A topological algorithm for identification of structural domains of proteins

Background: Identification of the structural domains of proteins is important for our understanding of the organizational principles and mechanisms of protein folding, and for insights into protein function and evolution. Algorithmic methods of dissecting protein of known structure into domains developed so far are based on an examination of multiple geometrical, physical and topological features. Successful as many of these approaches are, they employ a lot of heuristics, and it is not clear whether they illuminate any deep underlying principles of protein domain organization. Other well-performing domain dissection methods rely on comparative sequence analysis. These methods are applicable to sequences with known and unknown structure alike, and their success highlights a fundamental principle of protein modularity, but this does not directly improve our understanding of protein spatial structure.

The effect of teachers trained in a fundamental movement skills programme on children’s self-perceptions and motor competence

Perceived and actual motor competence are hypothesized to have potential links to children and young people’s physical activity (PA) levels with a potential consequential link to long-term health. In this cross-sectional study, Harter’s (1985, Manual for the Self-perception Profile for Children. Denver, CO: University of Denver) Competency Motivation-based framework was used to explore whether a group of children taught, during curriculum time, by teachers trained in the Fundamental Movement Skills (FMS) programme, scored higher on self-perception and on core motor competencies when compared to children whose teachers had not been so trained. One hundred and seventy seven children aged 7–8 years participated in the study. One hundred and seven were taught by FMS-trained teachers (FMS) and the remaining 70 were taught by teachers not trained in the programme (non-FMS). The Harter Self-Perception Profile for Children assessed athletic competence, scholastic competence, global self-worth and social acceptance. Three core components of motor competence (body management, object control and locomotor skills) were assessed via child observation. The FMS group scored higher on all the self-perception domains (p < 0.05). Statistically significant differences were found between the schools on all of the motor tasks (p < 0.05). The relationships between motor performance and self-perception were generally weak and non-significant. Future research in schools and with teachers should explore the FMS programme’s effect on children’s motor competence via a longitudinal approach.

Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains.

Macro domains constitute a protein module family found associated with specific histones and proteins involved in chromatin metabolism. In addition, a small number of animal RNA viruses, such as corona- and toroviruses, alphaviruses, and hepatitis E virus, encode macro domains for which, however, structural and functional information is extremely limited. Here, we characterized the macro domains from hepatitis E virus, Semliki Forest virus, and severe acute respiratory syndrome coronavirus (SARS-CoV). The crystal structure of the SARS-CoV macro domain was determined at 1.8-Å resolution in complex with ADP-ribose. Information derived from structural, mutational, and sequence analyses suggests a close phylogenetic and, most probably, functional relationship between viral and cellular macro domain homologs. The data revealed that viral macro domains have relatively poor ADP-ribose 1"-phosphohydrolase activities (which were previously proposed to be their biologically relevant function) but bind efficiently free and poly(ADP-ribose) polymerase 1-bound poly(ADP-ribose) in vitro. Collectively, these results suggest to further evaluate the role of viral macro domains in host response to viral infection.

Domains in three-dimensional ferroelectric nanostructures

We report the experimental measurement of domains in single- crystal nanocolumns of ferroelectric BaTiO3, together with a theory of domain size scaling in three- dimensional structures which explains the observations.

Wall thickness dependence of the scaling law for ferroic stripe domains

The periodicity of 180 degrees. stripe domains as a function of crystal thickness scales with the width of the domain walls, both for ferroelectric and for ferromagnetic materials. Here we derive an analytical expression for the generalized ferroic scaling factor and use this to calculate the domain wall thickness and gradient coefficients ( exchange constants) in some ferroelectric and ferromagnetic materials. We then use these to discuss some of the wider implications for the physics of ferroelectric nanodevices and periodically poled photonic crystals.

Functional domains of the human epididymal protease inhibitor, eppin

Eppin has two potential protease inhibitory domains: a whey acid protein or four disulfide core domain and a Kunitz domain. The protein is also reported to have antibacterial activity against Gram-negative bacteria. Eppin and its whey acid protein and Kunitz domains were expressed in Escherichia coli and their ability to inhibit proteases and kill bacteria compared. The Kunitz domain inhibits elastase (EC 3.4.21.37) to a similar extent as intact eppin, whereas the whey acid protein domain has no such activity. None of these fragments inhibits trypsin (EC 3.4.21.4) or chymotrypsin (EC 3.4.21.1) at the concentrations tested. In a colony forming unit assay, both domains have some antibacterial activity against E. coli, but this was not to the same degree as intact eppin or the two domains together. When bacterial respiratory electron transport was measured using a 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide assay, eppin and its domains caused an increase in the rate of respiration. This suggests that the mechanism of cell killing may be partly through the permeablization of the bacterial inner membrane, resulting in uncoupling of respiratory electron transport and consequent collapse of the proton motive force. Thus, we conclude that although both of eppin’s domains are involved in the protein’s antibacterial activity, only the Kunitz domain is required for selective protease inhibition.