On the use of dense matrix techniques within sparse simplex

In this paper we discuss some instances where dense matrix techniques can be utilized within a sparse simplex linear programming solver. The main emphasis is on the use of the Schur complement matrix as a part of the basis matrix representation. This approach enables to represent the basis matrix as an easily invertible sparse matrix and one or more dense Schur complement matrices. We describe our variant of this method which uses updating of the QR factorization of the Schur complement matrix. We also discuss some implementation issues of the LP software package which is based on this approach.     

In situ Fourier transform infrared spectroscopy as an efficient tool for determination of reaction kinetics

The performance of new FTIR-based monitoring technology to representatively determine reaction kinetics has been demonstrated on an example of homogeneously catalyzed liquid-phase sucrose hydrolysis to fructose and glucose. The reaction kinetics were investigated by using the ReactIR 1000 reaction analysis system, which enables determination of the component concentration from its characteristic FTIR spectrum. During the sucrose inversion, the ReactIR 1000 instrument connected to a computer controlled standard glass batch reactor provided the required operating conditions and information about the component concentration in real-time. We have studied the influence of hydrogen ion concentration, temperature and initial concentration of sucrose on the sucrose disappearance rate. It was found out that the inversion of sucrose is an irreversible reaction, which is not affected by the formation of fructose and glucose in the liquid-phase. Then, the parameters of the kinetic model (i.e., reaction rate constant and activation energy) were calculated. A comparison of the model output and the measured data showed that the kinetics of the sucrose inversion could be well described by means of the pseudo first-order kinetic model. Finally, the method of determining the kinetic model by FTIR spectroscopy was verified by comparing the results obtained in the batch reactor with the results obtained in the continuously stirred tank reactor.     

Heterogeneity of cardiac rat and human elongation factor 2

Elongation factor 2 (EF-2) catalyses the last step of the elongation cycle, translocation, in the course of protein biosynthesis. A system for analyzing post-translational modifications of EF-2, which is a single polypeptide of 857 amino acids, is reported and its application to cytosolic extracts of cultured neonatal rat heart myocytes, neonatal and adult rat cardiac tissue, and extracts of human left ventricular myocardium is described. Comparing different pH ranges in immobilized pH gradient-isoelectric focusing (IPG-IEF), a range of pH 3 - 10 and 4 - 9 resulted in a highly defined and reproducible resolution of six different EF-2 variants of all extracts in the first dimension. These six variants were detected by the "imaging plate" (phosphor radiation image sensor) after specific labeling with Pseudomonas exotoxin A catalyzed [32P]ADP-ribosylation. This finding could be confirmed in Western blot analysis with a specific polyclonal rabbit antibody. Using two-dimensional polyacrylamide gel electrophoresis (2-D-PAGE), five to six EF-2 variants could be demonstrated in all extracts. By application of a second IPG indicator strip to the 2-D gel, they could be aligned with corresponding spots in a silver-stained 2-D separation of human myocardial tissue, revealing that the EF-2 variants belong to the group of low-abundance proteins.     

Exploring the local conformational space of a membrane protein by site-directed spin labeling

Molecular modeling based on a hybrid evolutionary optimization and an information condensation algorithm, called GHOST, of spin label ESR spectra was applied to study the structure and dynamics of membrane proteins. The new method is capable of providing detailed molecular information about the conformational space of the spin-labeled segment of the protein in a membrane system. The method is applied to spin-labeled bacteriophage M13 major coat protein, which is used as a model membrane protein. Single cysteine mutants of the coat protein were labeled with nitroxide spin labels and incorporated in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. The new computational method allows us to monitor distributions of local spatial constraints and molecular mobility, in addition to information about the location of the protein in a membrane. Furthermore, the results suggest that different local conformations may coexist in the membrane protein. The knowledge of different local conformations may help us to better understand the function-structure relationship of membrane proteins.     

Phospholipid mesophases at solid interfaces: in-situ X-ray diffraction and spin-label studies

In this work, we report on recent investigations, both on the global and on the local molecular architecture of supported phospholipid model membranes. A brief theoretical introduction explains how global structural information on supramolecular lipid ensembles can be retrieved from surface X-ray diffraction measurements as well as how spin-label electron paramagnetic resonance spectroscopy (EPR) provides complementary information on the local environment of probe molecules. The combination of especially designed X-ray cells with the technique of small- and wide-angle X-ray surface scattering makes it possible to explore various fields of lipid research and its applications. Examples for different physico-chemical conditions are presented: (i) in situ chemistry under excess of water conditions demonstrating how solid-supported lipid films sense salinity, (ii) the 3D electron density reconstruction of a vesicle-fusion intermediate under controlled humidity, and (iii) complementary temperature and pressure effects on oriented phospholipid samples. Further, special attention has been given to the influence of different film preparation techniques with respect to quality and the defect structure manifestation. To resolve the proportions and local properties of defects in a hydrated lipid-deposited surface, spin-label EPR was applied. The results from 9.6 GHz EPR as well as from 1.2 GHz EPR suggest the alignment to be in the range between 30% and 80%. In addition, slow time-dependent EPR measurements point to nano-structural rearrangements due to water flow and reduction of alignment quality.     

MECHANISM OF BIOLUMINESCENCE, CHEMI-LUMINESCENCE AND ENZYME FUNCTION IN THE OXIDATION OF FIREFLY LUCIFERIN*,†

Abstract— The chemical steps and the products of the bioluminescent and chemiluminescent oxidations of firefly luciferin are elucidated. The colors of firefly bioluminescence can be explained in terms of different ionic excited states and spectral shifts due to changes in molecular environment. Firefly luciferase undergoes conformational changes during catalysis. There are two sites for light production per 100,000 mW. A regulatory mechanism involving dehydro-luciferin is proposed for control of firefly flashing.     

Synthesis of 3‐thiocyanato‐1H,3H‐quinoline‐2,4‐diones

4‐Hydroxy‐1H‐quinolin‐2‐ones ( 1 ) react with thiocyanogen in acetic acid to the corresponding 3‐thiocyanato‐1H,3H‐quinoline‐2,4‐diones ( 2 ) in good yields. In some cases, 3‐bromo‐1H,3H‐quinoline‐2,4‐diones ( 4 ) were isolated as minor reaction products. Compounds 2 are very reactive towards nucleophiles and easily hydrolyze to the corresponding 4‐hydroxy‐1H‐quinoline‐2‐ones ( 1 ).