1,721,075 research outputs found
Molecular Mechanics/Coarse-Grained Simulations as a Structural Prediction Tool for GPCRs/Ligand Complexes
No full textMolecular Modelling of the Ni(II)-Responsive Synechocystis PCC 6803 Transcriptional Regulator InrS in the Metal Bound Form
Full text linkInrS (internal nickel-responsive sensor) is a transcriptional regulator found in cyanobacteria that represses the transcription of the nickel exporter NrsD in the apo form and de-represses expression of the exporter upon Ni(II) binding. Although a crystal structure of apo-InrS from Synechocystis PCC 6803 has been reported, no structure of the protein with metal ions bound is available. Here we report the results of a computational study aimed to reconstruct the metal binding site by taking advantage of recent X-ray absorption spectroscopy (XAS) data and to envisage the structural rearrangements occurring upon Ni(II) binding. The modelled Ni(II) binding site shows a square planar geometry consistent with experimental data. The structural details of the conformational changes occurring upon metal binding are also discussed in the framework of trying to rationalize the different affnity of the apo- and holo-forms of the protein for DNA
Characterization and 1.57 Å resolution structure of the key fire blight phosphatase AmsI from Erwinia amylovora
No full textAmsI is a low-molecular-weight protein tyrosine phosphatase that regulates the production of amylovoran in the Gram-negative bacterium Erwinia amylovora, a specific pathogen of rosaceous plants such as apple, pear and quince. Amylovoran is an exopolysaccharide that is necessary for successful infection. In order to shed light on AmsI, its structure was solved at 1.57 Å resolution at the same pH as its highest measured activity (pH 5.5). In the active site, a water molecule, bridging between the catalytic Arg15 and the reaction-product analogue sulfate, might be representative of the water molecule attacking the phospho-cysteine intermediate in the second step of the reaction mechanism.The high-resolution (1.57 Å) structure and kinetic data of the key fire blight phosphatase AmsI are reported
Dynamic characterization and substrate binding of cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase-an enzyme used in bioremediation.
No full textIn recent years, techniques involving the use oforganisms to remove or neutralize pollutants from contaminatedsites have attracted great attention. The aim of bioremediationis to use naturally occurring organisms to degradedangerous substances to less toxic or non toxic molecules.The gram-negative bacterium Pandoraea pnomenusa strainB-356 (Pp) has been found to be able to transform a persistentclass of organic pollutant compounds, namely the biphenyland polychlorinated biphenyls (PCBs). A key enzyme in thePCB catabolic pathway is NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (BphB), for whichthe crystal structure from Pp has been crystallized in apo-,NAD-bound and biphenyldiol-/NAD-bound forms. The substratebinding loop structure has not been completely resolvedto date in the former two bound states. Here we report theresults of the first extensive molecular dynamics simulationson the three different states of PpBphB. This allowed an indepth characterization of the mechanism of ligand uptake andbinding, including unraveling of the gating mechanism. Oursimulations give a deep insight into several dynamic featuresof the enzyme that were not captured by crystal structure
Probing the transport of Ni(II) ions through the internal tunnels of the Helicobacter pylori UreDFG multimeric protein complex
No full textThe survival of several pathogenic bacteria, such as Helicobacter pylori (Hp), relies on the activity of the nickel dependent enzyme urease. Nickel insertion into urease is mediated by a multimeric chaperone complex (HpUreDFG) that is responsible for the transport of Ni(II) from a conserved metal binding motif located in the UreG dimer (CPH motif) to the catalytic site of the enzyme. The X-ray structure of HpUreDFG revealed the presence of water-filled tunnels that were proposed as a route for Ni(II) translocation. Here, we probe the transport of Ni(II) through the internal tunnels of HpUreDFG, from the CPH motif to the external surface of the complex, using microsecond-long enhanced molecular dynamics simulations. The results suggest a “bucketbrigade” mechanism whereby Ni(II) can be transported through a series of stations found along these internal pathways
Application of Molecular Dynamics to the Investigation of Metalloproteins Involved in Metal Homeostasis
No full textAvailable estimates indicate that 30–40 % of all proteins need at least one metal ion to perform their biological function. Therefore, they are called metalloproteins. The correct biosynthesis of metalloproteins requires living organisms to be able to cope with issues such as the limited bioavailability or the potential cytotoxicity of several essential metals. Thus, organisms have developed complex machineries that guarantee the proper intracellular concentration and distribution among compartments of each metal, i.e. metal homeostasis. To understand how the different proteins responsible for metal homeostasis carry out their function, it is necessary to investigate their three-dimensional (3D) structure and mobility at the atomic level. Nuclear magnetic resonance spectroscopy is one of the main experimental techniques providing this information. Computer simulations of molecular dynamics (MD) complement experimental information by showing how the 3D structure fluctuates over time and as a function of environmental conditions, with the possibility of exploring a wider range of timescales and conditions than usually amenable to experiment. Here we review numerous applications of MD for the investigation of the structure and dynamics of metalloproteins, and we also mention some technical aspects related to the parametrization of metals in commonly used force fields
Nickel-responsive transcriptional regulators
No full textNickel is an essential micronutrient for a large number of living organisms, but it is also a toxic metal ion when it accumulates beyond the sustainable level as it may result if and when its cellular trafficking is not properly governed. Therefore, the homeostasis and metabolism of nickel is tightly regulated through metal-specific protein networks that respond to the available Ni(II) concentration. These are directed by specific nickel sensors, able to couple Ni(II) binding to a change in their DNA binding affinity and/or specificity, thus translating the cellular level of Ni(II) into a modification of the expression of the proteins devoted to modulating nickel uptake, efflux and cellular utilization. This review describes the Ni(II)-dependent transcriptional regulators discovered so far, focusing on their structural features, metal coordination modes and metal binding thermodynamics. Understanding these properties is essential to comprehend how these sensors correlate nickel availability to metal coordination and functional responses. A broad and comparative study, described here, reveals some general traits that characterize the binding stoichiometry and Ni(II) affinity of these metallo-sensors
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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