the spontaneous formation of two compartments with highly dissimilar pH and ion concentrations, which cause electrochemical potential differences across the membrane. Initially generated gradients are relieved over time through dynamic diffusion and precipitation processes. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Kellermeier M.,University of Konstanz | Kellermeier M.,University of Regensburg | Glaab F.,University of Regensburg | Melero-Garcia E.,Laboratorio Of Estudios Cristalograficos | Garcia-Ruiz J.M.,Laboratorio Of Estudios Cristalograficos
Methods in Enzymology | Year: 2013

Silica biomorphs and silica gardens are canonical examples of precipitation phenomena yielding self-assembled nanocrystalline composite materials with outstanding properties in terms of morphology and texture. Both types of structures form spontaneously in alkaline environments and rely on simple, and essentially similar, chemistry. However, the underlying growth processes are very sensitive to a range of experimental parameters, distinct preparation procedures, and external conditions. In this chapter, we report detailed protocols for the synthesis of these extraordinary biomimetic materials and identify critical aspects as well as advantages and disadvantages of different approaches. Furthermore, modifications of established standard procedures are reviewed and discussed with respect to their benefit for the control over morphogenesis and the reproducibility of the experiments in both cases. Finally, we describe currently used techniques for the characterization of these fascinating structures and devise promising ways to analyze their growth behavior and formation mechanisms in situ and as a function of time. © 2013 Elsevier Inc.


Delgado-Lopez J.M.,Laboratorio Of Estudios Cristalograficos | Frison R.,CNR Institute of Crystallography | Cervellino A.,Paul Scherrer Institute | Gomez-Morales J.,Laboratorio Of Estudios Cristalograficos | And 2 more authors.
Advanced Functional Materials | Year: 2014

Bio-inspired apatite nanoparticles precipitated in the presence of citrate ions at increasing maturation times are characterized in terms of structure, size, morphology, and composition through advanced X-ray total scattering techniques. The origin of the platy crystal morphology, breaking the hexagonal symmetry, and the role of citrate ions is explored. By cross-coupling the size and shape information of crystal domains with those obtained by atomic force microscopy on multidomain nanoparticles, a plausible mechanism underlying the amorphous-to-crystal transformation is reconstructed. In the present study, citrate plays the distinct roles of inducing the platy morphology of the amorphous precursor and controlling the thickness of the Ca-deficient apatite nanocrystals. These findings can open new scenarios also in bone mineralization, where citrate might have a broader role to play than has been thought to date. Citrate bio-inspired apatite nanoparticles are characterized in terms of structure, size, morphology, and composition through advanced X-ray total scattering techniques. By cross-coupling size and shape information of crystal domains with atomic force microscopy data for multidomain nanoparticles, a plausible mechanism underlying the amorphous-to-crystal transformation is reconstructed and the origin of platy crystal morphology, breaking the hexagonal symmetry, explained. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


McPherson A.,University of California at Irvine | Gavira J.A.,Laboratorio Of Estudios Cristalograficos
Acta Crystallographica Section F:Structural Biology Communications | Year: 2014

Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of proteins, nucleic acids and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by the manipulation of various parameters that include temperature, ionic strength and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years owing to the advent of practical, easy-to-use screening kits and the application of laboratory robotics. A brief review will be given here of the most popular methods, some guiding principles and an overview of current technologies. © 2014 International Union of Crystallography. All rights reserved.


Ramirez-Rodriguez G.B.,Laboratorio Of Estudios Cristalograficos | Delgado-Lopez J.M.,Laboratorio Of Estudios Cristalograficos | Gomez-Morales J.,Laboratorio Of Estudios Cristalograficos
CrystEngComm | Year: 2013

The time-evolution of calcium phosphate precipitation by vapor diffusion has been studied by in situ confocal Raman microspectroscopy. A hanging drop configuration within a device known as "crystallization mushroom" was employed in order to improve the Raman signal coming from growing crystals. This innovative methodology allowed to identify and follow the evolution of the precipitates formed at different areas of the drops containing mixed solutions of Ca(CH3COO)2 and (NH4)2HPO 4 due to the diffusion of CO2 and NH3 gases released from NH4HCO3 solutions at different concentrations (30 mM, 100 mM and 2 M). Time-dependent in situ Raman spectra indicated that amorphous calcium phosphate (ACP) was the first precipitate appearing just after mixing the Ca- and PO4-containing solutions. A few minutes later, it transformed to dicalcium phosphate dihydrate (DCPD). The lifetime of DCPD strongly depends on the concentration of the NH 4HCO3 solutions and thus on the pH increase rate. The pathway for the phase transformation from ACP to DCPD and then to octacalcium phosphate (OCP) followed a dissolution-reprecipitation mechanism. Additionally, OCP acted as temporal template for the heterogeneous nucleation and crystallization of biomimetic carbonate-apatite nanocrystals (cAp). The characterization by TEM, XRPD and Raman spectroscopy of the freeze-dried powders obtained after seven days confirmed that OCP and cAp were the remaining phases when using 30 mM and 100 mM NH4HCO3 solutions. By contrast, working with the highest NH4HCO3 concentration the system evolved to the precipitation of elongated calcite crystals. © 2013 The Royal Society of Chemistry.


Choquesillo-Lazarte D.,Laboratorio Of Estudios Cristalograficos | Garcia-Ruiz J.M.,Laboratorio Of Estudios Cristalograficos
Journal of Applied Crystallography | Year: 2011

The use of poly(ethylene) oxide (PEO) as a gelator has been evaluated with a selected list of organic solvents. From the 26 solvents tested, eight formed gel matrices. This number was extended to 19 when poly(ethylene) oxide was used with a mixture of solvents. The procedure for the preparation of PEO organogels is described, and their application for the crystallization of small molecules using different crystallization techniques in the presence of organic solvents is discussed. © 2011 International Union of Crystallography Printed in Singapore-all rights reserved.

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