Interacting amino acid preferences of 3D pattern pairs at the binding sites of transient and obligate protein complexes

To assess the physico-chemical characteristics of protein-protein interactions, protein sequences and overall structural folds have been analyzed previously. To highlight this, discovery and examination of amino acid patterns at the binding sites defined by structural proximity in 3-dimensional (3D) space are essential. In this paper, we investigate the interacting preferences of 3D pattern pairs discovered separately in transient and obligate protein complexes. These 3D pattern pairs are not necessarily sequence-consecutive, but each residue in two groups of amino acids from two proteins in a complex is within certain °A threshold to most residues in the other group. We develop an algorithm called AA-pairs by which every pair of interacting proteins is represented as a bipartite graph, and it discovers all maximal quasi-bicliques from every bipartite graph to form our 3D pattern pairs. From 112 and 2533 highly conserved 3D pattern pairs discovered in the transient and obligate complexes respectively, we observe that Ala and Leu is the highest occuring amino acid in interacting 3D patterns of transient (20.91%) and obligate (33.82%) complexes respectively. From the study on the dipeptide composition on each side of interacting 3D pattern pairs, dipeptides Ala-Ala and Ala-Leu are popular in 3D patterns of both transient and obligate complexes. The interactions between amino acids with large hydrophobicity difference are present more in the transient than in the obligate complexes. On contrary, in obligate complexes, interactions between hydrophobic residues account for the top 5 most occuring amino acid pairings.

There is something about pairs trading

The process of pairs trading involves exhaustively matching and ranking pairwise stocks based on some prespecified measure of closeness; e.g., correlation, cointegration, sum-of-squared price difference. Pairs trading is popular for various reasons. It is simple to follow and execute. The pairwise portfolio can be nearly market-neutral, such that it does not require the comprehensive analysis of macroeconomic news. Since it is based on relative valuation, the actual worth of individual firms is not a pertinent consideration. The strategy is sufficiently flexible to accommodate various investment styles. Lastly, it does not evoke frequent intraday rebalancing, such that pairs trading can be automated to a certain extent and be cost-feasibly profitable. Despite its long history on Wall Street, pairs trading remains elusive in nature. The academic attention it attracts is modest compared to contrarian and momentum trading.

Genetic and environmental influences on variation in balance performance among female twin pairs aged 21-82 years

Genetic and environmental influences on variation in balance performance were measured in 93 monozygous and 83 dizygous female twin pairs aged 21–82 years (mean age, 50.5 years) in Melbourne, Australia, between 1999 and 2003. The authors administered clinical (Lord's Balance Test and Step Test) and laboratory tests of static and dynamic balance from the Chattecx Balance System with and without distractor tasks. The authors conducted factor analysis and estimated genetic and environmental variance components and heritability (defined as additive genetic variance as a proportion of all variance, after adjustment for age) using a multivariate normal model with the statistical package FISHER. Three factors were identified and adjusted for age. Heritability was 46% (standard error (SE), 9) for the "sensory balance tests" factor and 30% (SE, 9) for the "static and dynamic perturbations" factor. For both factors, the remaining variance was attributed to unique environmental effects. There was no evidence that genetic factors influenced variation in the "dynamic weight shift tests" factor, with environmental effects shared by twins accounting for 38% (SE, 7) of variance. Neither genetic nor environmental proportions of variance differed significantly between twin subgroups by age (≤50/>50 years). An age-related decline in performance measures was found across the whole sample. These results imply that balance impairments may have a heritable element.

Liquids intermediate between 'molecular' and 'ionic' liquids : liquid ion pairs?

Ionic liquids comprised of tetradecyltrihexyl- and tetrabutyl- phosphonium cations paired with chloride or sulfonyl amide anions exhibit properties that reflect strong ion association, including comparatively low viscosity as well as a degree of volatility, and hence exemplify an interesting intermediate state between true ionic and true molecular liquids.

