Demonstration of a protein with enhanced resistance to proteinase K in transmissible cytopathic condition elicited by cell-free lysate of free-living ameba Naegleria gruberi

The cell-free lysate of free-living amebae Naegleria gruberi and Naegleria fowleri were reported to elicit cytopathic effect in various cell lines that could be indefinitely transmitted by the culture media. The causative agent showed sensitivity to treatments detrimental to proteins while resisted exposures damaging to nucleic acids. Here we demonstrate that subsequent to exposure to N. gruberi lysate mild digestion with proteinase K reveals the presence of a protein band in HeLa cells absent from control cell lines. Though the small quantity of this protein with enhanced resistance to proteinase K relative to the total protein content of the sample has proved to date insufficient for its purification, we suppose that it is a human cellular protein that assumed altered conformation in a prion-like fashion. The conformational conversion could have been trigerred by an ameba protein in the lysate. In addition, we showed that HeLa cells treated with N. gruberi lysate display elevated cathepsin B activity which is assumed to be a secondary response to the accumulation of the proteinase K-resistant protein. We propose that a number of degenerative sequelae following previous microbial infections in mammals could have a similar pathomechanism. Moreover, epidemiological data strongly suggest that natural prion disease in sheep, goat and cervids may also have an etiology linked to prior infection/colonization with a microbe, as it had already been proposed by one of us.     

Linear C(n) clusters: are they acetylenic or cumulenic?

Uncapped linear Cn clusters have been studied with hybrid density functional theory focusing on the geometry, HOMO-LUMO gap, and the longitudinal optical (LO) vibrational mode. The latter two correlate well with the bond length alternation (BLA) of the optimized geometry. Due to end effects, the BLA is not constant along the chains. The degree of BLA changes continuously with increasing n: starting with essentially nonalternating structures (cumulenic), then turning into strongly alternating (acetylenic) structures. This transition has not yet been described or characterized and occurs at relatively large values of n. The implications for the widely observed characteristic LO vibrational bands of linear carbon clusters are discussed.     

The effect of numerical error on the reproducibility of molecular geometry optimizations

Geometry optimization is one of the most often applied techniques in computational drug discovery. Although geometry optimization routines are generally deterministic, the minimization trajectories can be extremely sensitive to initial conditions, especially in case of larger systems such as proteins. Simple manipulations such as coordinate transformations (translations and rotations), file saving and retrieving, and hydrogen addition can introduce small variations ( approximately 0.001 A) in the starting coordinates which can drastically affect the minimization trajectory. With large systems, optimized geometry differences of up to 1 A RMSD and final energy differences of several kcal/mol can be observed when using many commercially available software packages. Differences in computer platforms can also lead to differences in minimization trajectories. Here we demonstrate how routine structure manipulations can introduce small variations in atomic coordinates, which upon geometry optimization, can give rise to unexpectedly large differences in optimized geometries and final energies. We also show how the same minimizations run on different computer platforms can also lead to different results. The implications of these findings on routine computational chemistry procedures are discussed.     

Application of a novel linear/exponential hybrid force field scaling scheme to the longitudinal Raman active mode of polyyne

The properties of an infinite carbon chain (polyyne), an allotropic form of elemental carbon, are of importance in materials science as well as astronomy. The Raman active longitudinal optical (LO) frequencies are calculated with first-principles methods for oligoynes and polyyne and compared with experiments. Since traditional force constant scaling schemes fail in this case, we introduced a linear/exponential scaling scheme based on the exponential behavior of the carbon-carbon bond stretching force constant couplings in quasi-one-dimensional conjugated chains. The LO Raman active frequency is predicted at 1870-1877 cm-1. Our results provides further evidence for the assignment of the characteristic Raman peaks near 1850 cm-1 of the recently discovered long linear carbon chains encapsulated inside multiwalled or double-walled carbon nanotubes.     

A Simple HPLC/DAD Method Validation for the Quantification of Malondialdehyde in Rodent’s Brain

In the present study, a HPLC/DAD method was set up to allow for the determination and quantification of malondialdehyde (MDA) in the brain of rodents (rats). Chromatographic separation was achieved on Supelcosil LC-18 (3 μm) SUPELCO Column 3.3 cm × 4.6 mm and Supelco Column Saver 0.5 μm filter by using a mobile phase acetonitrile (A) and phosphate buffer (20 mM, pH = 6) (B). Isocratic elution was 14% for (A) and 86% for (B). The injection volume (loop mode) was 100 μL with an analysis time of 1.5 min. Flow rate was set at 1 mL/min. The eluted compound was detected at 532 nm by a DAD detector by keeping the column oven at room temperature. The results indicated that the method has good linearity in the range of 0.2–20 μg/g. Both intra- and inter-day precision, expressed as RSD, were ≤15% and the accuracies ranged between ±15%. The lower limit of quantification (LLOQ), stability, and robustness were evaluated and satisfied the validation criteria. The method was successfully applied in a study of chronic toxicology following different treatment regimens with haloperidol and metformin.     

