Factor Xa: Simulation studies with an eye to inhibitor design

Factor Xa is a serine protease which activates thrombin and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is at the crossroads of the extrinsic and intrinsic pathways of coagulation and, hence, has become an important target for the design of anti-thrombotics (inhibitors). It is not known to be involved in other processes than hemostasis and its binding site is different to that of other serine proteases, thus facilitating selective inhibition. The design of high-affinity selective inhibitors of factor Xa requires knowledge of the structural and dynamical characteristics of its active site. The three-dimensional structure of factor Xa was resolved by X-ray crystallography and refined at 2.2 Å resolution by Padmanabhan and collaborators. In this article we present results from molecular dynamics simulations of the catalytic domain of factor Xa in aqueous solution. The simulations were performed to characterise the mobility and flexibility of the residues delimiting the unoccupied binding site of the enzyme, and to determine hydrogen bonding propensities (with protein and with solvent atoms) of those residues in the active site that could interact with a substrate or a potential inhibitor. The simulation data is aimed at facilitating the design of high-affinity selective inhibitors of factor Xa.     

Photodetection with 5-Aminolevulinic acid-induced protoporphyrin IX in the rat abdominal cavity: drug-dose-dependent fluorescence kinetics

In 75% of cases, ovarian carcinoma has already metastasized in the abdominal cavity at the time of diagnosis. For determination of the necessity for a supplementary therapy, in addition to surgical resection, it is important to localize and stage microscopical intraperitoneal metastases of the tumor. Intraperitoneal photodetection of tumor metastases is based on preferential tumor distribution of a fluorescent tumor marker. The time-dependent differences in drug concentration between tumor and normal (T/N) tissues can be used to visualize small tumors. We performed fluorescence measurements on abdominal organs and tumor in the peritoneal cavity of rats. 5-Aminolevulinic acid (ALA)-induced protoporphyrin IX (PpIX) was used as the fluorescent marker. Three different drug doses (100, 25 and 5 mg/kg) were used and PpIX fluorescence profiles were followed up to 24 h after intravenous administration. Maximum T/N ratios were found 2-3 h after administration of ALA with all drug doses. A significant T/N tissue contrast was obtained for all abdominal organs tested after administration of 5 mg/kg.     

水+3-甲基吡啶+溴化钠三元溶液临界跨接现象

采用折射率法在较宽温度范围内研究了溴化钠、3-甲基吡啶和水的临界质量分数分别为0.240、0.192和0.568体系的临界性质, 发现在近临界点临界指数为0.365, 与Fishe重整化值一致. 有效临界指数随着温度逐渐远离临界点, 从0.365下降到0.20左右, 但当排除了“正规项”的影响后, 展现出向平均场理论值0.5单调跨接的行为.     

Metal speciation dynamics in colloidal ligand dispersions

In this work we propose a dynamic metal speciation theory for colloidal systems in which the complexing ligands are localized on the surface of the particles; i.e., there is spatial heterogeneity of binding sites within the sample volume. The differences between the complex formation and dissociation rate constants of complexes in colloidal dispersions and those in homogeneous solutions originate from the differences in kinetic and mass transport conditions. In colloidal systems, when the effective rate of dissociation of the surface complexes becomes fully diffusion controlled, its value is defined via the geometrical parameters of the particle. We assess the extent to which the conventional approach of assuming a homogeneously smeared-out ligand distribution overestimates the lability of surface complexes in colloidal ligand dispersions. The validity of the theory is illustrated by application to binding of lead and cadmium by carboxyl modified latex particles: our approach correctly predicts the formation/dissociation rate constants, which differ by several orders of magnitude from their homogeneous solution counterparts.     

Nonaqueous suspensions of laponite and montmorillonite

It is shown how stable, nonaqueous suspensions of fully exfoliated smectite clays such as Laponite and montmorillonite can be obtained. Suspensions in toluene and in a branched aliphatic solvent (polydecene) were characterized using elemental analysis, rheometry, and small-angle X-ray scattering. For Laponite, stable suspensions were obtained by adsorbing a dichain poly(isobutylene) based stabilizer to the particles. This approach did not result in full exfoliation for montmorillonite particles, possibly because the stabilizer was able to connect individual clay sheets at the edges during the treatment process. Instead, a quaternary ammonium surfactant, dimethyl dioctadecylammonium bromide (DODAB), was first adsorbed to the clay. Subsequently, adsorption of the poly(isobutylene) based stabilizer to this pretreated clay resulted in fully exfoliated suspensions of montmorillonite. Suspensions of clay particles treated only with DODAB have been studied by several authors before and are included in this study for comparison. A detailed discussion of the suspension behavior of the different clay samples is given. The suspension routes presented here may enable further studies of the structure and flow behavior of suspensions of thin, flexible clay platelets as a function of aspect ratio.     