An analysis of side chain interactions and pair correlations within antiparallel β-sheets : the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs

Cross-strand pair correlations are calculated for residue pairs in antiparallel β-sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H-bonded site) and pairs which are not (non-H-bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H-bonded site. Thestrongest observed correlations are for pairs of disulfide-bonded cystines, many of which adopt a close-packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine-rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for β- and γ-branched residues inthe non-H-bonded site. An examination of the structures showsa directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non-H-bonded β- and γ-branched residue pairs, (2) the handedness of the observed enantiomers of chiral β-branched side chains, and (3) the handedness of the twist of β-sheet. These findings have implications for the formation of β-sheets during protein folding and the mechanism by which the sheet becomes twisted

Conformational changes in redox pairs of protein structures

Disulfides are conventionally viewed as structurally stabilizing elements in proteins but emerging evidence suggests two disulfide subproteomes exist. One group mediates the well known role of structural stabilization. A second redox-active group are best known for their catalytic functions but are increasingly being recognized for their roles in regulation of protein function. Redox-active disulfides are, by their very nature, more susceptible to reduction than structural disulfides; and conversely, the Cys pairs that form them are more susceptible to oxidation. In this study, we searched for potentially redox-active Cys Pairs by scanning the Protein Data Bank for structures of proteins in alternate redox states. The PDB contains over 1134 unique redox pairs of proteins, many of which exhibit conformational differences between alternate redox states. Several classes of structural changes were observed, proteins that exhibit: disulfide oxidation following expulsion of metals such as zinc; major reorganisation of the polypeptide backbone in association with disulfide redox-activity; order/disorder transitions; and changes in quaternary structure. Based on evidence gathered supporting disulfide redox activity, we propose disulfides present in alternate redox states are likely to have physiologically relevant redox activity.

Context reinstatement effects in children’s cued recall of strongly and weakly associated word pairs

Typically, asking people to reinstate the context of events increases their recall of those events; however, research findings have been mixed with children. We tested whether the principle underlying context reinstatement applies to children as it does to adults. This underlying principle, encoding specificity, suggests that the greater the overlap between study context cues and retrieval context cues, the more information that people should recall. In the current experiment, four age groups (7-year-olds, 9-year-olds, 11-year-olds and adults) took part in an encoding specificity procedure. At study, participants saw cue– target word pairs in which the cue word was either a strong or a weak associate of the target word (e.g., ice–COLD; blow–COLD). During an immediate cued recall test, participants were presented with the same strong or weak cue words and new, extra-list cue words. Overall, children and adults recalled more targets when they were presented with the same cue words at study and test, regardless of whether the cues were strong or weak. This finding suggests that encoding specificity applies to children as well as adults. We discuss the implications of these results.

Interviewing pairs: discussions on migration and identity

This article examines a research method of conducting interviews with pairs of individuals, who may be friends or relatives. The authors critically reflect on their experiences of collecting qualitative data in an interview with two respondents. While one-on-one interviews and focus groups are more established and well-studied forms of gathering research data, we argue that paired interviews as a data collections method present additional advantages as well as some challenges for qualitative researchers. The researchers embraced the opportunity to interview pairs of individuals with the intention of minimising the asymmetry of power habitually inherent in interview situations. In the authors' experiences, paired interviews served to empower those being interviewed and reduced the discomfort felt by some in the personal interview situation. This form of interviewing tended to give more autonomy to the respondents and prompted them to provide more nuanced responses. Paired interviews assisted respondents in feeling relaxed and comfortable, provided a vibrant environment that encouraged respondents to build on each other's ideas and enabled them to enhance each other's stories. Respondents were better motivated to build discussions around an interview question and then illustrate their responses with examples. In our studies, we found that our respondents tended to offer more thorough and comprehensive narratives in the setting of a paired interview.

The effect of sliding speed on the wear of steel-tool steel pairs

This study examines the effect of sliding speed and surface temperature on the wear behavior of an unlubricated mild steel-tool steel contact pair using the pin-on-disc test. The operating conditions and contact pair are of interest to the automotive sheet metal stamping industry and the broader metal forming community, where high contact pressures and moderate forming speeds can result in significant frictional heating and thus affect tool life. It will be shown that, while adhesive wear is dominant at the tool steel surface for all sliding speeds examined, the adhesive wear rate is very sensitive to sliding speed during slow speed conditions but relatively insensitive to sliding speed during higher speed conditions. These higher sliding speeds result in high frictional heating, however, the effect of increasing bulk temperature results in a transition from adhesive wear to material removal-dominated mechanisms. It is concluded that there is a distinct difference in the wear response for comparable surface temperature and bulk temperature conditions, at the low to moderate sliding speeds and temperatures examined in this study. The SEM and profilometry analysis show that the technique of increasing sliding speed to replicate bulk temperature conditions (or vice versa), may not result in equivalent wear rates and mechanisms.