|Necessity of quantum mechanics for predicting binding free energy|
Ting Zhou, Danzhi Huang, Amedeo Caflisch
We demonstrate the necessity of quantum mechanics (QM) for predicting binding free energy by comparing the results of the linear interaction energy model with continuum model (LIECE) and the equivalent model with QM (QMLIECE).
|Resorufin - a lead for a new protein kinase CK2 inhibitor |
Iben Skjøth Sandholt1, Birgitte Brinkmann Olsen1, Barbara Guerra1, Olaf-Georg Issinger1, Brigitte Boldyreff2
Screening of a natural compound library led to the identification of resorufin, as a highly selective and potent inhibitor for protein kinase CK2. Out of 52 kinases tested only CK2 was inhibited. The IC50 values determined for the CK2 holoenzymes were 1.5 µM and for the free catalytic subunits ca. 4 µM. In different cancer cell lines treatment with resorufin led to cell death and endogenous CK2 was inhibited.
|MED-SuMo and MED-Hybridise: exploit all PDB macromolecule structures to design/optimize innovative leads|
Moriaud F., Oguievetskaia K., Adcock S.A., Vorotynsev A.M., Martin L., Doppelt-Azeroual O. and Delfaud F.
Obtaining structural information on fragment-protein target is a key factor and also a major limitation. We’ve used MED-SuMo and MED-Hybridise to query and mine the PDB seeking for similar interaction surfaces. MED-portions were used to design novel scaffolds (GPCR) and decorate a given scaffold (kinase). We have analysed the scaffolds in regard to their diversity, their presence in PubChem, PDB and other libraries.
|Production of prostanoids in the plant Arabidopsis thaliana|
Maged E. Mohamed and Colin M. Lazarus.
Prostanoids originate from PGHS action on the 20-carbon polyunsaturated fatty acid: DGLA, AA and EPA. We used cDNA expression in Saccharomyces cerevisiae and enzyme immunoassays to compare the activities of two mouse PGHS isoforms and cDNAs encoding mouse prostaglandin I synthase and thromboxane A synthase and genomic DNA encoding Trypanosoma brucei prostaglandin F synthase. All genes were active and were put in Transgenic Arabidopsis thaliana plants producing DGLA.
|Biosynthesis of Very Long Chain Polyunsaturated Fatty Acids in Chicory|
Hattem Mekky1, Michael R. Davey1, J. Brian Power1 , Maged E. Mohamed2 and Colin M. Lazarus2
Very long chain polyunsaturated fatty acids (VLCPUFAs) are declining in reserves, since they are produced by oily fish. VLCPUFAs are important in human nutrition because they are responsible for the production of inflammatory mediators such as prostaglandins, the regulation of cholesterol synthesis and its transport, and the maintenance of cellular membranes. This research aims to produce VLCPUFAs in edible plants.
|qPCRas a primary screen in drug discovery|
GauravJaggi, Frank Boeckler, Andreas Joerger and Alan Fersht
We report the use of qPCR technique to follow the thermal unfolding of proteins by the binding of the dye SYPRO Orange, and exploit its potential as a robust and high-throughput primary screen for small molecule drug discovery.
|Heterochromatin structure is induced by siRNA targeting HIV-1 promoter region |
K Suzuki1, H Lim1,3, T Ishida2, T Watanabe2, D Cooper1,3, A Kelleher1,3
We transfected siRNA targeting HIV-1 promoter region into a cell line productively infected with HIV-1. ChIP analysis revealed that the RNA duplex induced transcriptional gene silencing and enrichment of Ago1, H3K9me2, and HDAC1 in HIV promoter region to form heterochromatin structure. The data indicates RNA duplex induces the latent phase of HIV infection, since the chromosome formation is very similar to the state of HIV latently infected cell lines
|Evolution of the Contact Phase of Vertebrate Blood Coagulation|
M. B. Ponczek, D. Gailani and R. F. Doolittle
Three proteases involved in the contact phase of vertebrate blood coagulation were searched in genomes of amphibians, birds and mammals. Several data sources were used during this bioinformatics analysis. Our survey confirmed that the vertebrate contact phase has occurred by way of a series of gene duplications during the course of several hundred million years of evolution, beginning with the appearance of fXII and a PK-fXI predecessor in amphibians.
|Drop distribution determination in a liquid-liquid dispersion by image processing|
Brás, L.M.R., Gomes E.F., Ribeiro M. M. M., Guimarães M. M. L.
Image processing is a very relevant area of computer science with applications in many domains. Quantitative analysis and interpretation of digitized images is currently an important tool in several scientific domains. The aim of the present work is the development of shape discrimination and size classification algorithms for liquid drops in monochromatic digitized frames.