Folding thermodynamics of model four-strand antiparallel beta-sheet proteins

The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed for different sizes of the bias gap g, an artificial measure of a model protein's preference for its native state. The thermodynamic transition temperatures are obtained by calculating the squared radius of gyration, the root-mean-squared pair separation fluctuation, the specific heat, the internal energy of the system, and the Lindemann disorder parameter. In spite of the simplicity, the protein-like heteropolymers have shown a complex set of protein transitions as observed in experimental studies. Starting from high temperature, these transitions include a collapse transition, a disordered-to-ordered globule transition, a folding transition, and a liquid-to-solid transition. These transitions strongly depend on the native-state geometry of the model proteins and the size of the bias gap. A strong transition from the disordered globule state to the ordered globule state with large energy change and a weak transition from the ordered globule state to the native state with small energy change were observed for the large gap models. For the small gap models no native structures were observed at any temperature, all three beta-sheet proteins fold into a partially-ordered globule state which is geometrically different from the native state. For small bias gaps at even lower temperatures, all protein motions are frozen indicating an inactive solid-like phase.Comment: PDF file, 32 pages including 13 figure page

Quadrupoles for Remote Electrostimulation Incorporating Bipolar Cancellation

Introduction: A method that utilizes nanosecond bipolar cancellation (BPC) near a quadrupole electrodes to suppress a biological response but cancels the distal BPC at the quadrupole center, i.e., cancellation of cancellation (CANCAN), may allow for a remote focused stimulation at the quadrupole center. Objectives: The primary object of this study was to outline the requirement of the CANCAN implementation and select an effective quadrupole configuration. Results: We have studied three quadrupole electrode configurations, a rod quadrupole, a plate quadrupole (Plate-Q), and a resistor quadrupole. The pulse shapes of electric fields include monophasic pulses, cancellation pulses, and additive pulses. The Plate-Q appears the best for CANCAN as it shows the highest percentage of cancellation pulses among all pulse shapes, allowing for the best spatial focus. Conclusion: For the region of interest characterized in the Plate-Q configuration, the maximum magnitude of bipolar field is twice as that of the unipolar field, which allows for the CANCAN demonstration that involves membrane electropermeabilization

Protein Folding Pathways and Kinetics: Molecular Dynamics Simulations of β-Strand Motifs

AbstractThe folding pathways and the kinetic properties for three different types of off-lattice four-strand antiparallel β-strand protein models interacting via a hybrid Go-type potential have been investigated using discontinuous molecular dynamics simulations. The kinetic study of protein folding was conducted by temperature quenching from a denatured or random coil state to a native state. The progress parameters used in the kinetic study include the squared radius of gyration Rg2, the fraction of native contacts within the protein as a whole Q, and between specific strands Qab. In the time series of folding, the denatured proteins undergo a conformational change toward the native state. The model proteins exhibit a variety of kinetic folding pathways that include a fast-track folding pathway without passing through an intermediate and multiple pathways with trapping into more than one intermediate. The kinetic folding behavior of the β-strand proteins strongly depends on the native-state geometry of the model proteins and the size of the bias gap g, an artificial measure of a model protein's preference for its native state

Investigating the Impact of Recommendation Agents on E-commerce Ecosystem

The influence of recommendation agents on e-commerce ecosystem is profound. Technological impact of predictive intelligence could be explained more reasonably by taking a collective perspective. However, the ecosystem perspective has only served as a prologue for discussion regarding technological influence. The lack of research development associated with the technological influence on business in the ecological lens has constrained our understanding of the penetration and the role of technology in business ecosystem evolution. This paper therefore focuses on the impact of recommendation agents for online shopping environment on e-commerce ecosystem. Moreover, this paper observes and explains the phenomena that most participants in the e-commerce ecosystem are taking recommendation agents as one of the strategic technological investments towards further development as a common goal

Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e. alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments: http://as2ts.llnl.gov/AS2TS/LGA/lga_pdblist_plots.html

Myoclonic Epilepsy and Ragged Red Fibers (MERRF) Syndrome: Selective Vulnerability of CNS Neurons Does Not Correlate with the Level of Mitochondrial tRNA^(lys) Mutation in Individual Neuronal Isolates

Selective vulnerability of subpopulations of neurons is a striking feature of neurodegeneration. Mitochondrially transmitted diseases are no exception. In this study CNS tissues from a patient with myoclonus epilepsy and ragged red fibers (MERRF) syndrome, which results from an A to G transition of nucleotide (nt) 8344 in the mitochondrial tRNA^(Lys) gene, were examined for the proportion of mutant mtDNA. Either individual neuronal somas or the adjacent neuropil and glia were microdissected from cryostat tissue sections of histologically severely affected brain regions, including dentate nuclei, Purkinje cells, and inferior olivary nuclei, and from a presumably less affected neuronal subpopulation, the anterior horn cells of the spinal cord. Mutant and normal mtDNA were quantified after PCR amplification with a mismatched primer and restriction enzyme digestion. Neurons and the surrounding neuropil and glia from all CNS regions that were analyzed exhibited high proportions of mutant mtDNA, ranging from 97.6 ± 0.7% in Purkinje cells to 80.6 ± 2.8% in the anterior horn cells. Within each neuronal group that was analyzed, neuronal soma values were similar to those in the surrounding neuropil and glia or in the regional tissue homogenate. Surprisingly, as compared with controls, neuronal loss ranged from 7% of the Purkinje cells to 46% of the neurons of the dentate nucleus in MERRF cerebellum. Thus, factors other than the high proportion of mutant mtDNA, in particular nuclear-controlled neuronal differences among various regions of the CNS, seem to contribute to the mitochondrial dysfunction and ultimate cell death