Bond length alternation and energy band gap of polyyne

The bond length alternation (BLA) and energy band gap of polyyne are investigated by various first-principles theories, including Hartree-Fock, MP2, hybrid, and nonhybrid density functional theories. Both solid-state calculations utilizing periodic boundary conditions on polymers and molecular quantum mechanical calculations on extra-long oligomers were performed with consistent results. By validation on similar linear conjugated polymers, polyacetylene and polydiacetylene, the combination of hybrid-DFT schemes, B3LYP//BHandHLYP or B3LYP//KMLYP, is shown to give the best predictions for both geometry and band gap of polyyne based on available experimental data. We conclude that the best estimate of the BLA of polyyne is about 0.13 A and that of the band gap is about 2.2 eV.     

Stepwise cope rearrangement of cyclo-biphenalenyl via an unusual multicenter covalent pi-bonded intermediate

Multicenter covalent pi-bonding between pi-conjugated radicals has been recently recognized as a novel and important bonding interaction. The Cope rearrangement of cyclo-biphenalenyl 9 is studied by exploring its potential energy surface with density functional theory (DFT), and it is found that pi-bonding plays a critical role in the rearrangement process. Affected by this, the rearrangement of 9 takes place by a stepwise mechanism through an unusual pi-intermediate 10, of C2h symmetry, which can be characterized as a 2 x 13pi + 2 x 2pi system. The pi-intermediate has a long inter-phenalenyl distance of R approximately 2.8 angstroms, which is shorter than the sum of the van der Waals radii displaying multicenter covalent pi-bonding between the two phenalenyl units. The energy of the pi-intermediate 10 is higher than that of the sigma-bonded reactant 9 by approximately 2 kcal/mol according to the employed spin-restricted DFT. NMR chemical shift calculations support the sigma-bonded 9 as the global minimum. The calculated activation barrier of approximately 6 kcal/mol for the Cope rearrangement is consistent with the stepwise mechanism. A covalent pi-bonding effect in the pi-intermediate 10 is demonstrated indirectly by the shortening of inter-naphthalene distance of the dianion and dication of the cyclophane 14 compared to that of its neutral counterpart. The unusual pi-bonded structure with a long inter-phenalenyl distance becomes the most stable structure for the ethano-bridged derivative 13, which should have observable paramagnetism according to the calculated paramagnetic susceptibility.     

Numerical errors and chaotic behavior in docking simulations

This work examines the sensitivity of docking programs to tiny changes in ligand input files. The results show that nearly identical ligand input structures can produce dramatically different top-scoring docked poses. Even changing the atom order in a ligand input file can produce significantly different poses and scores. In well-behaved cases the docking variations are small and follow a normal distribution around a central pose and score, but in many cases the variations are large and reflect wildly different top scores and binding modes. The docking variations are characterized by statistical methods, and the sensitivity of high-throughput and more precise docking methods are compared. The results demonstrate that part of docking variation is due to numerical sensitivity and potentially chaotic effects in current docking algorithms and not solely due to incomplete ligand conformation and pose searching. These results have major implications for the way docking is currently used for pose prediction, ranking, and virtual screening.     

Jet flavor tomography of quark gluon plasmas at RHIC and LHC

A new Monte Carlo model of jet quenching in nuclear collisions, CUJET1.0, is applied to predict the jet flavor dependence of the nuclear modification factor for fragments f=π,D,B,e(-) from quenched jet flavors g,u,c,b in central collisions at RHIC and LHC. The nuclear modification factors for different flavors are predicted to exhibit a novel level crossing pattern over a transverse momentum range 5相似文献   

Analytical solutions of N‐person games

The possibility of analytical solutions of N‐person games is presented. A simple formula provides valuable information about the outcomes of such games with linear payoff functions and Pavlovian agents. Experiments performed with our simulation tool for the multiagent stag hunt dilemma game are presented. For the case of Pavlovian agents the game has nontrivial but remarkably regular solutions. If both payoff functions are linear and the real solutions of Eq. (2) are both positive, then the analytical solutions are remarkably accurate. © 2012 Wiley Periodicals, Inc. Complexity, 2012