Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials

We describe the application of knowledge-based potentials implemented in the MOE program to compare the ligand-binding sites of several proteins. The binding probabilities for a polar and a hydrophobic probe are calculated on a grid to allow easy comparison of binding sites of superimposed related proteins. The method is fast and simple enough to simultaneously use structural information of multiple proteins of a target family. The method can be used to rapidly cluster proteins into subfamilies according to the similarity of hydrophobic and polar fields of their ligand-binding sites. Regions of the binding site which are common within a protein family can be identified and analysed for the design of family-targeted libraries or those which differ for improvement of ligand selectivity. The field-based hierarchical clustering is demonstrated for three protein families: the ligand-binding domains of nuclear receptors, the ATP-binding sites of protein kinases and the substrate binding sites of proteases. More detailed comparisons are presented for serine proteases of the chymotrypsin family, for the peroxisome proliferator-activated receptor subfamily of nuclear receptors and for progesterone and androgen receptor. The results are in good accordance with structure-based analysis and highlight important differences of the binding sites, which have been also described in the literature.     

Segmentation of microscope images of living cells

This paper describes a segmentation method combining a texture based technique with a contour based method. The technique is designed to enable the study of cell behaviour over time by segmenting brightfield microscope image sequences. The technique was tested on artificial images, based on images of living cells and on real sequences acquired from microscope observations of neutrophils and lymphocytes as well as on a sequence of MRI images. The results of the segmentation are compared with the results of the watershed and snake segmentation methods. The results show that the method is both effective and practical.

Synthesis and crystal structure of the inter-alkali-metal chloride RbLiCl2

The crystal structure of RbLiCl₂ [a= 1441.3(3), b= 412.57(8), c= 720.9(1) pm, Guinier-Simon data, orthorhombic, Ccmm, No. 63, Z= 4] was determined and refined from single crystal data, R= 0.074, R_W= 0.062. The coordination polyhedron of Rb⁺ is a bicapped trigonal prism, Li⁺ is tetrahedrally coordinated. [LiCl₄] tetrahedra are connected via common corners to undulated layers $\text{∞}\text{2}\text{[}\text{LiCl}{}^{\mathrm{c}}{}_{\mathrm{<mtext>4</mtext><mtext>2</mtext>}}\text{]}{}^{\mathrm{?}}$ parallel to (100). The structure is closely related to that of SrZnO₂.     

Temperature measurements of a high-power microwave feedhorn window

Temperature measurements of a high-power microwave feedhorn window during transmitter operation at 365 kW CW and 8.5 GHz made using an imaging infrared radiometer are discussed. The window under investigation was constructed of HTP-6, a high-thermal-performance material developed to shield the Shuttle Orbiter from the heat of reentry. The measurement technique is described and experimental results are presented. The window performed adequately at 365 kW CW with a center temperature of 475°C. The tests verify that HTP-6 can be used as a window material or a support structure in high-power waveguide at power densities of 1.47 kW/cm² for extended periods of time, with no change in its mechanical characteristics     

Efficient polymer solar cell modules

Polymer solar cell modules based on the standard polymer–fullerene system of to-date, P3HT–PCBM, have been prepared and characterized. We have observed a loss of only 20% when up-scaling the active area of the solar cell by a factor somewhat larger than 10. An average solar cell efficiency of 3% and a module efficiency of 1.9% for three serially interconnected solar cells of 5.4 cm² each are reported. The route for further optimization of module performance is discussed based on analyzing the existing loss factors within this design.     

Comparison of solid-phase microextraction and dynamic headspace methods for the gas chromatographic-mass spectrometric analysis of light-induced lipid oxidation products in milk

This paper describes a general numerical method for the determination of rate constants that characterize the binding of a ligand L simultaneously and competitively to two different receptor molecules, R1 and R2. The experimental data consist of changes in the concentration of one receptor (e.g., R1) monitored over time. An example problem is represented by hirudin (L) binding to thrombin (R1) and to a chemical mutant of thrombin (R2). The published experimental data [Wedemeyer et al. (1997) Anal. Biochem. 248, 130-140], previously analyzed by using an appropriate algebraic method, were reanalyzed here by numerical integration [Kuzmic (1996) Anal. Biochem. 237, 260-273]. This general numerical method offers the following advantages. (1) It provides an estimate for the lower limit on feasible values of association rate constants. (2) It is many orders of magnitude more accurate. (3) It is easily extensible to more complicated reaction mechanisms. (4) It uses a simpler formalism and it is thus more accessible to nonmathematicians. (5) A suitable computer program for the analysis of competitive binding kinetics can be obtained via the Internet (http://www.biokin.com).     

Derivation of HLA-A11/Kb transgenic mice: functional CTL repertoire and recognition of human A11-restricted CTL epitopes

Transgenic mice expressing chimeric human (alpha1 and alpha2 HLA-A11 domains) and murine (alpha3, transmembrane, and cytoplasmic H-2Kb domains) class I molecules were derived. These mice were used as a model system to study the immunogenicity of human CTL epitopes and also to examine the aspects of Ag processing differences of mice vs man. Immunization of these mice with seven known HLA-A11-restricted CTL epitopes emulsified in IFA resulted in vigorous specific CTL responses. A larger panel of 45 A11-binding peptides was used to examine the relationship between immunogenicity in the HLA-A11/Kb transgenic mice and HLA-A11 binding capacity. Twenty-one of 28 (75%) peptides with high binding affinities (50% inhibitory concentration (IC50), 2-50 nM) and 7 of 13 (54%) intermediate binding peptides (IC50, 50-500 nM range) were immunogenic. In parallel, 19 of these peptides were used for in vitro primary immunizations of PBMC derived from HLA-A11 healthy human donors. It was found that 8 of 8 peptides that were able to elicit CTL in primary human in vitro cultures were also immunogenic in HLA-A11/Kb mice. Finally, HLA-A11/Kb transgenic mice were found to generate an A11/Kb restricted CTL response following immunization with influenza virus A/PR/8/34, suggesting that, at least to some extent, A11 epitopes are generated by transgenic mice as a result of natural in vivo processing and presentation.