Recent progress in protein 3D structure comparison

Quantitation of protein 3-D structure similarity is crucial in such fields as evolutionary studies, structural modeling and prediction of biological function. There are various approaches, many of which are tailored to specific problems. This review summarizes the recent developments in this field with particular interest in two main areas: i) improvements to and statistical interpretation of the root-man-square distance between equivalent atoms, rmsd; and ii) methods of protein structural classification based on geometrical features. Special attention is given to fast methods capable of analyzing large structural databases.     

The photoelectron spectrum of tetramethyldiazetine: The elucidation of ring size effects on azo group ionization potentials

The photoelectron spectrum of 3,3,4,4-tetramethyldiazetine (4-Me₄) has been measured. By comparison with the previously reported photoelectron spectra of 3,3-dimethyldiazirine and 3,3,5,5-tetramethylpyrazoline, 4-Me₄ has three resolved low energy ionization (8.87, 10.36, and 11.65 eV) with an anomalously low second ionization potential. MINDO/3-and ab initio STO-3G calculations on 3-, 4-, and 5-membered ring azo compounds (diazenes) have been carried out, and these allow definite conclusions about the order of n_?, n₊, and π ionization potentials to be made for the diazetine (n_? < N₊ < π) and for 3,3-dimethyldiazirine and 3,3,5,5-tetramethylpyrazoline(n_? < π n₊), in agreement with the predictions of Heilbronner. Ab initio STO-3G calculations on the nitrogen and alkyl fragments of the cyclic diazenes reveal the origin of ionization energy shifts with changes in ring size.     

Modeling the cluster formation during infrared and ultraviolet matrix-assisted laser desorption ionization of oligonucleotides in succinic acid matrix with molecular mechanics

A large succinic acid (HOOC(CH₂)₂COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation. Revised: 12 October 2001 / Accepted: 27 February 2002 / Published online: 13 June 2002     

Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps

Productive proton pumping by bacteriorhodopsin requires that, after the all-trans to 13-cis photoisomerization of the retinal chromophore, the photocycle proceeds with proton transfer and not with thermal back-isomerization. The question of how the protein controls these events in the active site is addressed here using quantum mechanical/molecular mechanical reaction-path calculations. The results indicate that, while retinal twisting significantly contributes to lowering the barrier for the thermal cis-trans back-isomerization, the rate-limiting barrier for this isomerization is still 5-6 kcal/mol larger than that for the first proton-transfer step. In this way, the retinal twisting is finely tuned so as to store energy to drive the subsequent photocycle while preventing wasteful back-isomerization.     

Need and use of reference materials in a comprehensive countrywide monitoring of radionuclides

The reliability of measurement results is essential for forming a common database of a laboratory network, because a well-maintained and consistent database is the crucial point of countrywide monitoring. Reference materials are important tools in realizing some aspects of quality assurance; they are especially useful in harmonizing work within the network. Among usual types of reference materials in radio analytics solutions, matrix reference materials and some special reference objects are used. All classes of reference materials should be used depending on the purpose of the demonstration of quality, even in-house reference materials. Interlaboratory measurement comparison and performance evaluation programs play important quality assurance role in radio analytical laboratories. Fortunately, nowadays, the main task is to determine a very low radioactivity concentration in the environment; therefore, pre-concentration is necessary. Generally, the radionuclide bearing natural materials collected from sites where there had been sufficient time for natural processes to redistribute various chemically different species of radionuclides are more reliable reference materials than spiked materials—the main difference is the chemical bounding which is crucial from the point of view of the bioavailability. The need of reference material is summarized according to the intended use, like quality control, measurement validation, and instrument calibration.     

