Conformation and concerted dynamics of the integrin-binding site and the C-terminal region of echistatin revealed by homonuclear NMR

Echistatin is a potent antagonist of the integrins αvβ3, α5β1 and αIIbβ3. Its full inhibitory activity depends on an RGD (Arg-Gly- Asp) motif expressed at the tip of the integrin-binding loop and on its C-terminal tail. Previous NMR structures of echistatin showed a poorly defined integrin-recognition sequence and an incomplete C-terminal tail, which left the molecular basis of the functional synergy between the RGD loop and the C-terminal region unresolved. We report a high-resolution structure of echistatin and an analysis of its internal motions by off-resonance ROESY (rotating-frame Overhauser enhancement spectroscopy). The fulllength C-terminal polypeptide is visible as a β-hairpin running parallel to the RGD loop and exposing at the tip residues Pro43, His44 and Lys45. The side chains of the amino acids of the RGD motif have well-defined conformations. The integrin-binding loop displays an overall movement with maximal amplitude of 30◦. Internal angular motions in the 100–300 ps timescale indicate increased flexibility for the backbone atoms at the base of the integrin- recognition loop. In addition, backbone atoms of the amino acids Ala23 (flanking the R24GD26 tripeptide) and Asp26 of the integrin-binding motif showed increased angular mobility, suggesting the existence of major and minor hinge effects at the base and the tip, respectively, of the RGD loop. A strong network of NOEs (nuclear Overhauser effects) between residues of the RGD loop and the C-terminal tail indicate concerted motions between these two functional regions. A full-length echistatin– αvβ3 docking model suggests that echistatin’s C-terminal amino acids may contact αv-subunit residues and provides new insights to delineate structure–function [email protected]; [email protected]; [email protected]; [email protected]

Metabolic Profile of chronic liver disease by NMR spectroscopy of human biopsies

Abstract Among the different processes occurring during the evolution of liver disease, fibrosis has a predominant role. Liver fibrosis mechanisms are fairly constant irrespective of the underlying etiology. Cirrhosis is the end-stage of this reaction. Metabolic profiles, which are affected by many physiological and pathological processes, may provide further insight into the metabolic consequences of this severe liver disease. The aim of this study was to demonstrate the applicability of 1H high resolution magic angle spinning (HR-MAS) NMR spectroscopy in the biochemical profile determination of human liver needle biopsy samples for the characterization of metabolic alterations related to the severity of liver disease. We recorded and analyzed HR-MAS spectra of 68 liver tissue samples obtained by needle biopsy from patients with chronic liver disease. Multivariate analysis was applied to these data to obtain discrimination patterns and to reveal relevant metabolites. The metabolic characterization of liver tissue from needle biopsies by HR-MAS NMR spectroscopy provided differential patterns for cirrhotic and non-cirrhotic chronic liver disease tissue. Metabolites closely related to the liver metabolism such as some fatty acids, glucose and amino acids show differences between the two groups. Phospholipid precursors, which have been previously correlated with hepatic lesions also show differences. Furthermore, the correlation between histologically assessed liver disease stages and the levels of the most discriminative metabolites show that liver dysfunction is present at the initial stages of chronic hepatic lesions. Overall, this work suggests that the additional information obtained by NMR metabolomics applied to needle biopsies of human liver may be useful for assessing metabolic alterations and liver dysfunction in chronic liver disease

Strategies for annotation and curation of translational databases: the eTUMOUR project

The eTUMOUR (eT) multi-centre project gathered in vivo and ex vivo magnetic resonance (MR) data, as well as transcriptomic and clinical information from brain tumour patients, with the purpose of improving the diagnostic and prognostic evaluation of future patients. In order to carry this out, among other work, a database—the eTDB—was developed. In addition to complex permission rules and software and management quality control (QC), it was necessary to develop anonymization, processing and data visualization tools for the data uploaded. It was also necessary to develop sophisticated curation strategies that involved on one hand, dedicated fields for QC-generated meta-data and specialized queries and global permissions for senior curators and on the other, to establish a set of metrics to quantify its contents. The indispensable dataset (ID), completeness and pairedness indices were set. The database contains 1317 cases created as a result of the eT project and 304 from a previous project, INTERPRET. The number of cases fulfilling the ID was 656. Completeness and pairedness were heterogeneous, depending on the data type involved

Microcámara y dispositivo de cultivo celular monitorizables por resonancia magnética nuclear

La presente invención hace referencia a una microcámara ya un dispositivo de cultivo celular, monitorizables por resonancia magnética nuclear y otras técnicas de imagen, donde dicha microcámara de cultivo se encuentra encapsulada y alojada en el interior de un chip. Dicha microcámara y dicho dispositivo resultan de fácil manejo para el usuario, permitiendo su manipulación o su reemplazo sin la necesidad de un montaje laborioso, beneficiando además notablemente el estudio de cultivos durante periodos largos de tiempo, superiores a 24 horas.Peer reviewedCentro de Investigación Biomecánica en Red en Bioingeniería Biomateriales y Nanomedicina, Universitat de Valencia, Consejo Superior de Investigaciones Científicas (España) , IKERLAN S. COOP.A1 Solicitud de patente con informe sobre el estado de la técnic

Microcámara y dispositivo de cultivo celular monitorizables por resonancia magnética nuclear

[EN] The invention relates to a cell culture device and microchamber which can be monitored using nuclear magnetic resonance and other imaging techniques, in which the culture microchamber is encapsulated and housed inside a chip. The microchamber and the device are easy for the user to handle, allowing same to be handled or repositioned without requiring complex mounting operations. In addition, the invention allows cultures to be studied for long periods, greater than 24 hours.[ES] La presente invención hace referencia a una micro cámara y a un dispositivo de cultivo celular, monitorizables por resonancia magnética nuclear y otras técnicas de imagen, donde dicha micro cámara de cultivo se encuentra encapsulada y alojada en el interior de un chip. Dicha micro cámara y dicho dispositivo resultan de fácil manejo para el usuario, pennitiendo su manipulación o su reemplazo sin la necesidad de un montaje laborioso, beneficiando además notablemente el estudio de cultivos durante periodos largos de tiempo, superiores a 24 horas.Peer reviewedCentro de Investigación Biomédica en Red en Bioingeniería Biomateriales y Nanomedicina, Universitat de Valencia, Consejo Superior de Investigaciones Científicas (España), Ikerlan S CCOPA1 Solicitud de patente con informe sobre el estado de la técnic

Strategies for annotation and curation of translational databases: the eTUMOUR project

The eTUMOUR (eT) multi-centre project gathered in vivo and ex vivo magnetic resonance (MR) data, as well as transcriptomic and clinical information from brain tumour patients, with the purpose of improving the diagnostic and prognostic evaluation of future patients. In order to carry this out, among other work, a database-the eTDB-was developed. In addition to complex permission rules and software and management quality control (QC), it was necessary to develop anonymization, processing and data visualization tools for the data uploaded. It was also necessary to develop sophisticated curation strategies that involved on one hand, dedicated fields for QC-generated meta-data and specialized quèries and global permissions for senior curators and on the other, to establish a set of metrics to quantify its contents. The indispensable dataset (ID), completeness and pairedness indices were set. The database contains 1317 cases created as a result of the eT project and 304 from a previous project, INTERPRET. The number of cases fulfilling the ID was 656. Completeness and pairedness were heterogeneous, depending on the data type involved