On the computation of protein backbones by using artificial backbones of hydrogens

NMR experiments provide information from which some of the distances between pairs of hydrogen atoms of a protein molecule can be estimated. Such distances can be exploited in order to identify the three-dimensional conformation of the molecule: this problem is known in the literature as the Molecular Distance Geometry Problem (MDGP). In this paper, we show how an artificial backbone of hydrogens can be defined which allows the reformulation of the MDGP as a combinatorial problem. This is done with the aim of solving the problem by the Branch and Prune (BP) algorithm, which is able to solve it efficiently. Moreover, we show how the real backbone of a protein conformation can be computed by using the coordinates of the hydrogens found by the BP algorithm. Formal proofs of the presented results are provided, as well as computational experiences on a set of instances whose size ranges from 60 to 6000 atoms.     

Determination of phenolic compounds,in vitro antioxidant activity and characterization of secondary metabolites in different parts of Passiflora cincinnata by HPLC-DAD-MS/MS analysis

Abstract

Ethanol extracts of different parts of Passiflora cincinnata were obtained by maceration. The total phenolic and flavonoid contents were evaluated. The antioxidant activities were determined by β-carotene-linoleic acid bleaching test, 2,2-diphenyl-1-picrylhydrazil (DPPH), and 2,2’-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical scavenging. The crude ethanol stem extract showed the highest amount of total polyphenols (45.53?mg gallic acid equivalent/g) while the highest total flavonoid contents (1.42?mg of quercetin equivalent/g) were observed in the leaf extract. The lowest IC₅₀ (25.65?μg/ml) by the DPPH method was observed for the stem extract. The ABTS method showed a significant antioxidant activity for all investigated extracts. The secondary metabolite composition of ethanol extracts was assessed by HPLC-DAD-MS/MS analysis, leading to the identification of fourteen secondary metabolites in P. cincinnata extracts. These results showed the potentiality of this species as a source of phenolic compounds and antioxidants.     

Discretization orders for protein side chains

Proteins are important molecules that are widely studied in biology. Since their three-dimensional conformations can give clues about their function, an optimal methodology for the identification of such conformations has been researched for many years. Experiments of Nuclear Magnetic Resonance (NMR) are able to estimate distances between some pairs of atoms forming the protein, and the problem of identifying the possible conformations satisfying the available distance constraints is known in the scientific literature as the Molecular Distance Geometry Problem (MDGP). When some particular assumptions are satisfied, MDGP instances can be discretized, and solved by employing an ad-hoc algorithm, named the interval Branch & Prune. When dealing with molecules such as proteins, whose chemical structure is known, a priori information can be exploited for generating atomic orderings that allow for the discretization. In previous publications, we presented a handcrafted order for the protein backbones. In this work, we propose 20 new orders for the 20 side chains that can be present in proteins. Computational experiments on artificial and real instances from NMR show the usefulness of the proposed orders.     

Binaural interference and auditory grouping

The phenomenon of binaural interference, where binaural judgments of a high-frequency target stimulus are disrupted by the presence of a simultaneous low-frequency interferer, can largely be explained using principles of auditory grouping and segregation. Evidence for this relationship comes from a number of previous studies showing that the manipulation of simultaneous grouping cues such as harmonicity and onset synchrony can influence the strength of the phenomenon. In this study, it is shown that sequential grouping cues can also influence whether binaural interference occurs. Subjects indicated the lateral position of a high-frequency sinusoidally amplitude-modulated (SAM) tone containing an interaural time difference. Perceived lateral positions were reduced by the presence of a simultaneous diotic low-frequency SAM tone, but were largely restored when the interferer was "captured" in a stream of identical tones. A control condition confirmed that the effect was not due to peripheral adaptation. The data lend further support to the idea that binaural interference is affected by processes related to the perceptual organization of auditory information. Modifications to existing grouping-based models are proposed that may help account for binaural interference effects more successfully.     

Separation of concurrent broadband sound sources by human listeners

The effect of spatial separation on the ability of human listeners to resolve a pair of concurrent broadband sounds was examined. Stimuli were presented in a virtual auditory environment using individualized outer ear filter functions. Subjects were presented with two simultaneous noise bursts that were either spatially coincident or separated (horizontally or vertically), and responded as to whether they perceived one or two source locations. Testing was carried out at five reference locations on the audiovisual horizon (0 degrees, 22.5 degrees, 45 degrees, 67.5 degrees, and 90 degrees azimuth). Results from experiment 1 showed that at more lateral locations, a larger horizontal separation was required for the perception of two sounds. The reverse was true for vertical separation. Furthermore, it was observed that subjects were unable to separate stimulus pairs if they delivered the same interaural differences in time (ITD) and level (ILD). These findings suggested that the auditory system exploited differences in one or both of the binaural cues to resolve the sources, and could not use monaural spectral cues effectively for the task. In experiments 2 and 3, separation of concurrent noise sources was examined upon removal of low-frequency content (and ITDs), onset/offset ITDs, both of these in conjunction, and all ITD information. While onset and offset ITDs did not appear to play a major role, differences in ongoing ITDs were robust cues for separation under these conditions, including those in the envelopes of high-frequency channels.     

Sodium self-diffusion coefficient in sodium silicate glass by quasielastic neutron scattering

Using pulsed neutrons of 19.8 Å wavelength a quasielastic line broadening as low as 0.03 eV (FWHM) has been observed due to Na⁺ diffusion in the glass Na₂O·2SiO₂. From the linewidths a Na⁺ self-diffusion coefficient of 3.1·10^–8 cm²/s at 420°C was obtained in excellent agreement with the diffusion coefficient determined for the same sample batch using²²Na radioactive tracers. The experimental Q dependence of the quasielasic linewidths gives a hint for deviations from a purely random walk in an ionic glass.     

Recent advances on the Discretizable Molecular Distance Geometry Problem

The Molecular Distance Geometry Problem (MDGP) consists in finding an embedding in R³${\mathbb{R}}^3$ of a nonnegatively weighted simple undirected graph with the property that the Euclidean distances between embedded adjacent vertices must be the same as the corresponding edge weights. The Discretizable Molecular Distance Geometry Problem (DMDGP) is a particular subset of the MDGP which can be solved using a discrete search occurring in continuous space; its main application is to find three-dimensional arrangements of proteins using Nuclear Magnetic Resonance (NMR) data. The model provided by the DMDGP, however, is too abstract to be directly applicable in proteomics. In the last five years our efforts have been directed towards adapting the DMDGP to be an ever closer model of the actual difficulties posed by the problem of determining protein structures from NMR data. This survey lists recent developments on DMDGP related research.