Showing papers by "José María Carazo published in 2011"
TL;DR: A two-step phase-shifting method, that can demodulate open- and closed-fringed patterns without local sign ambiguity is presented, based on determining first the fringe direction map by a regularized optical flow algorithm and applying the spiral phase transform to one of the fringe patterns.
Abstract: A two-step phase-shifting method, that can demodulate open- and closed-fringed patterns without local sign ambiguity is presented. The proposed method only requires a constant phase-shift between the two interferograms. This phase-shift does not need to be known and can take any value inside the range (0, 2π), excluding the singular case where it corresponds to π. The proposed method is based on determining first the fringe direction map by a regularized optical flow algorithm. After that, we apply the spiral phase transform (SPT) to one of the fringe patterns and we determine its quadrature signal using the previously determined direction. The proposed technique has been applied to simulated and experimental interferograms obtaining satisfactory results. A complete MATLAB software package is provided in [http://goo.gl/Snnz7].
113 citations
TL;DR: Structural data are consistent with p53 sliding along DNA via its C termini and the DNA-binding domains hopping on and off during searches for REs and point to a mechanism of enhancement of specificity by its binding to effector proteins.
Abstract: The multidomain homotetrameric tumor suppressor p53 has two modes of binding dsDNA that are thought to be responsible for scanning and recognizing specific response elements (REs). The C termini bind nonspecifically to dsDNA. The four DNA-binding domains (DBDs) bind REs that have two symmetric 10 base-pair sequences. p53 bound to a 20-bp RE has the DBDs enveloping the DNA, which is in the center of the molecule surrounded by linker sequences to the tetramerization domain (Tet). We investigated by electron microscopy structures of p53 bound to DNA sequences consisting of a 20-bp RE with either 12 or 20 bp nonspecific extensions on either end. We found a variety of structures that give clues to recognition and scanning mechanisms. The 44- and 60-bp sequences gave rise to three and four classes of structures, respectively. One was similar to the known 20-bp structure, but the DBDs in the other classes were loosely arranged and incompatible with specific DNA recognition. Some of the complexes had density consistent with the C termini extending from Tet to the DNA, adjacent to the DBDs. Single-molecule fluorescence resonance energy transfer experiments detected the approach of the C termini towards the DBDs on addition of DNA. The structural data are consistent with p53 sliding along DNA via its C termini and the DNA-binding domains hopping on and off during searches for REs. The loose structures and posttranslational modifications account for the affinity of nonspecific DNA for p53 and point to a mechanism of enhancement of specificity by its binding to effector proteins.
69 citations
TL;DR: Application of this three-dimensional maximum likelihood algorithm to cryo-electron tomographic data of ice-embedded thermosomes revealed distinct conformations that are in good agreement with results obtained by previous single particle studies.
62 citations
TL;DR: PRIDEViewer is a novel Java‐based application that presents the information available in a PRIDE XML file in a user‐friendly manner, facilitating the interaction among end users as well as the understanding and evaluation of the compiled information.
Abstract: Current standardization initiatives have greatly contributed to share the information derived by proteomics experiments. One of these initiatives is the XML-based repository PRIDE (PRoteomics IDEntification database), although an XML-based document does not appear to present a user-friendly view at the first glance. PRIDEViewer is a novel Java-based application that presents the information available in a PRIDE XML file in a user-friendly manner, facilitating the interaction among end users as well as the understanding and evaluation of the compiled information. PRIDEViewer is freely available at: http://proteo.cnb.csic.es/prideviewer/.
8 citations