Stroboskopisehe Untersuchungen über den zeitlichen Aufbau,die optische Absorption und das Nachleuchten gesteuerter Funkenentladungen

Zusammenfassung In elektrischen Funkenentladungen lassen sich Zündphase, Bogenphase und Abklingphase unterscheiden, die besondere charakteristische Eigenschaften aufweisen. Ihre Untersuchung wird durch ein neu entwickeltes Stroboskop ermöglicht, dessen Phasenlage beliebig gegenüber der periodischen Funkenfolge verstellt werden kann. Durch optische Absorption kann im abklingenden Funken nicht nur der atomare Metalldampf durch seine Grundlinien nachgewiesen werden, sondern auch seine molekularen Reaktionsprodukte mit der umgebenden Atmosphäre lassen sich durch Bandenabsorption feststellen. Das Nachleuchten abklingender Funkenentladungen wird im wesentlichen durch das Nachleuchten des aktiven Stickstoffs getragen, wenn der Metalldampfgehalt der Funkenstrecke gering gehalten wird. Gegen Ende der Nachleuchtphase lassen sich Sprüherscheinungen an den Elektroden feststellen, bei denen kleine Partikelchen mit unterschiedlichen, zum Teil spiralig verlaufenden Bahnkurven ausgeschleudert werden. Die Flugbahnen der Teilchen weisen auf starke Gasströmungen in der Funkenstrecke hin.

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Summary In electrical spark discharges it is possible to distinguish ignition phase, arc phase, and decay phase. These display special characteristic properties. It is possible to study them by means of a newly developed stroboscope, whose phase position can be adjusted at will against the periodic succession of sparks. Through optical absorption, not only the atomic metal vapor can be detected, through its ground lines, in the decaying sparks but also its molecular reaction products with the surrounding atmosphere can be established through the band spectrum. The phosphorescence of decaying spark discharges is essentially due to the afterglow of the active nitrogen, if the metal vapor of the spark gap is kept low. Toward the end of the phosphorescence phase, spray phenomena may be observed at the electrodes, in which tiny particles with distinctive, in part spiral, orbital curves are ejected. The flight paths of these particles indicate strong gas currents in the spark gap.

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Résumé On peut distinguer dans la décharge par étincelles, la phase d'ignition, la phase d'arc et la phase de décroissance. On explique ainsi certaines propriétés caractéristiques. On peut étudier ces diverses phases à l'aide d'un dispositif stroboscopique nouveau réglable à volonté pour observer la même phase d'étincelles qui se succèdent périodiquement. Grâce a l'absorption optique on peut détecter soit une vapeur atomique métallique par ses raies caractéristiques pendant la période de décroissance des étincelles, soit les réactions moléculaires qui se produisent dans les gaz environnants grâce aux spectres de bandes. La phosphorescence pendant la décroissance de l'étincelle est due essentiellement à la postluminescence de l'azote actif, si la tension de vapeur du métal entre les électrodes est suffisamment basse. Pendant la fin de la période de phosphorescence on observe sur les électrodes des phénomènes de pulvérisation avec formation de très petites particules qui sont éjectées en décrivant des trajectoires en spirales. Les trajectoires aériennes de ces particules révèlent l'existence de forts courants gazeux entre les électrodes.

     

Infrared spectra of gas-phase V(+)-(benzene) and V(+)-(benzene)(2) complexes

The organometallic ions V+-(benzene) and V+-(benzene)2 are produced by laser vaporization in a pulsed nozzle source. They are trapped and mass selected in an ion-trap/time-of-flight mass spectrometer, and their infrared spectra are measured with resonance-enhanced multiphoton photodissociation (IR-REMPD) spectroscopy with a tunable free-electron laser. Vibrational bands in the 600-1800 cm-1 region are characteristic of the benzene molecular moiety perturbed by the metal cation bonding. Experimental data are compared to the IR spectra derived from density functional calculations. Vibrational patterns in V+-(C6H6) indicate that the metal is bound in an eta6 pi-bonding configuration, while V+-(C6H6)2 is a sandwich. Trapped-ion IR-REMPD is a general method to access the vibrational spectroscopy of organometallic ions and their clusters.     

