Protein surface conservation in binding sites

An algorithm is described which uses the conservation of the 3D structure of protein surfaces, as opposed to their sequences, to detect protein-protein binding sites. The protein in which protein-protein binding sites are sought is compared with structures of multiple structurally related proteins and the surface that is conserved at least once is considered to be a part of the binding site. The binding site predictions obtained in this way for a set of protein-protein complexes correspond well with the actual protein-protein binding sites. A comparison of this method with an algorithm using the support vector machine approach for predicting protein-protein binding sites shows structural conservation to be an important characteristic that distinguishes binding sites from the remainder of protein surfaces.     

Application of X-ray fluorescence analytical techniques in phytoremediation and plant biology studies

Phytoremediation is an emerging technology that employs the use of higher plants for the clean-up of contaminated environments. Progress in the field is however handicapped by limited knowledge of the biological processes involved in plant metal uptake, translocation, tolerance and plant–microbe–soil interactions; therefore a better understanding of the basic biological mechanisms involved in plant/microbe/soil/contaminant interactions would allow further optimization of phytoremediation technologies. In view of the needs of global environmental protection, it is important that in phytoremediation and plant biology studies the analytical procedures for elemental determination in plant tissues and soil should be fast and cheap, with simple sample preparation, and of adequate accuracy and reproducibility. The aim of this study was therefore to present the main characteristics, sample preparation protocols and applications of X-ray fluorescence-based analytical techniques (energy dispersive X-ray fluorescence spectrometry—EDXRF, total reflection X-ray fluorescence spectrometry—TXRF and micro-proton induced X-ray emission—micro-PIXE). Element concentrations in plant leaves from metal polluted and non-polluted sites, as well as standard reference materials, were analyzed by the mentioned techniques, and additionally by instrumental neutron activation analysis (INAA) and atomic absorption spectrometry (AAS). The results were compared and critically evaluated in order to assess the performance and capability of X-ray fluorescence-based techniques in phytoremediation and plant biology studies. It is the EDXRF, which is recommended as suitable to be used in the analyses of a large number of samples, because it is multi-elemental, requires only simple preparation of sample material, and it is analytically comparable to the most frequently used instrumental chemical techniques. The TXRF is compatible to FAAS in sample preparation, but relative to AAS it is fast, sensitive and multi-elemental. The micro-PIXE technique requires rather expensive instrumentation, but offers multi-elemental analysis on the tissue and cellular level.     

Stacking and not solely topology of T3 loops controls rigidity and ammonium ion movement within d(G4T3G4)2 G-quadruplex

A solution state NMR study has shown that d(G4T3G4) in the presence of (15)NH4(+) ions folds into a single bimolecular G-quadruplex structure in which its G-tracts are antiparallel and the two T3 loops span along the edges of the outer G-quartets on the opposite sides of the G-quadruplex core. This head-to-tail topology is in agreement with the topology of the G-quadruplex recently found in the X-ray crystal structure formed by d(G4T3G4) in the presence of K(+) ions [Neidle et al. J. Am. Chem. Soc. 2006, 128, 5480]. In contrast, the presence of K(+) ions in solution resulted in a complex ensemble of G-quadruplex structures. Molecular models based on NMR data demonstrate that thymine loop residues efficiently base-base stack on the outer G-quartets and in this way stabilize a single structure in the presence of (15)NH4(+) ions. The use of heteronuclear NMR enabled us to localize three (15)NH4(+) ion binding sites between pairs of adjacent G-quartets and study the kinetics of their movement. Interestingly, no (15)NH4(+) ion movement within the G-quadruplex was detected at 25 degrees C. At 35 degrees C we were able to observe slow movement of (15)NH4(+) ions from the outer binding sites to bulk solution with the characteristic residence lifetime of 1.2 s. The slow movement of (15)NH4(+) ions from the outer binding sites into bulk solution and the absence of movement from the inner binding site were attributed to steric hindrance imposed by the T3 loops and the rigidity of the G-quadruplex.     

Infrared spectrum of 4-methoxypicolinic acid N-oxide: computation of asymmetric O-H stretching band

In this article we studied the strong intramolecularly hydrogen-bonded system 4-methoxypicolinic acid N-oxide. The potential energy surface V = V(rOH,rOO) and the corresponding dipole moment function were calculated using the DFT B3LYP/6-31+G(d,p) level of approximation. The time-independent vibrational Schr?dinger equation was solved using a rectangular grid basis set and shifted Gaussian basis set. The vibrational spectrum and metric parameters were also calculated. Effects of deuteration were considered. The calculated vibrational spectra were compared with the experimental spectra. The vibrational transition corresponding to asymmetric O-H stretching that occurs at about 1400 cm-1 compares well with the experimentally assigned O-H asymmetric stretching band centered at 1380 cm-1. The corresponding asymmetric O-D stretching band was predicted to be at 1154 cm-1, while the experimental O-D band was not assigned due to its very low intensity. Several overtones and hot transitions of significant intensities were located in the vicinity of the fundamental O-H stretching frequency, effectively broadening the infrared absorption attributed to the O-H stretching mode. This is in a good agreement with the observed broad protonic absorptions found in the infrared spectra of the title compound and its analogs. We have shown that the Gaussian basis set is the method of choice for a two-dimensional vibrational problem that requires several hundreds of vibrational basis functions and when high accuracy of the eigenvalues is required or when extending the calculations to more vibrational degrees of freedom. We have also demonstrated that for a large number of basis functions the Gramm-Schmidt orthogonalization procedure outperforms symmetric and canonical orthogonalization schemes.     

