Biomedical subjects

Bi Cheng Wang

Publications and source records attributed to Bi Cheng Wang.

5 recordsLinked to original sources

PubMed2005

SGXPro: a parallel workflow engine enabling optimization of program performance and automation of structure determination.

SGXPro consists of four components. (i) A parallel workflow engine that was designed to automatically manage communication between the different processes and build systematic searches of algorithm/program/parameter space to generate the best possible result for a given data set. This is performed by offering the user a palette of programs and techniques commonly used in X-ray structure determination in an environment that lets the user choose programs in a mix-and-match manner, without worrying about inter-program communication and file formats, during the structure-determination process. The current SGXPro program palette includes 3DSCALE, SHELXD, ISAS, SOLVE/RESOLVE, DM, SOLOMON, DMMULTI, BLAST, AMoRe, EPMR, XTALVIEW, ARP/wARP and MAID. (ii) A client/server architecture that allows the user to utilize the best computing facility available. (iii) Plug-in-and-play design, which allows easily integration of new programs into the system. (iv) User-friendly interface.

Crystallography, X-Ray↗

PubMed2005

Away from the edge II: in-house Se-SAS phasing with chromium radiation.

Recently, the demands of high-throughput macromolecular crystallography have driven continuous improvements in phasing methods, data-collection protocols and many other technologies. Single-wavelength anomalous scattering (SAS) phasing with chromium X-ray radiation opens a new possibility for phasing a protein with data collected in-house and has led to several successful examples of de novo structure solution using only weak anomalous scatterers such as sulfur. To further reduce data-collection time and make SAS phasing more robust, it is natural to combine selenomethionine-derivatized protein (SeMet protein) with Cr Kalpha radiation to take advantage of the larger anomalous scattering signal from selenium (f'' = 2.28 e(-)) compared with sulfur (f'' = 1.14 e(-)). As reported herein, the crystal structure of a putative chorismate mutase from Clostridium thermocellum was determined using Se-SAS with Cr Kalpha radiation. Each protein molecule contains eight selenomethionine residues in 148 amino-acid residues, providing a calculated Bijvoet ratio of about 3.5% at the Cr Kalpha wavelength. A single data set to 2.2 A resolution with approximately ninefold redundancy was collected using an imaging-plate detector coupled with a Cr source. Structure solution, refinement and deposition to the Protein Data Bank were performed within 9 h of the availability of the scaled diffraction data. The procedure used here is applicable to many other proteins and promises to become a routine pathway for in-house high-throughput crystallography.

Chorismate Mutase↗

PubMed2005

On increasing protein-crystallization throughput for X-ray diffraction studies.

Two recent developments, a novel screening/optimization strategy that considerably reduces the number of trials required to produce diffraction-size crystals and a simple modification that doubles the screening capacity of the Douglas Instruments ORYX 1-6 protein-crystallization robot, have been implemented into a structural genomics project. The new two-step screening/optimization strategy yields diffraction-quality crystals directly from the screening process, reducing the need for further optimization. The ORYX modification involves the addition of extensions to the sample- and oil-delivery arms and software modifications that allow two plates to be set up simultaneously.

Crystallization↗

PubMed2003

Crystallization and preliminary X-ray diffraction analysis of lectin-1 from Pseudomonas aeruginosa.

Carbohydrate recognition plays a role in the pathogenesis of Pseudomonas aeruginosa, a common cause of opportunistic infection in humans. Crystals of a carbohydrate-binding protein from P. aeruginosa, lectin PA-1, have now been obtained. The crystals belong to space group I222, with unit-cell parameters a = 40.25, b = 72.30, c = 133.82 A, and diffract to beyond 1.9 A resolution on a rotating-anode X-ray source. Details of crystal-growth conditions, diffraction data collection and processing are reported.

Crystallization↗

PubMed2002

Towards the crystal structure of glycerol dehydrogenase from Thermotoga maritima.

The NAD(+)-dependent glycerol dehydrogenase (EC 1.1.1.6) from the extremely thermophilic bacterium Thermotoga maritima has been crystallized in the presence of glycerol by the hanging-drop vapour-diffusion method using 2-methyl-2,4-pentanediol (MPD) as the precipitating agent. Crystals of the enzyme complexed with NAD(+) have also been obtained. The crystals belong to the tetragonal system with space group I422 and unit-cell parameters a = 105.3, c = 134.5 A. They diffract to a maximum resolution of 1.4 A using synchrotron radiation (lambda = 0.838 A). Crystals of the enzyme-NAD(+) complex diffract to 2.5 A resolution using in-house Cu Kalpha radiation.

Crystallography, X-Ray↗