Single molecule spectroscopy as a probe for dye-polymer interactions

Experimental (Single Molecule Spectroscopy) and theoretical (quantum-chemical calculations and Monte Carlo and molecular dynamics simulations) techniques are combined to investigate the behavior and dynamics of a polymer-dye molecule system. It is shown that the dye molecule of interest (1,1'-dioctadecyl-3,3,3',3'-tetramethylindo-dicarbocyanine) adopts two classes of conformations, namely planar and nonplanar ones, when embedded in a poly(styrene) matrix. From an in-depth analysis of the fluorescence lifetime trajectories, the planar conformers can be further classified according to the way their alkyl side chains interact with the surrounding poly(styrene) chains.     

Time-resolved EPR study of the photophysics and photochemistry of 1-(3-(methoxycarbonyl)propyl)-1-phenyl[6.6]C61

Time-resolved (TR) EPR was used to study the photophysics and photochemistry of 1-(3-(methoxycarbonyl)propyl)-1-phenyl[6.6]C61 (M1). The CW TREPR spectra of M1 in the photoexcited triplet state, frozen in a rigid matrix and in liquid solution at room temperature, were compared with those of 3C60. The introduction of the substituent on C60 has a striking effect on the spectra of the triplets, which is attributed to the lifting of the orbital degeneracy by the reduction in symmetry. Fourier transform (FT) EPR was used in an investigation of electron-transfer reactions in liquid solutions mediated by 3M1. Of particular interest was the system of M1/chloranil (CA)/perylene (Pe). Photoexcitation of M1 is found to lead to the formation of the chloranil anion radical and the perylene cation radical. From the chemically induced dynamic electron polarization (CIDEP) patterns in the FTEPR spectra and the dependence of the reaction kinetics on reactant concentrations, it was deduced that CA- is formed by two competing pathways following photoexcitation of M1: (1) direct electron transfer from 3M1 to CA followed by electron transfer from Pe to M1+ and (2) energy transfer from 3M1 to Pe followed by oxidative quenching of 3Pe by CA. In both pathways, M1 acts as a light-energy harvester and mediator of electron-transfer reactions from Pe to CA without itself being consumed in the process, that is, as a photocatalyst. It is found that the functionalization of C60 makes its triplet state a worse electron donor and acceptor, but it has no significant effect on the triplet energy transfer reaction.     

Characterisation of botulinum toxins type C, D, E, and F by matrix-assisted laser desorption ionisation and electrospray mass spectrometry

In a follow-up of the earlier characterisation of botulinum toxins type A and B (BTxA and BTxB) by mass spectrometry (MS), types C, D, E, and F (BTxC, BTxD, BTxE, BTxF) were now investigated. Botulinum toxins are extremely neurotoxic bacterial toxins, likely to be used as biological warfare agent. Biologically active BTxC, BTxD, BTxE, and BTxF are comprised of a protein complex of the respective neurotoxins with non-toxic non-haemagglutinin (NTNH) and, sometimes, specific haemagglutinins (HA). These protein complexes were observed in mass spectrometric identification. The BTxC complex, from Clostridium botulinum strain 003-9, consisted of a 'type C1 and D mosaic' toxin similar to that of type C strain 6813, a non-toxic non-hemagglutinating and a 33 kDa hemagglutinating (HA-33) component similar to those of strain C-Stockholm, and an exoenzyme C3 of which the sequence was in full agreement with the known genetic sequence of strain 003-9. The BTxD complex, from C. botulinum strain CB-16, consisted of a neurotoxin with the observed sequence identical with that of type D strain BVD/-3 and of an NTNH with the observed sequence identical with that of type C strain C-Yoichi. Remarkably, the observed protein sequence of CB-16 NTNH differed by one amino acid from the known gene sequence: L859 instead of F859. The BTxE complex, from a C. botulinum isolated from herring sprats, consisted of the neurotoxin with an observed sequence identical with that from strain NCTC 11219 and an NTNH similar to that from type E strain Mashike (1 amino acid difference with observed sequence). BTxF, from C. botulinum strain Langeland (NCTC 10281), consisted of the neurotoxin and an NTNH; observed sequences from both proteins were in agreement with the gene sequence known from strain Langeland. As with BTxA and BTxB, matrix-assisted laser desorption/ionisation (MALDI) MS provided provisional identification from trypsin digest peptide maps and liquid chromatography-electrospray (tandem) mass spectrometry (LC-ES MS) afforded unequivocal identification from amino acid sequence information of digest peptides obtained in trypsin digestion.