Analysis of sample of highly water-soluble Th-symmetric fullerenehexamalonic acid C66(COOH)12 by ion-chromatography and capillary electrophoresis

Ion chromatography (IC) was used to establish isomer purity of the highly water-soluble sample of fullerenehexamalonic acid, Th-symmetric hexakis-adduct C66(COOH)12. Sharp and symmetric peaks were obtained by IC using 1.0 M potassium hydroxide as eluent and applying gradient elution program. The identity of the two largest peaks in the chromatogram was assigned to Th-C66(COOH)12 and C66H(COOH)11. The developed IC procedure can be used for the semi-quantitative determination of the extent of the partial decarboxylation of the sample. As an alternative analytical technique, a CE procedure was introduced and its performance against IC was compared for this particular case.     

Approach to nonadiabatic transitions by density matrix evolution and molecular dynamics simulations

Many biological processes are characterized by an essentially quantum dynamical event, such as electron or proton transfer, in a complex classical environment. To treat such processes properly by computer simulation, allowing nonadiabatic transitions involving excited states, we recently developed a density matrix evolution (DME ) method [H. J. C. Berendsen and J. Mavri, J. Phys. Chem, 97 , 13464 (1993)] which simulates the dynamics of quantum systems embedded in a classical environment. The formalism of the method is presented and an overview of the applications ranging from collisions of a quantum harmonic oscillator with noble gas atoms to proton tunneling in a double-well hydrogen bond is given. The methodology for treatment of proton-transfer processes with inclusion of excited states is presented. Future application of the method on biologically interesting processes, such as proton transfer in enzymatic reactions, is discussed. © 1996 John Wiley & Sons, Inc.     

Monolithic chromatography for elemental and speciation analysis

Monolithic supports are increasingly used in the field of chromatography. They are appropriate for different applications (e.g., separation of biomolecules, organic acids and inorganic anions). However, only a few research groups are investigating the potential of using monolithic phases for rapid separation of metal cations and elemental speciation analysis.Monolithic supports based on porous monolithic silica have been successfully applied in separation of alkaline-earth and transition-metal cations in environmental waters and high ionic-strength samples.The present review covers applications of monolithic supports for chromatographic separation of metal cations and the potential for using monolithic chromatography in elemental speciation analysis. We critically evaluate the performances and the advantages of monolithic supports and compare them to conventional particle-packed chromatographic supports.     

Edge, vertex and mixed fault diameters

Let denote the maximum diameter among all subgraphs obtained by deleting q edges of G. Let denote the maximum diameter among all subgraphs obtained by deleting p vertices of G. We prove that for all meaningful a. We also define mixed fault diameter , where p vertices and q edges are deleted at the same time. We prove that for 0<la, , and give some examples.     

Influence of the soil matrices on the analytical performance of headspace solid-phase microextraction for organotin analysis by gas chromatography-pulsed flame photometric detection

Organotin compounds (OTCs) have been identified in a variety of environmental media (air, surface water, groundwater, soil and sediments). In the past, much attention was assigned to the study of the OTCs content in biological samples, water and sediments. Little information about OTCs in soil is available. In this work, a procedure for butyl and phenyltin determination in soils by headspace-solid-phase microextraction (HS-SPME) gas chromatography-pulsed flame photometric detection (GC-PFPD) was investigated. For SPME analysis, a polydimethylsiloxane (PDMS) coating was applied. Peat soil rich in organic matter and with a high cation-exchange capacity (CEC), and clay soil low in organic matter and with a low CEC were analysed. The influence of these different soil matrices on HS-SPME analysis was evaluated by spiking of samples. In general, the recoveries for the two spiked soils exceeded 80%. The repeatability of the method was better than 10%. The limits of detection (LODs) and limits of quantification (LOQs) were in the ng S ng(-1) range. The technique may be reliably applied for the determination of butyltins and monophenyltin in soils, while it shows some limitations for the analysis of di- and triphenyltin (TPhT).     

Differentiation of Borrelia burgdorferi sensu lato species by temperature gradient gel electrophoresis

Borrelia burgdorferi sensu lato is a multispecies complex of pathogenic spirochetes, causing Lyme borreliosis. Due to clinical, epidemiological, and taxonomical implications, there is a need for identification of isolated Borrelia strains. In the present study, we have optimized TGGE for B. burgdorferi sensu lato species differentiation and the results were compared with two reference methods, namely PFGE and restriction of 5S-23S intergenic space region PCR product. A differentiation of B. garinii, B. afzelii, and B. burgdorferi senso stricto species with TGGE was possible and intraspecies variation was detected. Results compared between TGGE, PFGE, and restriction of 5S-23S intergenic space region PCR product showed no difference in specificity of species identification.