Effect of polyelectrolytes and polyelectrolyte mixtures on the electrokinetic potential of dispersed particles. 1. Electrokinetic potential of polystyrene particles in solutions of surfactants, polyelectrolytes and their mixtures

The effect of cationic and anionic surfactants, as well as cationic and anionic polyelectrolytes (PE), their binary mixtures on the electrokinetic potential of monodisperse carboxylated polystyrene (PS) particles as a function of the reagents dose, pH, the charge density (CD) of polymers, the surfactant/PE and binary PE mixture composition, and sequence of components addition to the suspension has been studied. It has been shown that addition of increasing amount of anionic surfactant/polyelectrolytes increases the absolute value of the negative zeta-potential of PS particles; this increase is stronger the CD of the PE and pH of the system are higher. Adsorption of cationic surfactant/polyelectrolytes leads to a significant decrease in the negative ζ-potential and to overcharging the particles; changes in the ζ-potential are more pronounced for PE samples with higher CD and for suspensions with lower pH values. In mixtures of cationic and anionic PE, in a wide range of mixture composition, the ζ-potential of particles is determined by the adsorbed amount of the anionic polymer independently of the CD of PEs and the sequence of addition of the mixture components. The isoelectric point of the surface is reached at the adsorbed amount of positive charges of PE that is approximately equal to the surface CD of particles. The laws observed were explained by features of macromolecules conformation in adsorbed mixed PE layers. Considerations about the role of coulombic and non-coulombic forces in the mechanism of anionic/cationic PE adsorption are presented.     

Theory of variational calculation with a scaling correct moment functional to solve the electronic schrödinger equation directly for ground state one‐electron density and electronic energy

The reduction of the electronic Schrodinger equation or its calculating algorithm from 4N‐dimensions to a nonlinear, approximate density functional of a three spatial dimension one‐electron density for an N electron system which is tractable in practice, is a long‐desired goal in electronic structure calculation. In a seminal work, Parr et al. (Phys. Rev. A 1997, 55, 1792) suggested a well behaving density functional in power series with respect to density scaling within the orbital‐free framework for kinetic and repulsion energy of electrons. The updated literature on this subject is listed, reviewed, and summarized. Using this series with some modifications, a good density functional approximation is analyzed and solved via the Lagrange multiplier device. (We call the attention that the introduction of a Lagrangian multiplier to ensure normalization is a new element in this part of the related, general theory.) Its relation to Hartree–Fock (HF) and Kohn–Sham (KS) formalism is also analyzed for the goal to replace all the analytical Gaussian based two and four center integrals (∫g_i( r ₁)g_k( r ₂)rd r ₁d r ₂, etc.) to estimate electron‐electron interactions with cheaper numerical integration. The KS method needs the numerical integration anyway for correlation estimation. © 2012 Wiley Periodicals, Inc.     

In Vivo Endoscopic Tissue Identification by Rapid Evaporative Ionization Mass Spectrometry (REIMS)

Gastrointestinal cancers are a leading cause of mortality, accounting for 23 % of cancer‐related deaths worldwide. In order to improve outcomes from these cancers, novel tissue characterization methods are needed to facilitate accurate diagnosis. Rapid evaporative ionization mass spectrometry (REIMS) is a technique developed for the in vivo classification of human tissue through mass spectrometric analysis of aerosols released during electrosurgical dissection. This ionization technique was further developed by utilizing surface induced dissociation and was integrated with an endoscopic polypectomy snare to allow in vivo analysis of the gastrointestinal tract. We tested the classification performance of this novel endoscopic REIMS method in vivo. It was shown to be capable of differentiating between healthy layers of the intestinal wall, cancer, and adenomatous polyps based on the REIMS fingerprint of each tissue type in vivo.     

Large-scale temporal analysis of computer and information science

The main aim of the project reported in this paper was twofold. One of the primary goals was to produce an extensive source of network data for bibliometric analyses of field dynamics in the case of Computer and Information Science. To this end, we rendered the raw material of the DBLP computer and infoscience bibliography into a comprehensive collection of dynamic network data, promptly available for further statistical analysis. The other goal was to demonstrate the value of our data source via its use in mapping Computer and Information Science (CIS). An analysis of the evolution of CIS was performed in terms of collaboration (co-authorship) network dynamics. Dynamic network analysis covered three quarters of the XX. century (76 years, from 1936 to date). Network evolution was described both at the macro- and the mezo level (in terms of community characteristics). Results show that the development of CIS followed what appears to be a universal pattern of growing into a “mature” discipline.