Myoclonic Epilepsy and Ragged Red Fibers (MERRF) Syndrome: Selective Vulnerability of CNS Neurons Does Not Correlate with the Level of Mitochondrial tRNA^(lys) Mutation in Individual Neuronal Isolates

Selective vulnerability of subpopulations of neurons is a striking feature of neurodegeneration. Mitochondrially transmitted diseases are no exception. In this study CNS tissues from a patient with myoclonus epilepsy and ragged red fibers (MERRF) syndrome, which results from an A to G transition of nucleotide (nt) 8344 in the mitochondrial tRNA^(Lys) gene, were examined for the proportion of mutant mtDNA. Either individual neuronal somas or the adjacent neuropil and glia were microdissected from cryostat tissue sections of histologically severely affected brain regions, including dentate nuclei, Purkinje cells, and inferior olivary nuclei, and from a presumably less affected neuronal subpopulation, the anterior horn cells of the spinal cord. Mutant and normal mtDNA were quantified after PCR amplification with a mismatched primer and restriction enzyme digestion. Neurons and the surrounding neuropil and glia from all CNS regions that were analyzed exhibited high proportions of mutant mtDNA, ranging from 97.6 ± 0.7% in Purkinje cells to 80.6 ± 2.8% in the anterior horn cells. Within each neuronal group that was analyzed, neuronal soma values were similar to those in the surrounding neuropil and glia or in the regional tissue homogenate. Surprisingly, as compared with controls, neuronal loss ranged from 7% of the Purkinje cells to 46% of the neurons of the dentate nucleus in MERRF cerebellum. Thus, factors other than the high proportion of mutant mtDNA, in particular nuclear-controlled neuronal differences among various regions of the CNS, seem to contribute to the mitochondrial dysfunction and ultimate cell death

Microscopic and Macroscopic Stress with Gravitational and Rotational Forces

Many recent papers have questioned Irving and Kirkwood's atomistic expression for stress. In Irving and Kirkwood's approach both interatomic forces and atomic velocities contribute to stress. It is the velocity-dependent part that has been disputed. To help clarify this situation we investigate [1] a fluid in a gravitational field and [2] a steadily rotating solid. For both problems we choose conditions where the two stress contributions, potential and kinetic, are significant. The analytic force-balance solutions of both these problems agree very well with a smooth-particle interpretation of the atomistic Irving-Kirkwood stress tensor.Comment: Fifteen pages with seven figures, revised according to referees' suggestions at Physical Review E. See also Liu and Qiu's arXiv contribution 0810.080

Optimization of dynamic product offerings on online marketplaces: A network theory perspective

The fierce competition amongst brands on online marketplaces makes the optimization of offerings within this context a significant challenge. To address this challenge, we draw upon network theory and model the degree of competition through consumers’ consideration sets. We use a large empiricaldataset from one of the biggest online marketplaces to explore the dynamic relationship between network position and the degree of competition, and we depict the redistribution of market share of related offerings after adjusting their array. In doing so, we provide a theoretical reference on when and how brands should optimize their product offerings on online marketplaces. We further demonstrate that intra-brand cannibalization relations have a significantly greater impact on the degree of competition compared to inter-brand ones, while intra-brand cannibalization relations represent the main reason for fluctuations in the degree of competition. Hence, contrary to existing theoreticalinsights and practical intuitions, our findings demonstrate that brands should minimize the number and heterogeneity of their offerings within a market segment to increase their sales on online marketplaces

Ultra-Low Intensity Post-Pulse Affects Cellular Responses Caused by Nanosecond Pulsed Electric Fields

High-intensity nanosecond pulse electric fields (nsPEF) can preferentially induce various effects, most notably regulated cell death and tumor elimination. These effects have almost exclusively been shown to be associated with nsPEF waveforms defined by pulse duration, rise time, amplitude (electric field), and pulse number. Other factors, such as low-intensity post-pulse waveform, have been completely overlooked. In this study, we show that post-pulse waveforms can alter the cell responses produced by the primary pulse waveform and can even elicit unique cellular responses, despite the primary pulse waveform being nearly identical. We employed two commonly used pulse generator designs, namely the Blumlein line (BL) and the pulse forming line (PFL), both featuring nearly identical 100 ns pulse durations, to investigate various cellular effects. Although the primary pulse waveforms were nearly identical in electric field and frequency distribution, the post-pulses differed between the two designs. The BL’s post-pulse was relatively long-lasting (~50 µs) and had an opposite polarity to the main pulse, whereas the PFL’s post-pulse was much shorter (~2 µs) and had the same polarity as the main pulse. Both post-pulse amplitudes were less than 5% of the main pulse, but the different post-pulses caused distinctly different cellular responses. The thresholds for dissipation of the mitochondrial membrane potential, loss of viability, and increase in plasma membrane PI permeability all occurred at lower pulsing numbers for the PFL than the BL, while mitochondrial reactive oxygen species generation occurred at similar pulsing numbers for both pulser designs. The PFL decreased spare respiratory capacity (SRC), whereas the BL increased SRC. Only the PFL caused a biphasic effect on trans-plasma membrane electron transport (tPMET). These studies demonstrate, for the first time, that conditions resulting from low post-pulse intensity charging have a significant impact on cell responses and should be considered when comparing the results from similar pulse waveforms