Newman- Janis Algorithm Revisited. The purpose of the present article is to show that the Newman- Janis and Newman et al algorithm used to derive the Kerr and Kerr-Newman metrics respectively, automatically leads to the extension of the initial non negative polar radial coordinate r to a cartesian coordinate running from to , thus introducing in a natural way the region in the above spacetimes. Using Boyer-Lindquist and ellipsoidal coordinates, we discuss some geometrical aspects of the positive and negative regions of , like horizons, ergosurfaces, and foliation structures. It is available as a standalone Java program, downloadable and distributed on DVD and also a web application available on the NEA website. One of the main new features in JANIS is the scripting capability via command line, which notably automatizes plots generation and permits automatically extracting data from the JANIS database. New features added in this version of the JANIS software are described along this paper with some examples.
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High-throughput determination of RNA structure by proximity ligation. We present an unbiased method to globally resolve RNA structures through pairwise contact measurements between interacting regions. RNA proximity ligation RPL uses proximity ligation of native RNA followed by deep sequencing to yield chimeric reads with ligation junctions in the vicinity of structurally proximate bases.
RPL measurements correlate with established secondary structures for these RNA molecules, including stem-loop structures and long-range pseudoknots. We anticipate that RPL will complement the current repertoire of computational and experimental approaches in enabling the high-throughput determination of secondary and tertiary RNA structures.
An approach for high-throughput structure determination of proteins by NMR spectroscopy. Medek, Ales; Olejniczak, Edward T.
Using this strategy, the key NOEs that define the hydrophobic core and overall fold of the protein are easily obtained. NMR data are acquired using cryogenic probe technology which markedly reduces the spectrometer time needed for data acquisition. The approach is demonstrated by determining the overall fold of the antiapoptotic protein, Bcl-xL, from data collected in only 4 days.
Refinement of the Bcl-xL structure to a backbone rmsd of 0. A distance analysis of different proteins and structure calculations using simulated data suggests that our method will allow the global folds of a wide variety of proteins to be determined. NMR in a crystallography-based high-throughput protein structure-determination environment.
Application of in situ diffraction in high-throughput structure determination platforms. Macromolecular crystallography MX is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually.
A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment.
These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given. Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.
Directory of Open Access Journals Sweden. Full Text Available Acetylcholinesterase AChE is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used inter alia to treat cholinergic deficiencies e.
Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site CAS.
Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure -based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The CAS binding part of C could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule.
We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical. Fast iodide-SAD phasing for high-throughput membrane protein structure determination.
We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction I-SAD.
The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor GPCR , and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.
The JCSG high-throughput structural biology pipeline. The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than structures to the community over the past ten years and has made a significant contribution to the overall goal of the NIH Protein Structure Initiative PSI of expanding structural coverage of the protein universe.
The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than structures to the community over the past ten years. The JCSG has made a significant contribution to the overall goal of the NIH Protein Structure Initiative PSI of expanding structural coverage of the protein universe, as well as making substantial inroads into structural coverage of an entire organism.
Targets are processed through an extensive combination of bioinformatics and biophysical analyses to efficiently characterize and optimize each target prior to selection for structure determination.
The pipeline uses parallel processing methods at almost every step in the process and can adapt to a wide range of protein targets from bacterial to human. The construction, expansion and optimization of the JCSG gene-to- structure pipeline over the years have resulted in many technological and methodological advances and developments. The vast number of targets and the enormous amounts of associated data processed through the multiple stages of the experimental pipeline required the development of variety of valuable resources that, wherever feasible, have been converted to free-access web-based tools and applications.
High throughput screening of starch structures using carbohydrate microarrays. In this study we introduce the starch-recognising carbohydrate binding module family 20 CBM20 from Aspergillus niger for screening biological variations in starch molecular structure using high throughput carbohydrate microarray technology. Defined linear, branched and phosphorylated High throughput platforms for structural genomics of integral membrane proteins. Structural genomics approaches on integral membrane proteins have been postulated for over a decade, yet specific efforts are lagging years behind their soluble counterparts.
Indeed, high throughput methodologies for production and characterization of prokaryotic integral membrane proteins are only now emerging, while large-scale efforts for eukaryotic ones are still in their infancy.
Presented here is a review of recent literature on actively ongoing structural genomics of membrane protein initiatives, with a focus on those aimed at implementing interesting techniques aimed at increasing our rate of success for this class of macromolecules. All rights reserved. High throughput toxicokinetics HTTK is an approach that allows for rapid estimations of TK for hundreds of environmental chemicals.
HTTK-based reverse dosimetry i. Hura, Greg L. We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering SAXS.
Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution.
SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures , and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.
Standard nanoindentation tests are " high throughput " compared to nearly all other mechanical tests, such as tension or compression. However, the typical rates of tens of tests per hour can be significantly improved. These higher testing rates enable otherwise impractical studies requiring several thousands of indents, such as high-resolution property mapping and detailed statistical studies. Furthermore, since fast loading rates are required, the strain rate sensitivity must also be considered.
A review of these effects is given, with the emphasis placed on making complimentary standard nanoindentation measurements to address these issues. Experimental applications of the technique, including mapping of welds, microstructures, and composites with varying length scales, along with studying the effect of surface roughness on nominally homogeneous specimens, will be presented. Systematic efforts are currently under way to construct defined sets of cloned genes for high-throughput expression and purification of recombinant proteins.
To facilitate subsequent studies of protein function, we have developed miniaturized assays that accommodate extremely low sample volumes and enable the rapid, simultaneous processing of thousands of proteins.
A high-precision robot designed to manufacture complementary DNA microarrays was used to spot proteins onto chemically derivatized glass slides at extremely high spatial densities.
The proteins attached covalently to the slide surface yet retained their ability to interact specifically with other proteins, or with small molecules, in solution. Three applications for protein microarrays were demonstrated: screening for protein-protein interactions, identifying the substrates of protein kinases, and identifying the protein targets of small molecules.
High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all? Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology.
This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.
Variants of two candidate methods, those described by Vaintraub and Lapteva Anal Biochem In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously.
First, we have established an easy to follow experimental This protocol was subsequently applied to hydroxyl radical footprinting of three dimensional RNA structures to give a probing signal that correlates well with the RNA backbone solvent accessibility. Moreover, we applied Full Text Available Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis.
Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach.
We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors.
We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization.
Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines. Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Determining the optimal size of small molecule mixtures for high throughput NMR screening.
High-throughput screening HTS using NMR spectroscopy has become a common component of the drug discovery effort and is widely used throughout the pharmaceutical industry.
NMR provides additional information about the nature of small molecule-protein interactions compared to traditional HTS methods. In order to achieve comparable efficiency, small molecules are often screened as mixtures in NMR-based assays. Nevertheless, an analysis of the efficiency of mixtures and a corresponding determination of the optimum mixture size OMS that minimizes the amount of material and instrumentation time required for an NMR screen has been lacking.
A model for calculating OMS based on the application of the hypergeometric distribution function to determine the probability of a 'hit' for various mixture sizes and hit rates is presented. An alternative method for the deconvolution of large screening mixtures is also discussed.
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PubMed Central. Vincent, Amy E. Mitochondrial functions are intrinsically linked to their morphology and membrane ultrastructure. Characterizing abnormal mitochondrial structural features may thus provide insight into the underlying pathogenesis of inherited and acquired mitochondrial diseases.